Contacts of the helix formed by residues 83 - 109 (chain A) in PDB entry 5HJS
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 ARG 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER* 1.4 72.7 - - - +
84A GLU* 1.4 57.2 + - - +
86A ARG* 3.5 37.7 + - - +
87A GLN* 3.1 51.0 + - + +
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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
----------------------------------------------------------
82A SER* 3.3 7.0 + - - +
83A ARG* 1.4 77.0 - - - +
85A ALA* 1.4 58.2 + - - +
87A GLN* 3.2 20.0 + - - +
88A GLN* 2.9 48.6 + - + +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 3.5 23.7 - - + +
82A SER* 3.3 23.7 + - - +
83A ARG 3.5 0.2 - - - -
84A GLU* 1.4 73.9 - - - +
86A ARG* 1.3 56.0 + - - +
88A GLN* 3.4 2.1 + - - -
89A ARG* 2.9 55.5 + - - +
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Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A SER 3.4 14.1 + - - +
83A ARG* 3.5 52.7 + - - +
84A GLU 3.3 0.2 - - - -
85A ALA* 1.3 76.4 - - - +
87A GLN* 1.4 58.8 + - + +
89A ARG* 3.4 26.0 + - - +
90A PHE* 3.0 30.5 + - - +
164A LYS 4.4 7.5 - - - +
165A ALA 5.1 0.3 - - - -
269A LYS* 4.9 11.5 + - - +
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Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG* 3.1 41.4 + - + +
84A GLU* 3.2 23.3 + - - +
86A ARG* 1.4 80.9 - - + +
88A GLN* 1.3 63.7 + - - +
90A PHE* 3.8 8.6 - - - +
91A ALA* 3.1 25.6 + - - +
269A LYS* 5.9 2.0 - - + +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.5 26.4 - - + +
73A PRO* 4.3 3.6 - - - +
75A PRO* 4.2 17.3 - - + -
84A GLU* 2.9 33.9 + - + +
85A ALA* 3.8 5.6 - - - +
86A ARG 3.3 0.2 - - - -
87A GLN* 1.3 84.0 + - - +
89A ARG* 1.4 60.3 + - - +
90A PHE 3.4 0.2 - - - -
91A ALA* 3.6 7.6 - - - +
92A HIS* 2.9 27.9 + - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.6 50.4 - - + +
75A PRO* 3.7 23.3 - - + +
82A SER 4.9 4.9 + - - +
85A ALA* 2.9 42.3 + - - +
86A ARG* 3.7 22.8 - - - +
88A GLN* 1.4 72.5 - - - +
90A PHE* 1.4 64.7 + - - +
92A HIS* 3.2 4.0 + - - +
93A PHE 3.2 17.8 + - - -
164A LYS* 3.2 51.9 + - - +
165A ALA* 3.9 6.2 - - - +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ARG 3.0 19.3 + - - +
87A GLN* 3.8 8.1 - - - +
89A ARG* 1.4 76.9 - - - +
91A ALA* 1.4 64.4 + - + +
93A PHE* 3.3 4.7 + - - +
94A THR* 3.1 46.0 + - + +
165A ALA* 3.4 25.2 + - - +
166A GLY* 4.5 1.3 - - - -
264A LEU* 3.8 11.9 - - + -
269A LYS* 3.5 47.1 - - + +
270A LYS 3.6 24.5 - - - -
271A LEU* 4.4 11.0 - - + -
272A PRO* 5.5 0.2 - - + -
301A 668 3.8 23.3 - - + +
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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
----------------------------------------------------------
72A THR* 4.2 12.3 - - + +
87A GLN 3.1 19.9 + - - +
88A GLN* 3.6 13.0 - - - +
90A PHE* 1.4 77.6 - - + +
92A HIS* 1.4 64.0 + - - +
94A THR* 2.7 22.8 + - - -
95A GLU* 3.0 25.4 + - - +
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.8 11.8 - - + +
72A THR* 2.7 31.7 + - - +
73A PRO* 4.7 2.9 - - + +
74A TRP* 3.4 29.2 + + + -
88A GLN 2.9 15.5 + - - +
89A ARG 3.2 9.8 + - - +
91A ALA* 1.4 76.2 - - - +
93A PHE* 1.4 56.0 + + - +
95A GLU* 3.3 4.5 + - - +
96A LEU* 3.0 49.3 + - + +
155A PHE* 3.7 30.0 - + - -
157A TYR* 2.7 34.2 + + - -
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Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TRP* 3.6 28.0 - + - -
89A ARG 3.2 5.0 + - - +
90A PHE 3.8 7.2 - - - +
92A HIS* 1.4 80.0 - + - +
94A THR* 1.3 58.4 + - - +
96A LEU* 3.3 11.4 + - + +
97A ALA* 3.1 28.2 + - - +
151A PHE* 4.6 4.9 - + - -
157A TYR* 4.1 25.6 - + + -
161A ASP 4.4 1.3 - - - -
162A PHE* 3.7 53.4 - + - -
165A ALA* 3.7 19.7 - - + -
167A LEU* 3.7 20.2 - - + -
301A 668 3.6 33.7 - - + +
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Residues in contact with THR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 3.1 35.5 + - + +
91A ALA* 2.7 26.9 + - - -
93A PHE* 1.3 74.0 - - - +
95A GLU* 1.3 58.8 + - - +
97A ALA* 3.5 3.5 + - - +
98A ILE* 3.1 33.1 + - - +
271A LEU* 4.3 3.1 - - + -
272A PRO* 3.8 30.2 - - + +
275A LEU* 3.6 1.7 - - - +
301A 668 3.5 28.0 - - + -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG 3.8 6.0 - - - +
71A VAL* 3.6 16.4 - - + -
72A THR* 2.8 48.0 + - - -
91A ALA* 3.0 25.6 + - - +
92A HIS 3.6 5.2 - - - +
93A PHE 3.3 0.2 - - - -
94A THR* 1.3 76.7 - - - +
96A LEU* 1.3 64.0 + - - +
98A ILE* 3.4 14.6 + - + +
99A VAL* 3.2 28.4 + - + +
272A PRO* 6.2 0.2 - - + -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 4.2 10.8 - - + -
92A HIS* 3.0 40.8 + - + +
93A PHE* 3.3 14.1 + - + +
95A GLU* 1.3 75.5 - - - +
97A ALA* 1.3 57.8 + - - +
99A VAL* 3.3 6.1 + - + +
100A SER 3.0 22.3 + - - -
151A PHE* 3.8 33.4 - - + -
152A LEU* 3.9 17.9 - - + -
155A PHE* 3.8 28.5 - - + -
157A TYR* 4.3 3.4 - - + -
301A 668 3.4 31.2 - - + -
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Residues in contact with ALA 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 PHE 3.1 13.1 + - - +
94A THR 3.5 10.3 - - - +
95A GLU 3.3 0.2 - - - -
96A LEU* 1.3 74.2 - - - +
98A ILE* 1.4 57.7 + - - +
100A SER* 3.3 5.8 + - - -
101A VAL* 2.9 31.7 + - - +
134A MET* 3.6 25.8 - - + +
275A LEU* 3.8 12.1 - - + -
279A TRP* 4.7 0.2 - - + -
301A 668 3.7 24.8 - - + -
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR 3.1 18.6 + - - +
95A GLU* 3.7 15.0 - - + +
96A LEU 3.3 0.2 - - - -
97A ALA* 1.4 72.9 - - - +
99A VAL* 1.3 67.5 + - + +
101A VAL* 3.3 5.3 + - - +
102A GLN* 3.0 44.5 + - - +
272A PRO* 3.5 33.4 - - + -
274A LEU* 4.4 20.1 - - + +
275A LEU* 4.0 18.6 - - + -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.8 31.9 - - + -
71A VAL* 5.1 6.1 - - + -
95A GLU* 3.2 16.8 + - + +
96A LEU* 3.3 9.2 + - - +
98A ILE* 1.3 76.3 - - + +
100A SER* 1.3 62.5 + - - +
102A GLN* 3.4 16.4 + - - +
103A GLU* 3.1 39.7 + - + +
152A LEU* 4.4 14.1 - - + -
301A 668 4.0 16.4 - - + -
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU 3.0 13.2 + - - -
97A ALA 3.3 10.1 - - - -
98A ILE 3.2 0.2 - - - -
99A VAL* 1.3 76.2 - - - +
101A VAL* 1.4 61.7 + - - +
103A GLU* 3.1 4.7 + - - +
104A ILE* 3.0 32.1 + - - +
134A MET* 3.4 26.2 - - - +
137A GLU* 4.9 3.8 - - - +
301A 668 3.9 41.3 - - - -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA 2.9 21.7 + - - +
98A ILE 3.3 5.8 + - - +
100A SER* 1.4 69.1 - - - +
102A GLN* 1.3 62.3 + - - +
104A ILE* 3.2 11.4 + - + +
105A VAL* 3.0 34.9 + - + +
130A ALA* 4.8 8.3 - - + -
134A MET* 4.2 14.6 - - - -
274A LEU* 3.7 29.2 - - + -
275A LEU* 4.0 13.9 - - + -
278A ILE* 3.9 27.6 - - + -
5C LEU* 4.9 5.2 - - + -
8C LEU* 5.0 0.2 - - + -
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Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.0 34.1 + - + +
99A VAL* 3.6 18.1 - - - +
101A VAL* 1.3 75.4 - - - +
103A GLU* 1.3 56.6 + - + +
105A VAL* 3.5 3.2 + - - +
106A ASP* 3.1 34.2 + - - +
274A LEU* 4.6 3.6 - - + +
8C LEU* 4.1 36.7 - - + +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN 5.6 1.4 - - - +
99A VAL* 3.1 27.4 + - + +
100A SER 3.6 7.2 - - - +
102A GLN* 1.3 72.6 - - + +
104A ILE* 1.4 60.4 + - + +
106A ASP* 3.3 10.8 + - - +
107A PHE* 2.9 29.8 + - - +
137A GLU* 6.1 0.5 - - - -
141A ARG* 5.3 0.7 + - - -
152A LEU* 5.1 1.7 - - - +
301A 668 3.4 41.6 - - - -
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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
----------------------------------------------------------
100A SER* 3.0 26.0 + - - +
101A VAL* 3.2 10.5 + - + +
103A GLU* 1.4 73.3 - - + +
105A VAL* 1.4 55.2 + - + +
107A PHE* 3.3 7.7 + - + +
108A ALA* 2.8 33.7 + - - +
126A LEU* 4.0 20.4 - - + -
129A SER* 5.4 0.2 - - - +
130A ALA* 3.7 22.2 - - + +
133A VAL* 3.5 35.7 - - + -
134A MET* 3.7 31.0 - - + +
137A GLU* 5.5 4.9 - - + +
200A ILE* 4.6 8.5 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.0 27.1 + - + +
102A GLN 3.8 5.6 - - - +
104A ILE* 1.4 72.0 - - + +
106A ASP* 1.4 68.9 + - - +
108A ALA* 3.4 1.7 + - - +
109A LYS* 3.1 31.4 + - + +
126A LEU* 4.1 14.1 - - + -
5C LEU* 3.5 29.2 - - + -
8C LEU* 3.8 37.2 - - + +
9C LEU* 3.8 23.6 - - + -
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Residues in contact with ASP 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 GLN* 3.1 21.8 + - - +
103A GLU* 3.3 12.9 + - - +
105A VAL* 1.4 79.2 - - - +
107A PHE* 1.3 61.8 + - - +
109A LYS* 3.5 24.8 + - - +
110A GLN* 3.6 22.8 + - - +
8C LEU 5.2 0.9 - - - +
11C GLU* 4.8 8.8 - - - +
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Residues in contact with PHE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 3.4 26.9 - - + -
56A ALA* 4.0 17.3 - - + +
57A GLN* 3.4 44.2 - - + +
103A GLU 2.9 17.4 + - - +
104A ILE* 3.7 6.5 - - - +
106A ASP* 1.3 74.3 - - - +
108A ALA* 1.4 57.9 + - - +
110A GLN* 2.8 30.0 + - + +
111A LEU* 3.4 34.1 + - + +
133A VAL* 6.0 0.2 - - + -
193A ALA* 3.9 20.6 - - + -
196A ILE* 3.6 32.5 - - + -
197A ALA 4.7 0.4 - - - -
200A ILE* 4.6 5.4 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE 2.8 19.9 + - - +
105A VAL 3.8 4.0 - - - +
107A PHE* 1.4 71.8 - - - +
109A LYS* 1.3 62.5 + - - +
111A LEU* 3.1 23.5 + - - +
114A PHE* 3.2 38.8 - - + +
126A LEU* 3.8 25.1 - - + -
200A ILE* 4.3 9.9 - - + -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 3.1 36.2 + - + +
106A ASP* 3.7 17.0 + - - +
107A PHE 3.2 0.6 - - - -
108A ALA* 1.3 75.0 - - - +
110A GLN* 1.3 61.2 + - + +
111A LEU 3.4 2.5 + - - +
114A PHE* 4.2 6.1 - - + -
115A LEU* 3.4 39.3 - - + +
8C LEU 2.9 21.8 + - - -
9C LEU* 3.2 36.7 + - + +
11C GLU* 3.5 24.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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