Contacts of the helix formed by residues 113 - 145 (chain L) in PDB entry 3IS7
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 ASP 113 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 4.1 4.9 - - - +
128C GLU* 4.7 2.3 - - - +
4L ASP* 5.8 2.1 + - + +
7L VAL* 3.4 16.9 - - + +
61L ARG* 3.0 16.6 + - - -
65L LEU* 4.1 7.2 - - - +
108L CYS* 2.8 26.8 + - + +
111L VAL* 3.3 15.1 - - + +
112L HIS* 1.3 70.0 - - - +
114L TYR* 1.3 57.6 + - - +
115L VAL* 3.6 2.4 + - - +
116L SER* 2.7 39.0 + - - -
117L ARG 3.0 19.8 + - - -
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Residues in contact with TYR 114 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 3.9 18.1 - - + +
105C ILE* 3.6 36.5 - - + +
106C VAL* 3.3 18.5 + - - +
109C GLU* 6.0 0.2 - - - +
117C ARG* 3.9 14.5 + - - +
121C LYS* 4.4 16.2 - - + +
124C LEU* 4.0 17.0 - - + -
109L GLU* 3.5 40.6 + - - -
112L HIS* 3.2 59.0 + - + -
113L ASP* 1.3 70.1 - - - +
115L VAL* 1.3 60.1 + - - +
117L ARG* 3.6 9.7 - - - +
118L ASP* 3.1 25.6 + - - +
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Residues in contact with VAL 115 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LYS* 4.8 4.0 - - + +
124C LEU* 3.8 19.9 - - + +
125C GLU* 3.8 36.1 - - + +
128C GLU* 3.3 40.6 + - + +
61L ARG* 3.6 17.0 - - - +
113L ASP* 3.3 1.4 + - - -
114L TYR* 1.3 75.0 - - - +
116L SER* 1.3 66.1 + - - +
118L ASP* 3.1 6.8 + - + +
119L LEU* 3.1 23.8 + - + +
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Residues in contact with SER 116 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 4.4 3.1 - - - -
11L LEU* 4.1 10.8 - - - +
61L ARG* 2.9 27.4 + - - +
65L LEU* 3.9 7.4 - - - +
108L CYS* 3.7 15.0 - - - -
113L ASP* 2.7 35.3 + - - -
115L VAL* 1.3 72.7 - - - +
117L ARG* 1.3 67.0 + - - +
119L LEU* 3.3 6.1 + - - +
120L LEU* 2.9 26.3 + - - +
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Residues in contact with ARG 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B GLU* 2.6 41.8 + - - -
114B TYR* 3.9 17.8 + - - +
117B ARG* 4.1 17.0 - - - +
117C ARG* 4.4 15.0 - - - +
105L ILE* 3.7 27.5 - - + +
108L CYS* 3.8 16.5 - - + -
109L GLU* 2.8 42.3 + - - +
113L ASP 3.0 15.3 + - - +
114L TYR* 3.6 14.1 - - - +
116L SER* 1.3 75.8 - - - +
118L ASP* 1.3 57.8 + - - +
120L LEU* 3.1 7.2 + - - +
121L LYS* 2.8 38.3 + - + +
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Residues in contact with ASP 118 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 5.7 0.2 - - - +
121C LYS* 4.6 16.9 - - + +
122C ASP* 5.3 3.5 - - - +
125C GLU* 4.8 10.1 - - - +
114L TYR 3.1 17.7 + - - +
115L VAL* 3.6 9.0 - - + +
116L SER 3.0 1.4 - - - -
117L ARG* 1.3 78.5 - - - +
119L LEU* 1.3 66.5 + - - +
121L LYS* 3.3 16.9 + - - +
122L ASP* 3.1 35.0 + - - +
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Residues in contact with LEU 119 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L LEU* 5.6 1.3 - - + -
57L LYS* 3.9 42.2 - - + +
58L LEU* 4.3 7.9 - - + -
61L ARG* 4.1 23.8 - - + -
115L VAL* 3.1 13.6 + - + +
116L SER* 3.7 3.6 - - - +
118L ASP* 1.3 80.2 - - - +
120L LEU* 1.3 78.0 + - + +
122L ASP* 3.3 9.6 + - - +
123L ILE* 3.1 39.6 + - + +
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Residues in contact with LEU 120 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L HIS* 5.8 0.2 - - + -
11L LEU* 3.9 25.6 - - + -
14L ILE* 4.2 7.4 - - + -
58L LEU* 4.2 9.0 - - + -
101L LEU* 3.9 23.9 - - + +
104L ALA* 3.6 29.8 - - + -
105L ILE* 3.6 14.8 - - + +
108L CYS* 3.8 21.1 - - - -
116L SER 2.9 17.0 + - - +
117L ARG 3.5 6.3 - - - +
119L LEU* 1.3 90.0 - - + +
121L LYS* 1.3 58.4 + - - +
123L ILE* 3.3 6.5 + - + +
124L LEU* 3.0 26.7 + - - +
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Residues in contact with LYS 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.5 23.8 - - + +
115B VAL* 4.8 3.3 - - + +
118B ASP* 3.2 42.6 - - + +
105L ILE* 3.9 12.3 - - + +
117L ARG* 2.8 22.6 + - + +
118L ASP* 3.6 17.3 - - - +
119L LEU 3.2 0.2 - - - -
120L LEU* 1.3 77.6 - - - +
122L ASP* 1.3 83.5 + - - +
124L LEU* 3.2 5.6 + - + +
125L GLU* 2.9 35.6 + - - +
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Residues in contact with ASP 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L HIS* 4.9 1.5 + - - -
57L LYS* 6.5 0.4 - - - -
118L ASP* 3.1 23.5 + - - +
119L LEU* 3.3 9.6 + - - +
121L LYS* 1.3 89.3 - - - +
123L ILE* 1.3 66.4 + - + +
125L GLU* 3.3 10.0 + - - +
126L SER* 3.1 22.2 + - - -
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Residues in contact with ILE 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L ILE* 5.0 1.6 - - + -
18L GLU* 3.5 21.5 - - - +
54L HIS* 3.7 37.9 - - + +
57L LYS* 5.5 3.6 - - + -
58L LEU* 4.1 21.8 - - + -
101L LEU* 3.9 18.4 - - + -
119L LEU* 3.1 33.1 + - + +
120L LEU* 3.6 10.3 - - + +
122L ASP* 1.3 75.9 - - + +
124L LEU* 1.3 58.9 + - - +
126L SER* 3.1 9.2 + - - -
127L GLU* 2.8 34.1 + - - +
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Residues in contact with LEU 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.0 26.0 - - + -
115B VAL* 3.9 9.0 - - + -
98L THR* 3.0 32.8 - - - +
101L LEU* 4.2 22.4 - - + +
102L ARG* 3.9 24.0 - - + +
105L ILE* 4.0 14.4 - - + -
120L LEU 3.0 13.9 + - - +
121L LYS* 3.2 9.1 + - - +
123L ILE* 1.3 76.8 - - - +
125L GLU* 1.3 58.9 + - - +
127L GLU* 3.3 2.3 + - + +
128L GLU* 2.9 42.5 + - + +
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Residues in contact with GLU 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.9 30.3 - - + -
118B ASP* 4.6 4.2 - - - +
121L LYS* 2.9 30.8 + - - +
122L ASP* 3.8 9.6 - - - +
123L ILE 3.2 0.2 - - - -
124L LEU* 1.3 78.0 - - - +
126L SER* 1.3 63.1 + - - +
128L GLU* 3.3 3.5 + - - +
129L GLU* 3.0 40.2 + - + +
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Residues in contact with SER 126 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ASP* 4.8 9.0 + - - +
54L HIS* 3.3 30.2 + - - -
122L ASP 3.1 12.3 + - - -
123L ILE 3.1 9.2 + - - -
125L GLU* 1.3 79.0 - - - +
127L GLU* 1.3 61.8 + - - +
129L GLU* 3.3 17.6 + - - +
130L HIS* 3.1 20.8 + - - +
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Residues in contact with GLU 127 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 3.0 19.9 - - - +
51L GLU* 2.6 28.3 - - - +
54L HIS* 3.7 3.6 + - - -
94L GLU* 2.4 45.1 - - + +
97L ALA* 5.0 5.4 - - + -
98L THR* 5.1 11.4 - - - +
101L LEU* 3.9 22.4 - - + -
123L ILE* 2.8 27.1 + - + +
124L LEU* 3.3 4.9 + - - +
126L SER* 1.3 74.4 - - - +
128L GLU* 1.3 58.8 + - - +
130L HIS* 3.2 7.0 + - - +
131L ILE* 3.0 31.7 + - + +
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Residues in contact with GLU 128 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 2.9 39.4 + - - +
64B PHE* 3.5 25.5 - - + -
65B LEU* 6.1 0.4 - - - -
113B ASP* 4.5 0.3 - - - +
115B VAL* 3.6 20.8 - - + +
98L THR* 4.4 4.0 - - - +
102L ARG* 2.7 38.0 + - - +
124L LEU* 2.9 26.5 + - + +
125L GLU* 3.7 6.1 - - + +
127L GLU* 1.3 78.1 - - - +
129L GLU* 1.3 56.3 + - - +
131L ILE* 3.4 9.9 + - + +
132L ASP* 3.0 23.0 + - - +
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Residues in contact with GLU 129 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125L GLU* 3.0 37.2 + - + +
126L SER* 3.5 18.5 + - - +
128L GLU* 1.3 74.3 - - - +
130L HIS* 1.3 56.4 - - - +
132L ASP* 3.3 10.4 - - + +
133L TYR* 3.0 26.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 130 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L TYR* 3.3 39.4 - + - -
44L GLU* 4.7 4.8 + - - -
47L GLU* 3.3 45.4 + - + +
51L GLU* 5.6 0.4 + - - -
90L ASP* 4.6 2.0 - - + +
94L GLU* 2.7 24.6 + - - +
126L SER 3.1 12.7 + - - +
127L GLU* 3.2 11.4 + - - +
129L GLU* 1.3 73.4 - - - +
131L ILE* 1.3 59.4 + - - +
133L TYR* 3.1 9.5 + + - +
134L LEU* 2.9 54.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 4.3 10.3 - - + -
91L LEU* 3.8 16.6 - - + -
94L GLU* 3.6 37.7 - - + +
95L LEU* 4.2 18.2 - - + -
98L THR* 4.4 14.4 - - + +
127L GLU* 3.0 16.0 + - + +
128L GLU* 3.4 15.9 + - + +
130L HIS* 1.3 73.1 - - - +
132L ASP* 1.3 59.5 + - - +
134L LEU* 3.1 7.1 + - - -
135L GLU* 2.8 59.0 + - - +
----------------------------------------------------------
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Residues in contact with ASP 132 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 4.3 13.2 - - - +
64B PHE* 3.6 30.2 - - + +
128L GLU 3.0 14.8 + - - +
129L GLU* 3.3 14.5 - - - +
131L ILE* 1.3 76.4 - - - +
133L TYR* 1.3 61.2 + - - +
135L GLU* 3.6 4.6 + - - +
136L THR* 2.8 39.1 + - - -
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Residues in contact with TYR 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L LEU* 3.8 23.7 + - - +
43L HIS* 3.4 57.3 - + + +
44L GLU* 5.5 3.8 - - - -
47L GLU* 4.7 1.3 - - - +
87L LEU* 4.7 3.8 - - + -
129L GLU 3.0 13.3 + - - +
130L HIS* 3.1 16.1 + + - +
132L ASP* 1.3 75.9 - - - +
134L LEU* 1.3 80.2 + - + +
136L THR* 3.2 5.0 + - - -
137L GLN* 2.9 71.7 + - + +
153L HIS* 5.1 3.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44L GLU* 5.6 0.7 - - - +
87L LEU* 4.0 30.0 - - + +
90L ASP* 4.0 19.1 - - + +
91L LEU* 3.8 31.2 - - + +
94L GLU* 4.4 2.7 - - + -
130L HIS* 2.9 47.4 + - + +
131L ILE* 3.6 7.6 - - - +
133L TYR* 1.3 98.2 - - + +
135L GLU* 1.3 67.0 + - - +
136L THR 3.1 1.3 - - - -
137L GLN* 3.2 4.6 + - - +
138L LEU* 3.0 30.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 135 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 4.3 17.0 - - - +
66B GLU* 4.0 19.0 - - - +
91L LEU* 4.1 20.0 - - + +
95L LEU* 5.5 3.3 - - - +
131L ILE* 2.8 39.2 + - + +
132L ASP* 4.0 3.9 - - - +
134L LEU* 1.3 76.5 - - - +
136L THR* 1.3 58.5 + - - +
138L LEU* 3.4 8.4 + - - +
139L GLY* 2.9 26.2 + - - -
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Residues in contact with THR 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN 5.1 1.0 + - - +
34A ASP* 3.1 17.4 + - - +
35A TRP* 3.7 8.0 - - - +
36A GLY* 3.5 33.7 - - - +
132L ASP* 2.8 31.0 + - - -
133L TYR* 3.4 7.2 - - - -
135L GLU* 1.3 79.2 - - - +
137L GLN* 1.3 69.1 + - - +
139L GLY* 3.3 3.0 + - - -
140L LEU* 3.0 27.9 + - + +
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Residues in contact with GLN 137 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 5.4 0.2 - - - +
87L LEU* 4.1 13.5 - - + -
133L TYR* 2.9 67.8 + - + +
134L LEU* 3.2 6.2 + - - +
136L THR* 1.3 89.1 - - - +
138L LEU* 1.3 62.1 + - - +
140L LEU* 3.1 14.7 + - - +
141L ILE* 3.0 27.9 + - - +
149L TYR* 2.8 43.5 + - + +
153L HIS* 3.9 11.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L GLN* 3.6 33.3 + - + +
87L LEU* 3.7 40.6 - - + +
88L GLN* 4.0 15.5 - - + +
91L LEU* 3.9 26.9 - - + -
134L LEU 3.0 23.0 + - - +
135L GLU* 3.7 6.1 - - - +
137L GLN* 1.3 76.1 - - - +
139L GLY* 1.3 62.6 + - - +
141L ILE* 3.4 6.2 + - + +
142L GLN* 3.3 25.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP 5.5 0.4 - - - -
135L GLU 2.9 15.5 + - - -
136L THR* 3.6 5.4 - - - -
138L LEU* 1.3 77.6 - - - +
140L LEU* 1.3 60.8 + - - +
142L GLN* 3.3 10.8 + - - +
143L LYS* 3.0 39.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 140 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP 3.3 22.4 - - - +
36A GLY* 4.0 8.7 - - - +
37A LEU* 3.9 25.6 - - + -
154A MET* 4.0 28.7 - - + -
136L THR* 3.0 27.4 + - + +
137L GLN* 3.1 28.4 + - - +
139L GLY* 1.3 74.6 - - - +
141L ILE* 1.3 61.5 + - - +
143L LYS* 4.1 7.2 - - + +
144L VAL* 2.9 39.4 + - + +
149L TYR* 4.0 9.4 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L THR* 4.7 2.0 - - + -
84L GLN* 3.7 43.1 - - + +
87L LEU* 3.9 24.7 - - + -
137L GLN 3.0 17.5 + - - +
138L LEU* 3.5 8.1 - - + +
140L LEU* 1.3 76.7 - - - +
142L GLN* 1.3 65.6 + - - +
145L GLY* 3.1 28.2 + - - -
146L LEU* 3.8 26.2 + - + +
149L TYR* 3.5 35.0 - - + -
----------------------------------------------------------
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Residues in contact with GLN 142 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 4.8 4.2 - - - +
84L GLN* 4.2 13.7 + - - +
138L LEU 3.3 12.7 + - - +
139L GLY* 3.5 9.4 - - - +
140L LEU 3.1 0.4 - - - -
141L ILE* 1.3 91.6 - - - +
143L LYS* 1.3 63.3 + - + +
145L GLY* 4.3 2.8 + - - -
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Residues in contact with LYS 143 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 3.8 53.4 + - + +
37A LEU* 4.5 17.5 - - + -
146A LEU* 5.6 0.9 - - - +
147A GLU* 3.6 15.4 - - - +
150A LEU* 3.7 28.1 - - + +
139L GLY* 3.0 26.3 + - - +
140L LEU* 3.0 11.0 + - + +
142L GLN* 1.3 79.7 - - + +
144L VAL* 1.3 63.7 + - + +
145L GLY 3.5 0.2 - - - -
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Residues in contact with VAL 144 (chain L).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 3.4 25.4 - - - +
150A LEU* 3.8 11.4 - - + -
151A GLN* 3.6 27.8 - - + +
154A MET* 4.2 15.7 - - - -
140L LEU* 2.9 29.9 + - + +
143L LYS* 1.3 78.9 - - + +
145L GLY* 1.3 69.1 + - - +
148L ASN* 3.2 31.5 + - + +
149L TYR* 3.6 22.0 - - + +
----------------------------------------------------------
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Residues in contact with GLY 145 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 4.1 15.3 + - - -
141L ILE 3.1 15.3 + - - -
142L GLN 4.3 1.3 + - - -
143L LYS 3.5 1.6 - - - -
144L VAL* 1.3 83.2 - - - +
146L LEU* 1.3 68.3 + - - -
147L GLU 3.3 2.4 + - - -
148L ASN 3.4 1.0 + - - -
149L TYR* 2.9 20.8 + - - +
----------------------------------------------------------
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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