Contacts of the helix formed by residues 84 - 113 (chain A) in PDB entry 3N3B
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 THR 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.9 26.5 - - - +
16A ASP* 4.6 4.9 - - + +
19A ASP* 2.6 28.7 + - - +
82A ALA* 3.8 8.1 - - - +
83A LEU* 1.3 86.4 - - + +
85A PRO* 1.4 74.4 - - + +
86A HIS* 3.7 8.2 + - - -
87A GLU* 3.1 28.4 + - - +
88A GLU* 3.5 7.7 + - - +
202A LYS* 4.1 4.5 + - - +
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Residues in contact with PRO 85 (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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7A SER 6.1 1.3 - - - +
9A ILE* 3.4 30.1 - - + +
10A ASN 6.1 0.2 - - - +
15A SER* 5.9 1.8 - - - +
83A LEU 4.7 1.1 - - - +
84A THR* 1.4 87.4 - - + +
86A HIS* 1.3 75.2 + - + +
87A GLU 3.3 0.2 - - - -
88A GLU* 3.4 33.3 + - - +
89A ALA 3.4 3.3 + - - -
68B THR* 6.4 1.3 - - + -
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.0 16.3 - - + +
10A ASN 2.8 27.0 + - - -
11A TRP* 3.9 27.1 - + + -
13A LYS 3.4 22.4 - - - -
14A ILE* 3.6 25.6 - - + +
15A SER* 4.5 8.0 + - - -
19A ASP* 3.8 23.0 + - + +
84A THR* 3.1 9.9 - - - +
85A PRO* 1.3 90.7 - - + +
87A GLU* 1.3 60.5 + - - +
89A ALA* 3.4 3.7 + - - +
90A VAL* 3.1 32.1 + - - +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 4.2 0.2 - - - -
78A LEU* 5.1 1.4 - - - +
81A ASP 4.6 0.9 - - - +
82A ALA* 3.6 19.4 - - + +
83A LEU* 2.8 22.1 + - - +
84A THR* 3.1 22.2 + - - +
86A HIS* 1.3 76.4 - - - +
88A GLU* 1.3 59.3 + - - +
90A VAL* 3.3 2.1 + - - +
91A LEU* 3.0 45.2 + - + +
151A LYS* 4.6 9.0 + - - -
198A TYR* 3.3 29.5 - - + +
202A LYS* 3.2 43.4 + - - +
206A ASN* 5.5 0.3 + - - -
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 4.0 22.0 - - + +
82A ALA* 3.7 23.4 - - + +
84A THR 3.5 7.1 + - - +
85A PRO* 3.4 24.0 + - - +
86A HIS 3.3 0.4 - - - -
87A GLU* 1.3 77.3 - - - +
89A ALA* 1.3 59.6 + - - +
91A LEU* 3.5 10.2 + - - +
92A SER* 3.2 23.3 + - - -
71B ASN* 4.6 3.5 + - - +
72B VAL* 3.5 34.9 - - + +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 4.4 5.4 - - + -
11A TRP* 3.7 27.1 - - + -
23A TRP* 3.7 12.6 - - + -
85A PRO 3.4 7.2 + - - +
86A HIS 3.4 8.9 + - - +
87A GLU 3.3 0.4 - - - -
88A GLU* 1.3 76.7 - - - +
90A VAL* 1.3 64.6 + - - +
92A SER* 3.2 18.5 + - - -
93A ASN 3.3 4.7 + - - -
71B ASN* 4.2 12.3 - - - +
99B ALA* 4.1 17.1 - - + +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 4.8 0.7 - - + -
19A ASP 3.4 25.6 - - - +
22A VAL* 3.9 18.8 - - + -
23A TRP* 3.8 25.6 - - + +
26A LEU* 4.3 5.2 - - + -
86A HIS 3.1 15.4 + - - +
87A GLU 3.7 7.0 - - - +
89A ALA* 1.3 74.6 - - - +
91A LEU* 1.3 58.2 + - - +
93A ASN* 3.2 7.3 + - - +
94A ILE* 3.0 31.7 + - + +
198A TYR* 3.6 32.3 - - + +
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Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 4.2 9.4 - - + +
78A LEU* 3.9 35.4 - - + +
79A MET* 3.6 42.3 - - + +
82A ALA* 4.5 2.2 - - + -
87A GLU* 3.0 40.6 + - + +
88A GLU* 3.7 7.0 - - - +
89A ALA 3.3 0.2 - - - -
90A VAL* 1.3 73.8 - - - +
92A SER* 1.3 60.4 + - - +
94A ILE* 3.6 22.4 - - + +
95A SER* 2.9 30.5 + - - -
198A TYR* 5.1 6.3 - - + -
199A ILE* 5.1 5.2 - - + -
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Residues in contact with SER 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A MET* 3.7 13.7 - - - +
88A GLU 3.2 12.8 + - - -
89A ALA* 3.2 13.3 + - - -
91A LEU* 1.3 75.7 - - - +
93A ASN* 1.3 61.9 + - - +
95A SER* 3.7 3.3 + - - -
96A PHE* 3.2 16.6 + - - +
71B ASN* 2.8 30.0 + - - -
92B SER 4.2 2.4 - - - +
95B SER* 3.9 7.8 + - - -
96B PHE* 3.5 28.3 - - - +
99B ALA* 4.7 1.3 - - - -
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Residues in contact with ASN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 4.7 5.2 - - + -
26A LEU* 3.2 36.3 + - + +
27A THR* 3.7 15.8 - - + +
30A PHE* 6.1 1.2 - - - -
89A ALA 3.3 5.9 + - - +
90A VAL* 3.2 12.0 + - + +
92A SER* 1.3 76.9 - - - +
94A ILE* 1.3 59.4 + - - +
96A PHE* 3.4 2.5 + - - +
97A MET* 3.0 45.9 + - - +
195A HIS* 5.1 0.3 + - - -
96B PHE* 3.3 46.1 - - + -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.8 13.0 - - + -
75A ALA* 4.0 15.3 - - + -
90A VAL* 3.0 32.9 + - + +
91A LEU* 3.6 25.8 - - + +
93A ASN* 1.3 75.9 - - - +
95A SER* 1.3 59.6 + - - +
97A MET* 3.4 2.5 + - - +
98A GLU* 2.9 37.7 + - - +
195A HIS* 3.6 48.8 - - + +
198A TYR* 4.3 12.1 - - + -
199A ILE* 5.0 12.6 - - + -
321A MN 4.6 0.4 - - - +
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Residues in contact with SER 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 2.9 45.4 + - - +
75A ALA* 3.8 17.5 - - - -
76A PRO* 4.0 7.9 - - - +
79A MET* 4.6 6.1 - - - -
91A LEU 2.9 17.4 + - - -
92A SER* 3.9 7.0 - - - -
94A ILE* 1.3 76.9 - - - +
96A PHE* 1.3 61.5 + - - +
98A GLU* 3.2 16.7 + - - +
99A ALA 3.5 0.3 + - - -
79B MET* 5.8 1.2 - - - +
92B SER* 3.7 8.9 + - - -
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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
----------------------------------------------------------
30A PHE* 3.6 31.4 - + - -
92A SER 3.2 12.6 + - - +
93A ASN* 3.7 2.5 - - - +
95A SER* 1.3 77.9 - - - +
97A MET* 1.3 76.1 + - + +
99A ALA* 3.0 17.8 + - - +
100A VAL* 3.2 28.3 + - + +
23B TRP* 4.0 9.2 - + - -
27B THR* 4.0 14.4 - - + -
30B PHE* 5.3 0.7 - + - -
89B ALA 4.9 0.9 - - - -
92B SER* 3.5 25.7 - - - +
93B ASN* 3.3 45.8 - - + -
96B PHE* 3.6 28.9 - + + -
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Residues in contact with MET 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.5 5.6 - - + +
29A ASN 5.7 0.4 - - - -
30A PHE* 4.2 14.8 - - - -
31A TRP* 3.5 37.5 - - + +
93A ASN* 3.0 37.6 + - - +
94A ILE* 3.9 4.7 - - - +
96A PHE* 1.3 97.1 - - + +
98A GLU* 1.3 59.6 + - - +
100A VAL* 3.3 14.3 + - + +
101A HIS* 3.0 45.8 + - + +
191A ASP* 3.4 26.7 - - - +
195A HIS* 4.7 8.7 - - + +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.0 11.7 - - - +
70A GLN* 3.7 22.9 - - + +
71A ASN* 3.7 17.0 - - - +
75A ALA* 5.1 0.8 - - + +
94A ILE* 2.9 29.2 + - + +
95A SER* 3.4 9.2 - - - +
96A PHE 3.2 0.4 - - - -
97A MET* 1.3 76.9 - - - +
99A ALA* 1.3 57.9 + - - +
101A HIS* 3.2 4.8 + - - +
102A ALA* 3.1 26.3 + - - +
158A GLU* 2.9 5.7 - - - +
192A GLU* 3.1 1.4 - - - +
195A HIS* 3.4 5.2 + - - -
320A MN 2.1 34.5 + - - -
321A MN 2.0 31.9 + - - -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASN* 3.7 29.9 - - - +
95A SER 3.5 1.6 + - - -
96A PHE* 3.0 12.4 + - - +
98A GLU* 1.3 76.3 - - - +
100A VAL* 1.3 60.8 + - - +
102A ALA* 3.9 5.8 - - - +
103A ARG* 3.0 30.1 + - - +
11B TRP* 4.7 2.8 + - - -
23B TRP* 4.2 11.1 - - + -
89B ALA* 4.0 24.7 - - + +
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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
----------------------------------------------------------
31A TRP* 3.6 35.4 - - + +
32A LEU* 4.4 7.2 - - + -
33A PRO* 4.2 13.2 - - + +
96A PHE* 3.2 42.9 + - + +
97A MET* 3.3 26.4 + - + +
99A ALA* 1.3 75.0 - - - +
101A HIS* 1.3 58.8 + - - +
103A ARG* 3.4 6.2 + - - +
104A SER* 3.0 28.1 + - - -
23B TRP* 4.0 11.2 - - + -
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Residues in contact with HIS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.5 23.3 - + - -
67A ASP* 3.5 16.6 - - - +
97A MET* 3.0 27.2 + - + +
98A GLU* 3.2 10.6 + - - +
100A VAL* 1.3 77.0 - - + +
102A ALA* 1.3 61.2 + - - +
104A SER* 2.7 25.0 + - - -
105A TYR* 3.2 15.8 - - - +
188A ILE* 3.8 20.4 - - + +
191A ASP* 3.0 36.8 + - + +
192A GLU* 3.1 19.5 - - - -
195A HIS* 4.4 4.7 - + - -
320A MN 2.5 23.6 + - - -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 3.9 11.9 - - + +
67A ASP* 3.9 12.9 - - + +
68A THR* 4.0 13.0 - - - +
98A GLU 3.1 14.8 + - - +
99A ALA* 4.0 6.5 - - - +
101A HIS* 1.3 78.4 - - - +
103A ARG* 1.3 62.2 + - - +
105A TYR* 3.5 26.6 + - - +
106A SER* 3.8 5.9 + - - -
9B ILE* 3.8 24.5 - - + +
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Residues in contact with ARG 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.9 18.6 - - - -
34A GLU* 3.6 19.5 + - - -
99A ALA 3.0 19.7 + - - +
100A VAL* 3.6 4.7 - - - +
102A ALA* 1.3 77.1 - - - +
104A SER* 1.3 62.6 + - - +
106A SER* 3.1 12.6 + - - -
107A SER* 3.0 28.5 + - - +
110A SER* 6.2 0.2 - - - -
11B TRP* 3.5 53.1 + - + +
12B ASN* 5.4 3.0 + - - -
20B LEU* 4.1 20.0 - - - +
23B TRP* 3.9 32.2 - - + +
24B ASN* 5.1 1.6 + - - +
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Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 4.1 7.2 - - - -
33A PRO* 3.7 24.7 - - - -
100A VAL 3.0 15.2 + - - -
101A HIS 2.7 19.2 + - - -
103A ARG* 1.3 75.9 - - - +
105A TYR* 1.3 62.2 + - - +
107A SER* 3.3 4.7 + - - -
108A ILE* 3.2 25.9 + - - +
184A LEU* 3.5 27.9 - - - +
188A ILE* 3.7 10.2 - - - +
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.6 38.8 - + + +
63A LEU* 3.5 30.3 - - + +
64A THR* 3.4 30.5 - - - +
67A ASP* 3.0 27.5 + - - -
101A HIS 3.2 21.1 - - - -
102A ALA* 3.5 13.0 + - - +
103A ARG 3.2 0.8 - - - -
104A SER* 1.3 76.4 + - - +
106A SER* 1.3 61.9 + - - +
108A ILE* 3.3 14.9 + - + +
109A PHE* 3.1 31.1 + - + -
162A PHE* 3.9 5.9 - - - -
166A PHE* 4.2 5.0 - - - -
185A ILE* 4.1 6.3 - - + -
188A ILE* 3.8 28.0 - - + +
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 5.3 0.3 - - - +
102A ALA 3.8 2.3 + - - -
103A ARG* 3.1 15.2 + - - -
105A TYR* 1.3 75.4 - - - +
107A SER* 1.3 60.6 + - - +
109A PHE* 3.4 9.1 + - - -
110A SER* 2.9 26.4 + - - -
122A TYR* 4.0 7.8 + - - -
9B ILE 4.0 10.2 + - - -
10B ASN* 4.0 1.6 + - - -
11B TRP* 3.2 42.3 + - - +
12B ASN* 3.0 19.1 + - - +
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PRO* 3.7 25.5 - - - +
34A GLU* 4.3 3.5 + - - -
38A LEU* 3.9 11.9 - - - +
103A ARG* 3.0 30.6 + - - +
104A SER 3.4 10.8 - - - -
105A TYR 3.2 0.4 - - - -
106A SER* 1.3 75.0 - - - +
108A ILE* 1.3 61.0 + - - +
110A SER* 3.9 5.0 - - - -
111A THR* 2.8 33.3 + - - -
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.4 18.4 - - + -
56A THR* 5.6 3.8 - - + -
60A PHE* 4.3 29.8 - - + -
104A SER 3.2 15.9 + - - +
105A TYR* 3.5 20.4 - - + +
106A SER 3.3 0.2 - - - -
107A SER* 1.3 77.7 - - - +
109A PHE* 1.3 60.9 + - + +
111A THR* 4.1 1.1 - - - -
112A LEU* 3.1 52.4 + - + +
113A CYS* 4.2 3.3 - - - -
181A THR* 4.0 27.6 - - + -
184A LEU* 4.3 16.6 - - + -
185A ILE* 4.6 1.6 - - + -
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Residues in contact with PHE 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 6.3 0.2 - - + -
57A MET* 4.0 20.9 - - + -
60A PHE* 3.5 36.6 - + + -
61A THR* 3.7 25.4 - - + -
64A THR* 4.4 6.7 - - - -
105A TYR 3.1 23.3 + - - -
106A SER* 3.7 10.5 - - - +
107A SER 3.4 0.2 - - - -
108A ILE* 1.3 79.5 - - + +
110A SER* 1.3 59.8 + - - +
113A CYS* 3.0 46.5 + - - +
118A VAL* 3.9 34.2 - - + +
122A TYR* 3.9 19.5 - + - -
10B ASN* 6.0 0.4 - - - -
12B ASN* 4.0 9.2 - - - +
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER 2.9 18.2 + - - -
107A SER* 3.9 7.6 - - - -
108A ILE 3.4 0.2 - - - -
109A PHE* 1.3 77.2 - - - +
111A THR* 1.3 61.9 + - - +
113A CYS 4.6 3.3 - - - +
12B ASN* 3.5 21.1 + - - +
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.8 21.2 - - + +
39A SER* 3.8 34.5 - - - +
42A ILE* 4.0 20.4 - - + +
107A SER* 2.8 23.4 + - - -
108A ILE 4.2 1.8 - - - -
110A SER* 1.3 80.9 + - - +
112A LEU* 1.3 61.9 + - + +
113A CYS 5.2 0.2 - - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 3.7 17.0 - - + +
41A ASP* 3.7 8.3 - - + +
42A ILE* 3.7 41.8 - - + +
45A TRP* 3.2 38.9 + - + -
56A THR* 6.4 0.2 - - + -
108A ILE* 3.1 30.2 + - + +
111A THR* 1.3 82.8 - - - +
113A CYS* 1.3 70.0 + - - +
178A LEU* 4.2 15.7 - - + -
181A THR* 3.8 22.7 - - + +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.6 34.8 - - + +
56A THR* 6.0 1.1 - - - -
57A MET* 3.8 20.4 - - - -
108A ILE* 4.2 7.4 - - - -
109A PHE* 3.0 37.5 + - - +
110A SER 4.6 4.2 - - - +
111A THR 5.2 0.2 - - - -
112A LEU* 1.3 82.5 - - - +
114A GLN* 1.3 64.2 + - - +
115A THR 4.1 1.0 + - - -
118A VAL* 3.5 18.8 - - + -
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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