Contacts of the helix formed by residues 101 - 132 (chain B) in PDB entry 1ZV0
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 CYS 101 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 3.3 38.9 - - + -
98B ASN* 4.8 12.1 - - + -
99B TYR 3.2 3.6 - - - +
100B LEU* 1.3 74.0 - - - +
102B LYS* 1.3 61.4 + - - +
103B ILE 3.6 0.9 - - - -
104B ALA* 3.3 20.2 + - - -
105B SER* 3.4 7.6 + - - -
170B PHE* 3.8 4.6 - - + -
172B ILE* 4.6 5.4 - - + -
179B VAL* 3.8 2.9 - - - -
180B CYS* 2.0 64.7 - - + -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN 4.0 19.3 - - - +
99B TYR* 3.4 29.7 - - - +
100B LEU 3.2 1.0 - - - -
101B CYS* 1.3 75.0 - - - +
103B ILE* 1.3 65.3 + - + +
104B ALA 3.2 0.9 - - - -
106B ALA* 3.8 11.6 - - - +
164B ILE* 4.1 45.0 - - + +
165B ILE* 4.6 20.4 - - - +
170B PHE* 3.4 27.1 - - + -
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.7 16.0 - - + +
84B TRP* 5.0 14.6 - - + +
100B LEU* 4.0 14.8 + - + +
101B CYS 3.6 0.2 - - - -
102B LYS* 1.3 76.6 - - + +
104B ALA* 1.3 62.8 + - - +
106B ALA* 4.1 3.8 - - - -
107B SER* 3.1 44.6 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 4.4 8.3 - - - +
81B LEU* 4.5 2.9 - - + +
84B TRP* 4.8 15.7 - - + -
100B LEU 4.3 3.4 + - - +
101B CYS* 3.3 38.2 + - - +
102B LYS 3.2 0.8 - - - -
103B ILE* 1.3 79.5 - - - +
105B SER* 1.3 59.9 + - - +
107B SER* 4.5 0.9 - - - -
108B VAL* 2.9 29.7 + - - +
179B VAL* 4.2 14.8 - - + -
180B CYS* 3.7 1.6 - - - -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B CYS 3.5 2.0 + - - -
102B LYS 4.1 0.4 + - - -
104B ALA* 1.3 79.3 - - - +
106B ALA* 1.3 59.6 + - - +
108B VAL* 3.5 6.8 + - - +
109B SER* 3.3 26.4 + - - -
163B ALA* 6.2 0.2 - - - -
170B PHE* 3.1 36.3 - - - -
179B VAL 4.6 0.4 - - - -
180B CYS* 2.8 46.9 + - - +
181B ALA* 4.0 7.2 - - - -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS 3.8 15.2 + - - +
103B ILE* 3.8 4.0 + - - +
104B ALA 3.5 0.6 - - - -
105B SER* 1.3 76.2 - - - +
107B SER* 1.3 59.7 + - - +
108B VAL 3.2 0.2 + - - -
109B SER* 3.3 4.3 + - - -
110B PHE* 2.9 30.6 + - - +
160B SER* 3.9 35.4 - - - +
163B ALA* 5.7 0.7 - - - -
164B ILE* 4.6 8.3 - - + -
170B PHE* 3.7 9.7 - - + -
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B CYS* 4.8 6.4 - - - +
77B PHE* 4.7 2.0 + - - -
80B THR* 3.6 26.3 + - - +
81B LEU* 5.5 0.9 - - - -
103B ILE* 3.1 32.6 + - - +
106B ALA* 1.3 77.0 - - - +
108B VAL* 1.3 51.6 + - - +
110B PHE* 4.2 6.9 - - - +
111B ASN* 2.6 36.5 + - - +
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Residues in contact with VAL 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.6 9.6 - - + -
77B PHE* 6.0 0.7 - - + -
81B LEU* 3.3 42.8 - - + -
104B ALA 2.9 24.0 - - - +
105B SER* 3.6 7.2 - - - +
106B ALA 3.2 0.4 - - - -
107B SER* 1.3 75.8 - - - +
109B SER* 1.3 64.5 + - - +
111B ASN* 3.1 13.1 - - - +
112B LEU* 2.9 52.3 + - + +
179B VAL 4.1 11.0 - - - +
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B SER* 3.3 16.1 + - - -
106B ALA* 3.8 5.4 - - - -
108B VAL* 1.3 78.8 - - - +
110B PHE* 1.3 60.1 + - - +
112B LEU* 3.1 1.8 + - - +
113B TYR* 2.8 57.4 + - - -
156B ALA* 5.5 1.1 - - - +
159B ALA* 5.0 10.1 - - - -
160B SER* 5.4 4.0 - - - -
199B LYS* 3.9 23.5 + - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 6.0 3.6 - - + -
76B CYS* 6.3 2.9 - - + -
106B ALA 2.9 18.0 + - - +
107B SER* 4.2 7.2 - - - +
109B SER* 1.3 74.4 - - - +
111B ASN* 1.3 60.1 + - + +
113B TYR* 4.2 0.2 - - - -
114B ALA* 3.0 38.0 + - + +
153B TRP* 3.9 30.5 - + + -
156B ALA* 3.6 33.9 + - + +
157B GLY* 3.7 19.1 - - - -
160B SER* 3.9 13.1 - - - -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 3.6 28.4 - - + +
74B ASP* 5.6 2.6 + - - +
76B CYS* 5.3 1.6 - - + -
77B PHE* 3.1 45.0 - - + +
81B LEU* 4.1 0.5 - - - +
107B SER 2.6 24.7 + - - +
108B VAL* 3.1 18.9 + - - +
109B SER 3.2 0.2 - - - -
110B PHE* 1.3 80.9 - - + +
112B LEU* 1.3 76.5 + - - +
114B ALA* 4.0 4.8 - - - +
115B SER* 3.0 26.2 + - - -
294B ASN* 5.6 0.6 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 4.2 15.0 - - + -
8A PBF 3.7 48.5 - - + +
77B PHE* 5.4 3.6 - - + -
108B VAL* 2.9 40.1 + - + +
109B SER* 4.0 1.1 - - - +
111B ASN* 1.3 87.3 - - - +
113B TYR* 1.3 84.5 + - + +
115B SER* 3.3 7.2 + - - +
116B VAL* 3.0 28.6 + - - +
294B ASN* 4.3 13.7 - - - +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS 3.5 15.5 + - - -
7A PRO* 5.1 0.5 - - - +
8A PBF 4.1 8.1 - - - -
109B SER* 2.8 37.6 + - - -
110B PHE 4.2 0.2 - - - -
112B LEU* 1.3 89.5 - - + +
114B ALA* 1.3 60.7 + - - +
115B SER 3.1 0.2 - - - -
116B VAL* 3.8 17.9 - - + -
117B PHE* 2.7 46.1 + + + -
156B ALA* 4.9 4.3 - - - +
159B ALA* 5.4 5.6 - - + -
183B HIS* 5.7 1.6 - - - -
199B LYS* 3.5 43.7 - - + +
200B ASN* 5.1 3.0 + - - -
203B GLY* 2.7 36.8 - - - +
204B PHE* 3.9 19.7 - + + -
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASN* 4.7 10.1 - - - +
73B ALA* 4.4 18.4 - - + -
110B PHE* 3.0 27.8 + - + +
111B ASN 4.0 4.3 - - - +
113B TYR* 1.3 76.0 - - - +
115B SER* 1.3 57.9 + - - +
117B PHE* 3.8 2.4 - - - +
118B LEU* 2.8 39.1 + - + +
152B ILE* 4.4 12.7 - - + +
153B TRP* 5.3 2.7 - - + -
156B ALA* 4.5 8.5 - - + +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PBF 4.2 36.9 - - - -
70B LEU* 4.1 14.2 + - - +
73B ALA* 5.3 4.5 - - - +
74B ASP* 4.7 9.0 + - - -
111B ASN 3.0 14.5 + - - -
112B LEU* 3.3 13.5 + - - +
113B TYR 3.1 0.4 - - - -
114B ALA* 1.3 76.2 - - - +
116B VAL* 1.3 59.2 + - - +
118B LEU* 3.4 1.4 + - - +
119B LEU* 3.0 35.8 + - - +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PBF 3.2 31.4 - - + +
112B LEU 3.0 21.6 + - - +
113B TYR* 3.1 21.7 + - + -
115B SER* 1.3 75.6 - - - +
117B PHE* 1.3 60.8 + - - +
119B LEU* 3.0 12.4 + - + -
120B THR* 3.2 10.7 + - - -
203B GLY 4.6 1.8 - - - +
204B PHE* 4.0 6.3 - - - +
207B PRO* 3.5 21.3 - - + -
208B PHE* 3.3 32.8 - - + +
211B ILE* 3.4 10.8 - - + +
249B PHE* 5.2 1.3 - - + -
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 2.7 38.6 + + + +
114B ALA* 4.2 2.9 - - - +
116B VAL* 1.3 69.2 - - - +
118B LEU* 1.3 62.9 + - - +
120B THR* 3.3 13.8 + - + +
121B CYS* 3.2 18.9 + - - +
152B ILE* 3.7 47.1 - - + +
155B LEU* 3.6 33.7 - - + -
156B ALA* 3.9 11.9 - - - -
202B LEU* 3.2 37.0 - - + -
203B GLY* 3.8 13.7 - - - -
207B PRO* 3.5 15.7 - - + -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 4.2 13.9 - - + +
69B ASN* 3.6 35.4 - - - +
70B LEU* 3.6 33.9 - - + +
73B ALA* 5.4 0.4 - - + -
114B ALA* 2.8 29.2 + - + +
115B SER 3.8 0.2 - - - +
117B PHE* 1.3 76.2 - - - +
119B LEU* 1.3 58.3 + - - +
121B CYS* 2.6 45.6 + - - -
122B LEU* 2.9 11.7 + - + +
149B CYS* 3.9 26.5 - - + -
152B ILE* 4.1 12.8 - - + -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PBF 4.2 35.0 - - + -
70B LEU* 5.2 1.6 - - + -
115B SER 3.0 23.0 + - - +
116B VAL* 3.0 2.0 + - + -
118B LEU* 1.3 76.3 - - - +
120B THR* 1.3 55.4 + - - +
122B LEU* 4.0 23.2 - - + +
123B SER* 3.1 23.2 + - - -
211B ILE* 3.1 36.6 - - + +
242B ILE* 4.6 14.4 - - + -
245B ILE* 5.8 1.6 - - + -
246B VAL* 5.2 10.5 - - + -
249B PHE* 3.7 34.1 - - + -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL 3.2 3.2 + - - -
117B PHE* 3.4 14.6 - - + +
118B LEU 3.1 0.2 - - - -
119B LEU* 1.3 73.7 - - - +
121B CYS* 1.3 67.7 + - - +
123B SER* 3.1 19.6 + - - -
124B ILE* 3.2 27.3 + - + +
152B ILE* 6.3 1.8 - - + -
207B PRO* 2.9 39.5 + - + +
210B ILE* 3.2 22.2 - - + -
211B ILE* 3.4 3.1 - - - +
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Residues in contact with CYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.1 48.8 - - + -
117B PHE 3.2 5.3 + - - +
118B LEU* 2.6 49.5 + - - -
120B THR* 1.3 82.4 - - - +
122B LEU* 1.3 61.8 + - - +
124B ILE* 3.4 6.8 + - - +
125B ASP* 3.1 25.1 + - - +
148B THR* 4.2 18.6 - - + +
149B CYS* 5.3 1.3 - - - -
152B ILE* 5.7 2.2 - - + -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA* 4.9 3.8 - - + -
66B PHE* 3.6 35.0 - - + -
67B LEU* 4.3 15.0 - - + -
70B LEU* 3.9 28.0 - - + -
118B LEU* 2.9 17.2 + - + +
119B LEU* 4.0 25.1 - - + +
121B CYS* 1.3 75.1 - - - +
123B SER* 1.3 62.2 + - - +
126B ARG* 3.1 52.1 + - - +
242B ILE* 4.6 19.3 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU 3.1 15.7 + - - -
120B THR 3.1 12.3 + - - -
122B LEU* 1.3 75.8 - - - +
124B ILE* 1.3 60.1 + - - +
126B ARG* 4.3 3.2 - - - +
127B TYR* 3.6 11.4 + - - +
210B ILE 3.3 9.2 + - - -
211B ILE* 3.3 38.1 + - - -
214B SER* 2.6 29.1 + - - -
215B TYR* 4.9 1.8 - - - -
218B ILE* 5.7 0.2 - - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B THR* 3.2 26.2 + - + +
121B CYS* 3.9 6.1 - - - +
123B SER* 1.3 76.9 + - - +
125B ASP* 1.3 62.0 + - - +
127B TYR* 3.5 4.0 + - - +
128B LEU* 3.4 26.1 + - + +
148B THR* 6.5 0.9 - - + -
210B ILE* 3.8 32.8 - - + -
214B SER* 4.0 7.0 - - - +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 3.6 12.4 - - - +
66B PHE* 3.6 20.3 - - + -
121B CYS 3.1 16.7 + - - +
122B LEU 4.3 0.2 - - - +
124B ILE* 1.3 77.3 - - - +
126B ARG* 1.3 100.3 + - - +
129B ALA* 3.3 10.0 + - - +
140B ARG* 3.0 45.1 + - - +
144B VAL* 4.3 2.9 - - - +
145B ALA* 3.9 11.4 - - - +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 5.6 0.8 - - - +
62B VAL* 3.6 16.0 - - - +
63B ALA* 3.8 24.9 - - - +
66B PHE* 3.7 19.6 - - - -
122B LEU* 3.1 38.0 + - + +
123B SER* 4.3 4.3 - - - +
125B ASP* 1.3 119.6 + - - +
127B TYR* 1.3 63.5 + - - +
129B ALA* 4.8 3.8 - - - +
130B ILE* 3.7 4.9 + - - +
218B ILE* 3.5 17.5 - - + +
239B PHE* 3.2 56.2 - - + -
242B ILE* 3.9 25.6 - - + -
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B SER 3.6 4.2 + - - +
124B ILE* 3.5 4.3 + - - +
125B ASP 3.4 0.6 - - - -
126B ARG* 1.3 79.8 - - - +
128B LEU* 1.3 66.9 + - + +
129B ALA 3.2 0.9 + - - -
130B ILE* 3.3 5.5 + - + +
131B VAL* 3.2 47.6 + - + +
214B SER* 3.9 23.3 - - - +
217B LEU* 3.5 53.2 + - + +
218B ILE* 3.7 30.2 - - + +
220B LYS* 5.2 6.2 - - + +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.4 14.4 + - + +
127B TYR* 1.3 83.3 - - + +
129B ALA* 1.3 61.2 + - - +
131B VAL* 3.6 10.2 + - + +
132B HIS 3.5 14.7 + - - -
133B PRO* 3.8 28.0 - - + +
136B SER* 5.5 2.0 - - - +
138B LEU* 4.3 20.6 - - + -
140B ARG* 3.5 22.9 - - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B VAL* 5.9 1.6 - - + -
125B ASP* 3.3 19.4 + - - +
126B ARG* 4.1 7.6 - - - +
127B TYR 3.2 0.6 + - - -
128B LEU* 1.3 78.1 - - - +
130B ILE* 1.3 59.1 + - - +
131B VAL 3.6 0.2 + - - -
132B HIS* 3.3 28.1 + - - -
140B ARG* 3.3 25.0 - - + +
239B PHE* 4.6 11.4 - - + -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG 3.7 10.3 + - - +
127B TYR* 3.3 12.5 + - + +
129B ALA* 1.3 76.1 - - - +
131B VAL* 1.3 63.1 + - + +
132B HIS* 3.2 18.8 + - + -
218B ILE* 4.1 17.7 - - + -
219B TRP* 4.3 5.8 - - + -
220B LYS* 3.8 30.3 - - + +
222B LEU* 3.8 10.1 - - + +
223B LYS* 5.2 0.7 - - - +
235B ASN* 5.1 1.3 - - + -
236B ASP* 3.2 45.1 - - + +
239B PHE* 4.0 18.3 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 3.2 57.6 + - + +
128B LEU* 3.8 11.0 - - + +
129B ALA 3.4 0.4 - - - -
130B ILE* 1.3 77.4 - - + +
132B HIS* 1.3 72.2 + - - +
133B PRO* 4.6 9.6 - - + -
220B LYS* 3.2 48.0 + - + +
222B LEU* 3.5 3.3 - - - +
----------------------------------------------------------
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU 3.5 3.6 + - - -
129B ALA 3.3 20.8 + - - -
130B ILE* 3.2 26.0 + - + -
131B VAL* 1.3 79.7 - - - +
133B PRO* 1.4 72.1 - - - +
134B MET* 3.6 8.3 + - - +
220B LYS* 4.8 3.3 + - - -
222B LEU* 3.6 17.4 - - + +
232B LYS* 4.7 21.5 - - + +
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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