Contacts of the helix formed by residues 82 - 120 (chain A) in PDB entry 4U1D
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 4.3 9.1 - - - +
79A ILE* 3.5 6.7 + - - +
81A GLY* 1.3 77.7 - - - +
83A THR* 1.3 63.9 + - - +
84A GLU* 3.3 14.9 + - - -
85A GLY* 3.0 24.9 + - - -
86A LEU* 3.2 22.6 + - - +
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Residues in contact with THR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 1.3 69.2 - - - +
84A GLU* 1.3 74.5 + - - +
85A GLY 3.0 1.6 - - - -
86A LEU* 3.1 5.8 + - - +
87A VAL* 2.9 33.1 + - + +
174A LEU* 3.7 28.9 - - + +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.8 19.5 - - + +
46A SER* 6.4 1.1 - - - -
82A SER* 3.3 19.2 - - - -
83A THR* 1.3 80.1 + - - +
85A GLY* 1.3 55.5 + - - +
87A VAL* 3.4 12.3 + - - +
88A SER* 2.9 28.6 + - - -
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Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.9 2.7 - - - +
79A ILE* 3.3 44.1 - - - +
82A SER* 3.0 14.5 + - - -
83A THR 3.0 0.6 - - - -
84A GLU* 1.3 74.4 - - - +
86A LEU* 1.3 57.9 + - - +
88A SER* 3.1 6.1 + - - -
89A VAL* 2.9 28.8 + - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.1 39.9 - - + +
82A SER 3.2 21.3 + - - +
83A THR* 3.1 8.1 + - - +
85A GLY* 1.3 71.4 - - - +
87A VAL* 1.3 66.4 + - + +
89A VAL* 3.1 12.1 + - + +
90A GLY 2.9 19.4 + - - -
172A ASN* 3.4 37.2 - - - +
174A LEU* 3.5 33.2 - - + -
175A LEU* 3.4 14.6 - - + +
223A ASN* 3.7 17.9 - - - +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 2.9 30.7 + - + +
84A GLU* 3.4 13.2 - - + +
85A GLY 3.2 0.2 - - - -
86A LEU* 1.3 76.9 - - + +
88A SER* 1.3 58.2 + - - +
90A GLY* 3.2 3.5 + - - -
91A ALA* 2.9 29.0 + - + +
94A ARG* 4.0 8.4 + - - +
174A LEU* 6.2 0.9 - - + -
175A LEU* 5.5 0.7 - - - -
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Residues in contact with SER 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.9 11.8 + - - -
46A SER* 5.2 0.4 - - - -
49A GLU* 3.5 32.9 + - - +
75A TYR* 2.6 28.0 + - - -
84A GLU 2.9 14.4 + - - -
85A GLY 3.3 9.0 - - - -
87A VAL* 1.3 73.1 - - - +
89A VAL* 1.3 59.6 + - - +
91A ALA* 3.2 2.7 + - - +
92A VAL* 2.9 33.8 + - - +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 4.2 4.7 - - + -
76A LYS* 3.9 34.8 - - + +
79A ILE* 3.7 20.4 - - + -
80A GLN* 5.4 2.5 - - + +
85A GLY 2.9 17.1 + - - +
86A LEU* 3.1 15.0 + - + +
88A SER* 1.3 75.4 - - - +
90A GLY* 1.3 63.4 + - - +
92A VAL* 3.0 12.4 - - + +
93A ALA* 3.0 22.7 + - - +
168A LEU* 4.9 8.0 - - + +
169A LEU* 4.8 9.0 - - + -
175A LEU* 4.0 23.3 - - + -
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 2.9 13.7 + - - -
87A VAL* 3.7 3.4 - - - -
89A VAL* 1.3 76.6 - - - +
91A ALA* 1.3 57.4 + - - +
93A ALA* 3.5 6.0 + - - +
94A ARG* 2.9 41.9 + - - +
169A LEU* 5.2 1.6 - - - -
175A LEU* 4.0 14.8 - - - -
178A THR* 3.6 14.7 - - - +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 3.3 26.0 - - - +
53A PHE* 4.1 5.6 - - + -
87A VAL* 2.9 19.1 + - + +
88A SER* 3.6 3.6 - - - +
89A VAL 3.1 0.2 - - - -
90A GLY* 1.3 75.6 - - - +
92A VAL* 1.3 61.2 + - - +
94A ARG* 3.3 25.4 + - - +
95A LYS* 2.9 27.0 + - - +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 4.0 10.5 - - + -
52A VAL* 3.6 37.7 - - + -
53A PHE* 3.7 22.7 - - + -
56A LEU* 3.2 13.3 - - + +
72A LEU* 4.7 14.5 - - + +
75A TYR* 4.4 13.5 - - + -
88A SER* 2.9 22.0 + - - +
89A VAL* 3.0 24.2 - - + +
91A ALA* 1.3 73.5 - - - +
93A ALA* 1.3 61.0 + - + +
95A LYS* 4.2 0.2 - - - -
96A PHE* 3.0 24.9 + - - +
168A LEU* 6.0 0.7 - - + -
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 4.8 6.5 - - - -
89A VAL 3.0 16.4 + - - +
90A GLY* 3.5 6.3 - - - +
92A VAL* 1.3 78.6 - - - +
94A ARG* 1.3 63.2 + - - +
96A PHE* 3.2 8.7 + - - +
97A ILE* 3.0 28.8 + - - +
165A VAL* 4.2 12.6 - - + -
168A LEU* 4.8 6.5 - - + -
169A LEU* 3.7 31.2 - - + -
178A THR* 4.8 1.3 - - + -
182A VAL* 6.0 0.4 - - - -
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Residues in contact with ARG 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.0 10.9 + - - +
90A GLY* 2.9 18.9 + - - +
91A ALA* 3.3 47.0 + - - +
93A ALA* 1.3 76.0 - - - +
95A LYS* 1.3 62.1 + - - +
97A ILE* 3.3 7.6 + - - +
98A ASP* 3.0 32.0 + - - +
178A THR* 3.7 27.4 + - + +
182A VAL* 6.1 2.7 - - + -
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 3.6 53.3 - - + -
56A LEU* 3.9 8.1 - - + -
57A GLU* 4.2 17.4 + - - -
91A ALA 2.9 17.6 + - - +
92A VAL 3.6 5.4 - - - +
94A ARG* 1.3 75.0 - - - +
96A PHE* 1.3 64.2 + - - +
98A ASP* 3.1 7.7 + - + +
99A LEU* 2.9 55.0 + - + +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.5 21.9 - - + +
60A VAL* 3.7 20.0 - - + -
65A GLY* 5.9 1.3 - - - -
68A LEU* 3.7 30.1 - - + -
69A LYS* 5.8 1.6 - - - -
72A LEU* 3.8 17.9 - - + -
92A VAL 3.0 15.1 + - - +
93A ALA* 3.2 9.2 + - - +
95A LYS* 1.3 75.0 - - - +
97A ILE* 1.3 63.9 + - + +
99A LEU* 3.0 5.4 + - - +
100A VAL* 3.0 40.1 + - + +
157A PHE* 4.9 0.2 - + - -
161A SER* 3.3 34.5 - - - -
164A ALA* 5.2 6.3 - - + -
165A VAL* 3.6 25.8 - - + -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA 3.0 17.8 + - - +
94A ARG* 3.7 8.7 - - - +
96A PHE* 1.3 75.7 - - + +
98A ASP* 1.3 58.2 + - - +
100A VAL* 3.1 10.0 - - + +
101A GLU* 2.9 49.5 + - - +
161A SER 4.4 1.8 - - - +
162A TYR* 3.8 37.7 - - + +
165A VAL* 3.5 38.1 - - + -
182A VAL* 4.3 12.6 - - + -
185A LYS* 3.7 20.4 - - + -
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ARG* 3.0 20.2 + - - +
95A LYS* 3.7 11.4 - - + +
97A ILE* 1.3 77.1 - - - +
99A LEU* 1.3 62.0 + - + +
101A GLU* 3.4 13.8 + - - +
102A SER* 3.0 36.0 + - - +
185A LYS* 4.2 12.5 + - - -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE 4.7 0.2 - - - +
56A LEU* 3.5 21.8 - - + +
57A GLU* 3.5 44.6 - - + +
60A VAL* 4.1 13.3 - - + +
95A LYS* 2.9 53.7 + - + +
96A PHE 3.0 8.3 + - - +
98A ASP* 1.3 80.5 - - + +
100A VAL* 1.3 57.1 + - - +
102A SER* 3.2 5.3 + - - -
103A LYS* 2.9 28.7 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A VAL* 3.8 5.8 - - + -
96A PHE* 3.0 34.2 + - + +
97A ILE* 3.1 29.4 - - + +
99A LEU* 1.3 76.3 - - - +
101A GLU* 1.3 56.6 + - + +
103A LYS* 3.2 7.8 + - - +
104A ILE* 3.0 25.5 + - - +
157A PHE* 3.4 33.2 - - + -
158A THR* 3.6 24.6 - - + +
161A SER* 3.7 17.5 - - - +
162A TYR* 5.7 4.0 - - + -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 2.9 28.1 + - - +
98A ASP* 3.7 8.1 - - - +
100A VAL* 1.3 80.2 - - + +
102A SER* 1.3 60.0 + - - +
104A ILE* 3.8 9.0 + - - +
105A ALA* 3.8 14.2 + - - +
158A THR* 5.3 0.7 - - - -
162A TYR* 3.2 25.5 + - - +
185A LYS* 3.1 40.2 + - - +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ASP* 3.0 19.1 + - - +
99A LEU* 3.9 4.0 - - - -
101A GLU* 1.3 74.3 - - - +
103A LYS* 1.3 61.4 + - - +
104A ILE 3.2 0.4 - - - -
105A ALA* 3.1 10.2 + - - +
106A SER* 3.0 31.9 + - - -
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 3.9 13.9 - - + -
61A GLU* 3.1 40.5 + - - +
99A LEU 2.9 18.0 + - - +
100A VAL* 3.2 6.9 + - - +
102A SER* 1.3 77.6 - - - +
104A ILE* 1.3 61.9 + - - +
106A SER* 3.3 12.3 + - - +
107A GLU* 3.0 57.5 + - + +
110A ARG* 4.7 8.1 - - - +
154A TRP* 3.7 41.3 - - + -
158A THR* 5.9 0.9 - - + -
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL 3.0 8.1 + - - +
101A GLU* 3.8 11.2 - - - +
102A SER 3.2 0.2 - - - -
103A LYS* 1.3 77.3 - - - +
105A ALA* 1.3 58.9 + - - +
107A GLU* 3.4 2.3 + - + +
108A GLN* 2.9 33.1 + - + +
151A ILE* 5.2 2.9 - - + +
154A TRP* 3.5 37.9 - - + +
155A LEU* 3.6 22.7 - - + +
158A THR* 3.3 25.6 - - + +
189A PHE* 5.2 3.6 - - + -
192A LYS* 5.9 0.2 - - - +
193A TYR* 3.1 31.4 - - + +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU 3.8 6.8 + - - +
102A SER* 3.1 15.2 + - - +
104A ILE* 1.3 79.7 - - - +
106A SER* 1.3 57.8 + - - +
108A GLN* 3.3 7.0 + - - +
109A THR* 3.0 30.7 + - - -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 3.0 15.0 + - - -
103A LYS* 3.7 18.5 - - - +
105A ALA* 1.3 76.3 - - - +
107A GLU* 1.3 65.6 + - - +
109A THR* 3.1 14.2 - - - +
110A ARG* 3.0 31.5 + - - +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 3.0 47.0 + - - +
104A ILE* 4.0 3.1 - - + +
106A SER* 1.3 76.8 - - - +
108A GLN* 1.3 57.6 + - - +
110A ARG* 3.1 39.0 + - - +
111A ALA* 2.9 28.2 + - - +
151A ILE* 4.2 13.1 - - + +
154A TRP* 3.5 53.8 + - + +
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ILE* 2.9 21.1 + - + +
105A ALA* 3.5 8.3 - - - +
107A GLU* 1.3 77.7 - - - +
109A THR* 1.3 57.2 + - - +
111A ALA* 3.2 5.4 + - - +
112A ASP* 3.0 53.5 + - - +
151A ILE* 4.6 19.9 - - - +
155A LEU* 5.3 1.0 - - - +
192A LYS* 6.1 0.4 - - - +
193A TYR* 3.6 35.1 + - - +
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Residues in contact with THR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ALA 3.0 14.9 + - - +
106A SER* 3.1 23.6 - - - +
108A GLN* 1.3 75.8 - - - +
110A ARG* 1.3 56.9 + - - +
112A ASP* 4.0 9.1 - - - +
113A GLU* 3.0 54.2 + - - +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 4.7 6.7 - - - +
106A SER* 3.0 16.9 + - - +
107A GLU* 3.3 43.0 + - - +
108A GLN 3.1 0.4 - - - -
109A THR* 1.3 77.4 - - + +
111A ALA* 1.3 60.4 + - - +
113A GLU* 3.8 5.5 - - - +
114A LEU* 2.9 39.9 + - + +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A GLU 2.9 6.4 + - - +
108A GLN* 3.2 11.4 + - - +
110A ARG* 1.3 74.0 - - - +
112A ASP* 1.3 70.3 + - - +
114A LEU* 2.9 25.5 + - + +
115A GLN* 3.0 25.1 + - - +
151A ILE* 3.5 39.3 - - + -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLN* 3.0 38.8 + - - +
109A THR* 4.0 7.7 - - - +
111A ALA* 1.3 78.5 - - - +
113A GLU* 1.3 61.3 + - + +
115A GLN* 4.1 13.1 + - - +
116A LYS* 3.9 23.2 + - - +
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A THR* 3.0 38.5 + - - +
110A ARG* 4.0 5.2 - - - +
112A ASP* 1.3 79.7 - - + +
114A LEU* 1.3 62.4 + - - +
115A GLN 3.3 0.8 + - - -
116A LYS* 3.7 18.1 + - - +
117A GLN* 4.5 5.7 + - - +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 2.9 33.1 + - + +
111A ALA* 2.9 25.1 + - + +
113A GLU* 1.3 75.3 - - - +
115A GLN* 1.3 77.5 + - + +
116A LYS 3.3 0.9 + - - -
117A GLN* 3.9 4.4 + - - +
118A GLU* 3.7 34.6 + - - +
151A ILE* 5.6 5.2 - - + -
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Residues in contact with GLN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA* 3.0 22.4 + - - +
112A ASP* 4.3 12.6 + - - +
113A GLU 3.3 0.4 - - - -
114A LEU* 1.3 89.0 - - + +
116A LYS* 1.3 61.3 + - + +
118A GLU* 3.3 9.1 + - - +
119A ILE* 3.0 36.3 + - + +
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Residues in contact with LYS 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP 3.9 20.2 + - - +
113A GLU* 3.9 10.8 - - - +
114A LEU 3.3 0.4 - - - -
115A GLN* 1.3 79.7 - - + +
117A GLN* 1.3 63.7 + - + +
119A ILE* 3.0 9.8 + - + +
120A ASP* 2.9 30.2 + - - +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU 4.5 5.5 + - - +
114A LEU* 3.9 6.0 + - - +
115A GLN 3.6 0.2 - - - -
116A LYS* 1.3 81.1 - - + +
118A GLU* 1.3 61.5 + - + +
120A ASP* 3.7 20.1 - - - +
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Residues in contact with GLU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 3.7 29.8 + - - +
115A GLN* 3.3 11.3 + - - +
116A LYS 3.1 0.6 - - - -
117A GLN* 1.3 78.6 - - + +
119A ILE* 1.3 66.1 + - + +
120A ASP 4.5 1.6 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 3.0 21.9 + - + +
116A LYS* 3.0 10.5 + - + +
118A GLU* 1.3 81.3 - - + +
120A ASP* 1.3 64.3 + - + +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LYS 2.9 15.1 + - - +
117A GLN* 3.7 16.4 - - - +
118A GLU 3.5 1.7 - - - -
119A ILE* 1.3 85.0 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il