Contacts of the helix formed by residues 114 - 144 (chain L) in PDB entry 1BCF
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 TYR 114 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 3.8 12.8 - - - +
105C ILE* 3.3 39.7 - - + -
106C GLY* 3.5 18.4 - - - -
117C ARG* 3.7 17.5 + - - -
121C ILE* 3.7 26.2 - - + +
124C LEU* 4.2 12.9 - - + +
109L ASP* 3.3 40.2 + - - -
112L HIS* 2.9 51.1 + + + -
113L ASP* 1.3 75.6 - - - +
115L VAL* 1.3 53.1 + - - +
117L ARG* 3.5 9.1 - - + +
118L ASP* 2.8 33.4 + - - +
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Residues in contact with VAL 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.1 6.5 - - + +
124C LEU* 3.8 13.6 - - + +
125C ARG* 2.7 93.8 + - + +
128C GLU* 3.7 19.3 + - + +
61L ARG* 3.9 21.7 - - - +
113L ASP* 3.3 1.4 + - - -
114L TYR* 1.3 74.7 - - - +
116L SER* 1.3 64.7 + - - +
118L ASP* 4.0 1.1 - - - -
119L MET* 3.1 11.6 + - - +
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Residues in contact with SER 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 4.2 8.8 - - - +
11L LEU* 4.4 4.4 - - - +
61L ARG* 2.9 27.5 + - - +
65L LEU* 3.9 5.5 - - - +
108L ALA* 4.7 0.4 - - - -
113L ASP* 2.7 36.5 + - - -
115L VAL* 1.3 77.6 - - - +
117L ARG* 1.3 61.8 + - - +
119L MET* 3.5 8.3 + - - +
120L MET* 3.2 39.6 + - - +
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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 ASP* 3.5 27.7 + - - -
114B TYR* 3.7 23.2 + - - -
117B ARG* 5.0 9.1 - - - +
117C ARG* 4.9 7.9 - - - +
121C ILE* 5.6 3.4 - - + -
105L ILE* 3.3 30.3 + - + +
106L GLY* 4.2 2.6 - - - -
108L ALA* 3.7 13.9 - - + +
109L ASP* 3.2 40.6 + - - +
113L ASP 3.1 13.0 + - - +
114L TYR* 3.5 26.5 - - + +
116L SER* 1.3 75.8 - - - +
118L ASP* 1.3 63.0 + - - +
120L MET* 4.0 9.0 - - - +
121L ILE* 3.1 44.9 + - - +
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Residues in contact with ASP 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.3 14.8 - - + +
125C ARG* 2.9 41.9 + - - +
114L TYR 2.8 17.9 + - - +
115L VAL* 4.0 1.1 - - - -
117L ARG* 1.3 79.3 - - - +
119L MET* 1.3 61.8 + - - +
121L ILE* 3.4 8.6 + - - +
122L GLU* 3.3 35.9 + - - +
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Residues in contact with MET 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 3.4 21.2 - - - +
11L LEU* 4.1 11.0 - - + -
57L ARG* 3.1 46.9 + - - +
58L TYR* 3.8 31.2 - - + -
61L ARG* 3.8 36.8 - - + -
115L VAL* 3.1 10.8 + - + +
116L SER* 3.7 5.8 - - - +
118L ASP* 1.3 79.3 - - - +
120L MET* 1.3 62.6 - - + +
122L GLU* 3.1 1.8 - - - +
123L ILE* 3.1 34.4 + - + +
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Residues in contact with MET 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L VAL* 5.6 2.5 - - + -
10L TYR* 6.0 0.9 - - + -
11L LEU* 3.9 15.5 - - + -
14L LEU* 3.6 28.5 - - - -
58L TYR* 4.4 6.1 - - + +
101L LEU* 3.6 17.5 - - + +
104L ALA* 3.8 33.0 - - + +
105L ILE* 3.7 16.2 - - + +
108L ALA* 4.1 8.7 - - + -
116L SER* 3.2 29.4 + - - +
117L ARG* 4.0 7.9 - - - +
119L MET* 1.3 87.3 - - + +
121L ILE* 1.3 59.2 + - - +
122L GLU 3.2 0.2 - - - -
123L ILE* 3.3 4.9 + - - +
124L LEU* 2.8 28.9 + - - +
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Residues in contact with ILE 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.0 28.0 - - + +
115B VAL* 4.3 5.5 - - + +
117B ARG* 6.0 2.2 - - + -
118B ASP* 4.2 31.9 - - + +
105L ILE* 3.8 19.3 - - + -
117L ARG* 3.1 42.8 + - - +
118L ASP* 3.4 7.6 + - - +
120L MET* 1.3 73.4 - - - +
122L GLU* 1.3 59.7 + - + +
124L LEU* 3.5 6.4 + - - +
125L ARG* 3.0 28.0 + - + +
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Residues in contact with GLU 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 3.5 10.5 + - - -
57L ARG* 2.7 32.5 + - - +
118L ASP* 3.3 33.7 + - - +
119L MET 3.1 7.9 - - - +
121L ILE* 1.3 77.6 - - + +
123L ILE* 1.3 61.9 + - - +
125L ARG* 3.3 11.8 + - - +
126L ASP* 3.3 25.4 + - - +
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Residues in contact with ILE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 4.0 3.8 - - - +
54L HIS* 3.7 33.7 - - + +
57L ARG* 3.7 24.2 - - + +
58L TYR* 3.7 35.9 - - + +
101L LEU* 4.4 7.6 - - + -
119L MET* 3.1 38.0 + - + +
120L MET* 3.6 7.0 - - - +
122L GLU* 1.3 80.1 - - - +
124L LEU* 1.3 56.3 + - - +
126L ASP* 3.1 6.8 - - - +
127L GLU* 3.0 46.6 + - - +
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Residues in contact with LEU 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.6 11.4 - - + -
115B VAL* 3.9 18.4 - - + -
98L ALA* 4.0 25.6 - - + +
101L LEU* 3.6 27.8 - - + +
102L ARG* 4.2 25.6 - - + +
105L ILE* 3.8 22.2 - - + -
120L MET 2.8 17.7 + - - +
121L ILE* 3.8 6.1 - - - +
122L GLU 3.3 0.2 - - - -
123L ILE* 1.3 72.2 - - - +
125L ARG* 1.3 65.1 + - - +
126L ASP 3.1 2.2 - - - -
127L GLU* 3.3 3.0 + - + +
128L GLU* 3.0 34.8 + - + +
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Residues in contact with ARG 125 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 3.7 21.8 - - - +
115B VAL* 3.2 54.5 + - + +
118B ASP* 3.0 25.9 + - - +
119B MET* 4.0 10.9 - - - +
122B GLU* 3.4 19.8 + - - -
121L ILE* 3.0 14.2 + - - +
122L GLU* 3.4 14.6 - - - +
124L LEU* 1.3 75.5 - - - +
126L ASP* 1.3 63.1 + - - +
128L GLU* 3.7 5.0 + - - +
129L GLY* 3.4 14.7 + - - -
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Residues in contact with ASP 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L ASP* 6.0 1.0 - - - +
54L HIS* 2.9 30.4 + - + +
122L GLU 3.3 12.7 + - - +
123L ILE* 3.1 11.1 + - - +
124L LEU 3.1 0.2 - - - -
125L ARG* 1.3 79.9 - - - +
127L GLU* 1.3 59.6 + - - +
129L GLY* 3.0 16.0 + - - -
130L HIS* 3.1 22.1 + - + +
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Residues in contact with GLU 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU* 3.2 5.1 - - - +
54L HIS* 3.0 6.0 + - - -
94L GLU* 3.4 9.6 - - - +
97L GLY 6.1 0.4 - - - -
98L ALA* 5.2 5.8 - - + +
101L LEU* 3.9 22.1 - - + +
123L ILE* 3.0 16.4 + - - +
124L LEU* 3.3 10.1 + - + +
126L ASP* 1.3 74.4 - - - +
128L GLU* 1.3 52.2 + - - +
130L HIS* 2.8 27.0 + - - +
131L ILE* 2.8 25.4 + - + +
600L MN 2.0 37.0 + - - -
601L MN 2.0 33.1 + - - -
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Residues in contact with GLU 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.6 13.1 - - - +
61B ARG* 3.1 36.3 + - - +
64B PHE* 3.5 27.7 - - + -
115B VAL* 3.7 18.0 - - + +
98L ALA* 5.6 0.2 - - + -
102L ARG* 2.7 34.4 + - - +
124L LEU* 3.0 24.6 + - + +
125L ARG* 3.8 7.4 - - - +
126L ASP 3.3 0.2 - - - -
127L GLU* 1.3 75.2 - - - +
129L GLY* 1.3 55.5 + - - +
131L ILE* 3.8 11.9 - - + -
132L ASP* 3.2 21.0 + - - +
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Residues in contact with GLY 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125L ARG 3.4 7.5 + - - -
126L ASP* 3.0 11.3 + - - -
128L GLU* 1.3 78.1 - - - +
130L HIS* 1.3 64.6 + - - +
132L ASP* 3.4 7.3 + - - +
133L TRP* 3.3 20.8 + - - +
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Residues in contact with HIS 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L TYR* 3.8 2.2 - - - +
47L GLU* 3.4 35.3 - - + +
50L ASP* 3.8 29.4 + - + +
51L GLU* 2.9 18.1 + - - -
54L HIS* 4.3 6.5 - + - -
94L GLU* 3.6 13.9 - - - +
126L ASP* 3.1 16.2 + - - +
127L GLU* 2.8 13.1 + - - +
129L GLY* 1.3 77.0 - - - +
131L ILE* 1.3 62.4 + - - +
133L TRP* 3.4 4.3 + - - +
134L LEU* 3.2 29.1 + - - +
600L MN 1.8 35.8 + - - -
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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
----------------------------------------------------------
1B MET* 4.3 11.4 - - + -
64B PHE* 4.2 11.7 - - + -
91L LEU* 4.0 14.9 - - + +
94L GLU* 3.6 33.4 - - + +
95L LEU* 3.7 25.8 - - + -
98L ALA* 4.3 13.2 - - + -
127L GLU 2.8 20.7 + - - +
128L GLU* 3.7 15.5 - - + +
130L HIS* 1.3 77.5 - - - +
132L ASP* 1.3 59.6 + - - +
134L LEU* 3.6 2.1 + - - +
135L GLU* 3.0 51.6 + - - +
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Residues in contact with ASP 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 4.5 11.6 - - - +
64B PHE* 3.8 26.8 - - + -
128L GLU 3.2 19.0 + - - +
129L GLY* 3.7 8.5 - - - +
130L HIS 3.3 0.4 - - - -
131L ILE* 1.3 74.8 - - - +
133L TRP* 1.3 64.0 + - - +
135L GLU* 3.4 6.7 + - - +
136L THR* 3.0 37.7 + - - -
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Residues in contact with TRP 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L ARG* 4.0 14.6 - - - +
40L LEU* 4.4 12.3 - - + -
43L VAL* 3.3 38.5 - - + +
44L GLU* 3.6 30.5 - - + -
47L GLU* 3.6 20.2 - - - +
87L LEU* 5.0 7.2 - - + -
129L GLY 3.3 11.0 + - - +
130L HIS* 3.4 5.8 + - - +
132L ASP* 1.3 76.0 - - - +
134L LEU* 1.3 92.8 + - + +
136L THR* 3.4 6.1 + - + -
137L GLU* 3.0 65.9 + - + +
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Residues in contact with LEU 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L TYR* 3.8 20.2 - - - +
44L GLU* 4.3 1.3 - - - +
47L GLU* 4.8 0.4 - - - +
87L LEU* 3.5 31.6 - - + +
90L ASP* 3.6 20.0 - - + +
91L LEU* 3.8 36.3 - - + +
94L GLU* 4.1 6.1 - - + -
130L HIS 3.2 20.4 + - - +
131L ILE 4.0 3.1 - - - +
133L TRP* 1.3 103.6 - - + +
135L GLU* 1.3 62.9 + - - +
137L GLU* 3.2 4.7 + - - +
138L LEU* 3.0 29.1 + - + +
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Residues in contact with GLU 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.0 41.2 + - - +
64B PHE* 3.9 12.0 - - - +
66B GLU* 4.2 3.8 - - - +
91L LEU* 4.2 22.8 - - + +
95L LEU* 5.6 1.6 - - - +
131L ILE* 3.0 30.5 + - - +
132L ASP* 3.8 7.1 - - - +
133L TRP 3.3 0.2 - - - -
134L LEU* 1.3 76.0 - - - +
136L THR* 1.3 63.8 + - - +
138L LEU* 3.5 4.5 + - - +
139L ASP* 3.3 30.8 + - - +
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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
----------------------------------------------------------
34A ASN 3.2 17.3 + - - -
35A TRP* 3.2 26.2 - - - +
36A GLY* 3.4 18.6 - - - -
132L ASP* 3.0 24.9 + - - -
133L TRP* 3.8 7.9 - - + -
135L GLU* 1.3 77.2 - - - +
137L GLU* 1.3 66.3 + - - +
139L ASP* 3.3 7.0 + - - +
140L LEU* 3.2 29.7 + - + +
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Residues in contact with GLU 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L ARG* 3.1 32.3 + - - -
87L LEU* 4.1 10.8 - - + -
133L TRP* 3.0 58.5 + - + +
134L LEU* 3.5 5.6 - - - +
136L THR* 1.3 79.3 - - - +
138L LEU* 1.3 61.9 + - - +
140L LEU* 3.2 28.4 + - - +
141L ILE* 3.2 19.3 + - - +
149L TYR* 2.6 36.5 + - - +
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Residues in contact with LEU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L GLU* 3.7 30.4 - - + +
87L LEU* 4.2 16.4 - - + +
88L ARG* 3.5 67.4 + - + +
91L LEU* 4.0 25.8 - - + -
134L LEU 3.0 15.6 + - - +
135L GLU* 3.9 5.2 - - - +
136L THR 3.3 0.2 - - - -
137L GLU* 1.3 76.2 - - - +
139L ASP* 1.3 60.5 + - - +
141L ILE* 3.8 11.3 + - + +
142L GLN* 3.5 17.2 + - - +
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Residues in contact with ASP 139 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 5.6 7.6 - - + +
135L GLU* 3.3 19.2 + - - +
136L THR* 3.3 10.3 + - - +
137L GLU 3.2 0.6 - - - -
138L LEU* 1.3 76.2 - - - +
140L LEU* 1.3 57.5 + - + +
141L ILE 3.3 0.4 - - - -
142L GLN* 2.6 32.5 - - - +
143L LYS* 2.7 48.6 + - + +
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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 20.0 - - - +
36A GLY* 4.6 3.6 - - - +
37A LEU* 4.0 19.7 - - + -
150A LEU* 6.1 0.4 - - + -
154A ILE* 4.1 14.4 - - + -
39L ARG* 5.6 1.6 - - - +
136L THR* 3.2 30.5 + - + +
137L GLU* 3.3 25.8 - - - +
139L ASP* 1.3 74.5 - - + +
141L ILE* 1.3 60.3 + - - +
142L GLN 3.1 0.2 - - - -
143L LYS* 4.2 13.2 - - + +
144L MET* 2.8 57.2 + - + +
149L TYR* 4.1 12.8 - - + -
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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 VAL* 4.5 3.4 - - + -
84L GLU* 3.8 35.9 - - + +
87L LEU* 4.0 21.8 - - + -
137L GLU 3.2 12.5 + - - +
138L LEU* 3.8 10.1 - - + +
140L LEU* 1.3 74.9 - - - +
142L GLN* 1.3 58.2 + - - +
145L GLY* 2.9 31.9 + - - -
146L LEU* 3.7 33.6 + - + +
149L TYR* 3.7 38.8 - - + -
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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 GLN* 4.9 3.3 + - - -
84L GLU* 6.1 0.4 - - - +
88L ARG* 6.3 0.2 - - - +
138L LEU 3.5 13.1 + - - +
139L ASP* 2.6 37.5 - - - +
141L ILE* 1.3 82.4 - - - +
143L LYS* 1.3 88.2 + - - +
145L GLY* 4.2 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* 4.6 26.9 - - - +
37A LEU* 4.5 14.6 - - - +
146A LEU* 5.4 2.8 - - - +
147A GLN* 3.6 15.6 + - - +
150A LEU* 3.6 36.3 - - + +
139L ASP* 2.7 34.3 + - + +
140L LEU* 3.3 19.0 + - + +
142L GLN* 1.3 103.3 - - - +
144L MET* 1.3 60.5 + - + +
----------------------------------------------------------
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Residues in contact with MET 144 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN* 3.0 51.5 - - - +
150A LEU* 3.8 9.0 - - + +
151A GLN* 3.4 43.3 - - - +
154A ILE* 3.6 29.2 - - + -
140L LEU* 2.8 45.3 + - + +
143L LYS* 1.3 73.9 - - + +
145L GLY* 1.3 69.1 + - - +
148L ASN* 3.6 11.0 + - + +
149L TYR* 3.8 23.6 - - + +
----------------------------------------------------------
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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