Contacts of the helix formed by residues 94 - 123 (chain Y) in PDB entry 3J7Y
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 94 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186V THR* 3.3 38.9 + - - -
187V TYR* 3.7 11.4 - - - +
188V VAL 4.8 1.6 - - - -
197V GLU* 4.6 5.5 + - - -
93Y LYS* 1.3 74.6 - - - +
95Y ASN* 1.3 55.7 + - - +
96Y GLU* 3.5 9.2 + - - +
97Y ASP* 3.2 16.9 + - - +
98Y LEU* 2.7 36.7 + - - +
149Y ARG* 3.9 3.4 - - - +
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Residues in contact with ASN 95 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187V TYR* 5.3 7.3 - - - -
193V THR* 3.4 15.8 + - - +
194V LEU* 3.5 37.2 - - + +
197V GLU* 2.7 33.4 + - + +
198V VAL* 4.6 1.1 - - - -
94Y SER* 1.3 74.2 - - - +
96Y GLU* 1.3 56.6 + - - +
98Y LEU* 3.2 6.2 + - - +
99Y HIS* 2.9 30.3 + - - +
146Y VAL* 5.3 2.6 - - - +
149Y ARG* 2.5 40.7 + - - +
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Residues in contact with GLU 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197V GLU* 3.4 33.9 + - + +
198V VAL* 4.3 10.5 - - + -
201V ALA* 3.7 30.5 - - + +
94Y SER* 3.5 7.1 + - - +
95Y ASN* 1.3 77.7 - - - +
97Y ASP* 1.3 64.8 + - - +
99Y HIS* 3.4 4.3 + - - +
100Y LYS* 3.2 33.7 + - - +
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Residues in contact with ASP 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689 PHE* 3.1 25.2 - - - -
709 LEU* 3.6 13.6 - - - +
184V GLU* 5.6 0.2 - - - +
186V THR* 3.8 12.0 + - - +
93Y LYS* 3.7 32.4 + - + +
94Y SER* 3.2 25.7 + - - +
96Y GLU* 1.3 79.4 - - - +
98Y LEU* 1.3 57.9 + - - +
100Y LYS* 3.2 8.4 + - - +
101Y LEU* 2.9 25.7 + - - +
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Residues in contact with LEU 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194V LEU* 4.5 6.1 - - + -
90Y LEU* 3.3 39.9 - - + +
93Y LYS* 3.4 32.5 - - + +
94Y SER 2.7 25.1 + - - +
95Y ASN* 3.2 7.6 + - - +
97Y ASP* 1.3 73.7 - - - +
99Y HIS* 1.3 55.9 - - - +
101Y LEU* 3.2 12.1 + - + +
102Y TRP* 2.9 26.4 + - - +
142Y LEU* 3.8 10.3 - - + +
145Y VAL* 4.0 14.1 - - + -
146Y VAL* 3.5 26.9 - - + -
149Y ARG* 4.1 9.6 - - - +
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Residues in contact with HIS 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619 VAL* 3.1 28.5 + - - +
639 PRO* 3.7 25.8 - - + +
20U PHE* 3.8 27.8 - + + +
21U ARG* 4.9 6.0 + - + +
194V LEU* 4.3 10.3 - - + +
198V VAL* 3.6 40.7 - - + +
202V MET* 5.9 0.8 - - - -
95Y ASN 2.9 13.0 + - - +
96Y GLU 3.5 9.2 - - - +
98Y LEU* 1.3 75.9 - - - +
100Y LYS* 1.3 64.4 + - + +
102Y TRP* 3.2 17.4 + - - +
103Y TYR* 3.2 23.5 + + - -
142Y LEU* 6.0 0.2 - - - -
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Residues in contact with LYS 100 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639 PRO* 3.8 28.7 - - + -
649 ASP* 4.0 32.9 + - - +
659 LEU* 3.8 4.4 - - + +
679 GLY 5.7 2.8 + - - -
689 PHE* 3.3 40.7 - - + +
96Y GLU* 3.2 20.6 + - - +
97Y ASP* 3.2 6.1 + - - +
99Y HIS* 1.3 82.2 - - + +
101Y LEU* 1.3 60.6 + - - +
103Y TYR* 3.2 13.0 + - - +
104Y VAL* 3.2 16.6 + - - +
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Residues in contact with LEU 101 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689 PHE* 3.6 8.4 - - + -
709 LEU* 4.2 17.9 - - + +
719 LYS 3.9 12.8 - - - +
85Y TRP* 3.7 52.0 - - + +
90Y LEU* 4.6 11.2 - - + -
93Y LYS* 5.9 3.1 - - + -
97Y ASP* 2.9 14.8 + - - +
98Y LEU* 3.3 15.0 - - + +
100Y LYS* 1.3 76.2 - - - +
102Y TRP* 1.3 57.3 + - - +
104Y VAL* 3.2 6.1 + - + +
105Y LEU* 2.9 45.3 + - + +
142Y LEU* 3.9 14.8 - - + -
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Residues in contact with TRP 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379 ARG* 3.5 22.9 - - - -
21U ARG* 3.5 29.8 - - + -
22U THR* 3.1 37.8 + - - +
23U ASN* 5.6 0.4 - - - -
25U PHE* 4.6 4.0 - + - -
98Y LEU 2.9 13.4 + - - +
99Y HIS* 3.2 13.4 + - - +
101Y LEU* 1.3 75.4 - - - +
103Y TYR* 1.3 73.6 + + + +
105Y LEU* 3.2 10.3 + - - +
106Y LEU* 2.9 32.8 + - + +
139Y MET* 3.6 57.4 - - + +
142Y LEU* 3.5 27.3 - - + +
143Y ASP* 4.3 9.6 - - + -
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Residues in contact with TYR 103 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609 PHE* 4.4 2.5 - - + +
619 VAL 3.2 20.4 + - - -
629 VAL* 3.6 40.6 - - + -
639 PRO* 3.9 13.2 - - + -
659 LEU* 4.8 3.6 - - + -
19U VAL 3.7 16.1 + - - -
21U ARG* 3.7 24.9 + - - -
22U THR* 4.4 11.5 - - + +
60U ILE* 3.7 26.7 - - + -
99Y HIS* 3.2 27.6 + + - +
100Y LYS 3.2 9.3 + - - +
102Y TRP* 1.3 86.5 - + + +
104Y VAL* 1.3 62.4 - - - +
106Y LEU* 3.2 16.7 + - + +
107Y LYS* 3.2 29.2 + - - +
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Residues in contact with VAL 104 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659 LEU* 4.2 13.5 - - + -
689 PHE* 3.7 26.0 - - + -
709 LEU 4.0 9.6 - - - +
719 LYS* 4.4 0.7 - - - -
729 PRO* 3.8 35.2 - - + -
100Y LYS 3.2 13.3 + - - +
101Y LEU* 3.2 11.4 + - + +
103Y TYR* 1.3 79.3 - - - +
105Y LEU* 1.3 62.4 + - - +
107Y LYS* 3.6 10.2 + - - +
108Y GLU* 3.4 18.9 + - - +
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Residues in contact with LEU 105 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729 PRO* 3.6 33.0 - - + +
85Y TRP* 4.1 9.0 - - + +
90Y LEU* 6.0 0.2 - - + -
101Y LEU* 2.9 31.4 + - + +
102Y TRP* 3.2 7.6 + - - +
104Y VAL* 1.3 78.2 - - - +
106Y LEU* 1.3 57.8 + - - +
108Y GLU* 3.2 7.7 + - - +
109Y ARG* 2.9 28.2 + - - +
135Y VAL* 4.1 9.4 - - + +
138Y SER* 3.4 26.7 - - - +
139Y MET* 3.6 26.2 - - + +
142Y LEU* 3.8 27.8 - - + -
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Residues in contact with LEU 106 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22U THR* 4.1 20.4 - - - +
24U PHE 4.3 0.4 - - - +
25U PHE* 3.5 32.8 - - + -
56U TYR* 3.1 33.0 - - + +
60U ILE* 4.1 14.8 - - + -
61U TYR* 4.5 0.4 - - + -
102Y TRP* 2.9 20.3 + - + +
103Y TYR* 3.2 14.1 + - + +
105Y LEU* 1.3 77.7 - - - +
107Y LYS* 1.3 70.2 + - + +
109Y ARG* 3.2 7.2 + - - +
110Y ASN* 2.8 42.7 + - - +
139Y MET* 4.4 6.3 - - + -
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Residues in contact with LYS 107 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629 VAL* 5.5 0.2 - - - +
659 LEU* 3.8 29.0 - - - +
60U ILE* 3.5 41.2 + - + +
61U TYR* 3.2 23.7 + - + +
66Y GLU* 3.1 36.0 - - + +
103Y TYR* 3.2 20.1 + - - +
104Y VAL* 4.0 8.7 - - - +
106Y LEU* 1.3 79.8 - - - +
108Y GLU* 1.3 57.9 + - - +
110Y ASN* 3.2 4.2 + - - +
111Y MET* 2.9 29.0 + - - +
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Residues in contact with GLU 108 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729 PRO* 3.9 23.4 - - + +
739 TYR* 2.7 35.2 + - - -
175V LYS* 4.4 16.6 - - + +
104Y VAL 3.4 10.5 + - - +
105Y LEU 3.2 10.4 + - - +
107Y LYS* 1.3 79.1 - - - +
109Y ARG* 1.3 55.7 + - - +
111Y MET* 3.0 34.5 + - + +
112Y LEU* 2.9 43.3 + - - +
131Y ARG* 5.1 0.5 - - - -
135Y VAL* 3.0 17.5 - - + +
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Residues in contact with ARG 109 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE* 3.1 55.1 - - + -
105Y LEU 2.9 13.8 + - - +
106Y LEU* 3.3 10.3 - - - +
108Y GLU* 1.3 76.9 - - - +
110Y ASN* 1.3 57.1 + - - +
112Y LEU* 3.2 8.9 + - - +
113Y LEU* 2.9 44.7 + - + +
132Y LEU* 4.3 8.0 - - + +
135Y VAL* 3.9 16.1 - - + +
136Y VAL* 3.2 51.5 - - - +
139Y MET* 3.9 19.9 - - + +
140Y ASP* 4.8 2.0 + - - -
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Residues in contact with ASN 110 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE* 3.0 24.1 - - - +
26U ILE* 3.6 34.5 - - - +
56U TYR* 3.0 27.0 + - - -
61U TYR* 3.2 20.3 + - - +
67Y PHE* 3.9 8.0 - - + -
106Y LEU* 2.8 24.1 + - - +
107Y LYS 3.3 7.2 - - - +
109Y ARG* 1.3 74.5 - - - +
111Y MET* 1.3 57.7 + - - +
113Y LEU* 3.2 6.5 + - - +
114Y THR* 2.9 34.2 + - - +
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Residues in contact with MET 111 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175V LYS* 4.0 13.0 - - - +
66Y GLU 3.8 9.4 - - - +
67Y PHE* 3.5 16.8 - - - +
68Y PHE* 3.5 28.3 - - - +
69Y ASP* 3.7 28.0 - - + -
107Y LYS 2.9 13.0 + - - +
108Y GLU* 3.0 40.4 + - + +
110Y ASN* 1.3 75.6 - - - +
112Y LEU* 1.3 72.3 + - + +
114Y THR* 2.3 23.0 + - - -
115Y LEU* 2.9 23.5 + - - -
131Y ARG* 4.6 6.1 - - - +
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Residues in contact with LEU 112 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739 TYR* 3.8 2.5 - - - +
108Y GLU* 2.9 47.1 + - - +
109Y ARG 3.2 6.9 + - - +
111Y MET* 1.3 87.0 - - + +
113Y LEU* 1.3 58.3 + - - +
115Y LEU* 3.2 5.3 + - + +
116Y GLU* 2.9 34.1 + - - +
126Y MET* 4.5 5.4 - - + +
131Y ARG* 3.2 37.0 - - + +
132Y LEU* 3.5 43.7 - - + +
135Y VAL* 3.7 11.9 - - + -
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Residues in contact with LEU 113 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25U PHE* 4.4 18.8 - - + +
26U ILE 3.8 15.9 - - - +
27U GLN* 3.5 40.5 - - + +
109Y ARG* 2.9 40.3 + - + +
110Y ASN* 3.2 6.7 + - - +
112Y LEU* 1.3 76.1 - - - +
114Y THR* 1.3 56.5 + - - +
116Y GLU* 3.2 22.2 + - + +
117Y GLN* 2.9 24.4 + - - +
132Y LEU* 4.8 8.5 - - + -
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Residues in contact with THR 114 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U GLN* 3.7 8.5 - - - +
28U LEU* 3.4 42.4 - - + +
107U PHE* 5.7 1.8 - - - -
110U LEU* 5.5 0.8 - - - +
67Y PHE* 2.7 34.6 + - + +
68Y PHE* 4.3 10.3 - - - -
110Y ASN 2.9 19.8 + - - +
111Y MET 2.3 25.5 + - - -
113Y LEU* 1.3 75.1 - - - +
115Y LEU* 1.3 60.1 + - - +
117Y GLN* 3.2 6.3 + - - +
118Y GLU* 2.9 29.0 + - - +
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Residues in contact with LEU 115 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110U LEU* 4.1 22.2 - - + -
111U PHE* 3.5 14.1 - - + -
68Y PHE* 6.2 0.7 - - - -
69Y ASP* 4.0 17.5 - - - +
74Y TRP* 5.5 2.5 - - + -
111Y MET* 2.9 17.4 + - - +
112Y LEU* 3.4 11.4 - - - +
114Y THR* 1.3 82.5 + - - +
116Y GLU* 1.3 55.9 + - - +
118Y GLU* 3.2 8.8 + - - +
119Y ALA* 2.9 25.6 + - - +
126Y MET* 3.5 10.3 - - + -
127Y PRO* 3.4 36.3 - - + -
131Y ARG* 3.4 24.2 - - - +
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Residues in contact with GLU 116 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Y LEU 2.9 9.1 + - - +
113Y LEU* 3.3 32.6 - - + +
115Y LEU* 1.3 74.9 - - - +
117Y GLN* 1.3 59.6 + - - +
119Y ALA* 3.2 4.2 + - - +
120Y LYS* 2.9 44.4 + - - +
126Y MET* 3.4 37.4 - - + +
129Y PRO* 5.6 2.9 - - - +
132Y LEU* 3.6 33.7 - - - +
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Residues in contact with GLN 117 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2368A C 5.0 1.0 + - - -
2369A A 3.1 26.0 + - - -
27U GLN* 4.3 13.2 - - - +
29U VAL* 3.7 26.6 - - + +
43U ARG* 3.1 41.1 + - - +
113Y LEU 2.9 12.5 + - - +
114Y THR* 3.2 10.0 + - - +
116Y GLU* 1.3 77.9 - - - +
118Y GLU* 1.3 56.9 + - - +
120Y LYS* 3.2 24.0 + - - +
121Y ARG* 2.9 27.4 + - - +
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Residues in contact with GLU 118 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U ARG* 2.7 32.0 + - + -
107U PHE* 3.6 27.9 - - + -
110U LEU* 4.0 28.6 + - + +
111U PHE* 3.2 17.6 - - + -
114Y THR 2.9 12.8 + - - +
115Y LEU 3.4 9.6 - - - +
117Y GLN* 1.3 75.5 - - - +
119Y ALA* 1.3 58.0 + - - +
121Y ARG* 3.2 10.3 + - + +
122Y GLN* 2.9 55.9 + - - +
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Residues in contact with ALA 119 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111U PHE* 3.7 24.0 - - + -
115Y LEU 2.9 12.6 + - - +
116Y GLU 3.2 10.1 + - - +
118Y GLU* 1.3 75.7 + - - +
120Y LYS* 1.3 64.3 + - + +
122Y GLN* 3.2 4.4 + - - -
123Y ARG 3.2 2.9 + - - -
124Y LEU 3.1 42.8 + - - +
125Y PRO 4.4 0.7 - - - +
126Y MET* 4.2 18.8 - - + +
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Residues in contact with LYS 120 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2367A A 4.4 4.7 + - - +
2368A C 3.6 39.8 + - - +
116Y GLU* 2.9 25.6 + - - +
117Y GLN* 3.2 28.9 + - - +
119Y ALA* 1.3 78.4 - - + +
121Y ARG* 1.3 62.1 + - - +
123Y ARG* 3.4 11.8 + - - +
124Y LEU 5.1 0.4 - - - -
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Residues in contact with ARG 121 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2368A C 3.2 36.0 + - - +
2369A A 3.2 51.9 + - - +
29U VAL* 6.5 0.7 - - + -
30U ARG* 3.5 49.6 + - + +
31U PRO 4.7 0.2 + - - -
32U GLY* 3.9 15.7 - - - +
117Y GLN* 2.9 16.3 + - - +
118Y GLU* 3.4 14.1 - - + +
120Y LYS* 1.3 76.9 - - - +
122Y GLN* 1.3 69.9 + - + +
123Y ARG* 3.4 6.6 + - - +
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Residues in contact with GLN 122 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30U ARG* 4.6 12.0 + - - +
110U LEU 3.8 16.1 - - - +
111U PHE* 4.2 10.4 - - + +
118Y GLU* 2.9 43.4 + - - +
119Y ALA* 3.2 5.8 + - - +
121Y ARG* 1.3 83.9 + - - +
123Y ARG* 1.3 68.3 + - - +
124Y LEU* 3.2 30.7 + - + +
----------------------------------------------------------
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Residues in contact with ARG 123 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2347A C 2.9 43.3 + - - +
2348A A 3.9 14.7 + - - -
2366A G 3.5 16.6 + - - +
2367A A 4.5 24.0 + - - +
119Y ALA 3.2 5.2 + - - -
120Y LYS 3.4 7.4 + - - +
121Y ARG 3.3 9.3 - - - +
122Y GLN* 1.3 79.5 - - - +
124Y LEU* 1.3 63.5 + - + +
125Y PRO* 4.6 1.9 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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