Contacts of the helix formed by residues 109 - 137 (chain M) in PDB entry 5X6E
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 ASN 109 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11M TYR* 5.9 1.6 - - - -
107M SER 2.9 6.7 + - - -
108M LYS* 1.3 128.4 + - + +
110M LEU* 1.3 64.8 + - - +
111M THR* 2.4 34.4 + - - +
112M HIS* 4.3 6.2 + - - -
113M PHE* 3.6 3.5 - - - +
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Residues in contact with LEU 110 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M SER 3.3 24.7 - - - +
109M ASN* 1.3 75.7 + - - +
111M THR* 1.3 60.7 + - - +
112M HIS 3.6 0.4 - - - -
113M PHE* 3.5 24.0 - - + -
114M PHE* 2.8 52.3 + - + +
107N SER* 3.0 45.1 - - - +
110N LEU* 3.9 12.3 - - + -
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Residues in contact with THR 111 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M GLN* 5.0 6.4 + - - +
7M GLU* 4.6 8.9 + - - +
109M ASN* 2.4 27.6 + - - +
110M LEU* 1.3 80.7 - - - +
112M HIS* 1.3 78.2 + - - +
114M PHE* 4.1 3.3 - - - +
115M TYR* 3.3 19.1 + - - +
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Residues in contact with HIS 112 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M GLN 4.5 4.0 - - - -
7M GLU* 3.1 39.9 + - + +
8M PHE* 3.4 48.6 - + + -
11M TYR* 3.5 22.3 - + + +
106M LEU* 3.8 2.1 - - + +
108M LYS* 3.1 33.7 + - - +
109M ASN* 4.3 5.8 - - - -
111M THR* 1.3 92.1 + - - +
113M PHE* 1.3 61.6 + - - +
114M PHE 3.4 0.2 - - - -
115M TYR* 3.4 9.0 - - + +
116M VAL* 3.4 27.4 + - - +
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Residues in contact with PHE 113 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M LEU* 3.0 57.0 - - + +
108M LYS* 3.7 1.6 - - - +
109M ASN 3.6 2.2 - - - +
110M LEU* 3.5 32.1 - - + +
111M THR 3.1 0.2 - - - -
112M HIS* 1.3 77.2 - - - +
114M PHE* 1.3 70.0 + + - +
115M TYR 3.3 0.2 - - - -
116M VAL* 4.1 3.3 + - - +
117M PHE* 3.6 17.3 + - - +
106N LEU 5.2 0.7 - - - -
110N LEU* 4.3 14.8 - - + -
113N PHE* 3.2 62.4 - + + -
114N PHE* 4.2 22.9 - + - -
117N PHE* 5.2 4.6 - + - -
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Residues in contact with PHE 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M GLN* 5.5 3.1 - - - +
110M LEU* 2.8 46.8 + - + +
111M THR* 4.2 3.8 - - - +
113M PHE* 1.3 86.3 - + - +
115M TYR* 1.3 55.1 + - - +
117M PHE* 3.4 7.4 - + - +
118M GLN* 2.8 34.5 + - - +
74N ILE* 4.0 33.4 - - + +
75N ASP* 6.1 2.0 - - + -
103N LYS* 2.8 46.9 - - + -
104N GLU* 4.9 1.1 - - + -
106N LEU* 4.5 3.4 - - + -
107N SER* 4.4 14.8 - - - -
113N PHE* 4.1 21.3 - + - -
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Residues in contact with TYR 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M ASN 5.0 1.8 - - - -
4M GLN* 3.7 41.0 - - + +
5M ALA* 3.4 35.4 - - + +
8M PHE* 4.1 32.8 - + + -
40M PHE* 3.8 12.0 - + - -
66M ALA 4.4 12.1 + - - -
67M PHE* 4.5 2.8 - - - -
68M VAL* 4.3 7.9 - - + -
111M THR 3.3 14.0 + - - +
112M HIS* 3.4 12.3 - - - +
114M PHE* 1.3 75.5 - - - +
116M VAL* 1.3 73.7 + - + +
118M GLN* 2.9 20.4 + - + +
119M THR* 3.1 37.4 + - + +
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Residues in contact with VAL 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8M PHE* 4.2 20.2 - - + -
38M CYS* 5.6 2.5 - - - -
68M VAL* 4.2 17.5 - - + -
70M MET* 4.2 14.4 - - - -
102M LEU* 5.5 2.7 - - + -
106M LEU* 4.1 22.9 - - + -
112M HIS 3.4 15.5 + - - +
113M PHE 4.4 4.5 - - - +
115M TYR* 1.3 81.8 - - + +
117M PHE* 1.3 61.6 + - - +
119M THR* 2.6 26.2 + - - -
120M LEU* 3.1 7.9 + - + +
117N PHE* 3.7 25.6 - - + -
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Residues in contact with PHE 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113M PHE 3.6 13.6 + - - +
114M PHE* 3.4 11.9 + + - +
115M TYR 3.1 0.6 - - - -
116M VAL* 1.3 76.5 - - - +
118M GLN* 1.3 57.2 - - - +
120M LEU* 3.2 4.8 + - + +
121M GLN* 2.9 50.1 + - - +
70N MET* 4.8 9.9 - - + -
74N ILE* 3.5 32.5 - - + -
102N LEU* 6.0 0.9 - - + -
106N LEU* 5.3 5.2 - - + -
113N PHE* 3.4 35.7 - + + -
116N VAL* 4.4 20.9 - - + -
117N PHE* 4.0 19.4 - + + -
120N LEU* 3.5 29.2 - - + -
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Residues in contact with GLN 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4M GLN* 4.7 11.9 + - - +
114M PHE 2.8 16.8 + - - +
115M TYR* 2.9 15.0 + - + +
117M PHE* 1.3 76.2 - - - +
119M THR* 1.3 54.8 + - + +
121M GLN* 3.0 7.1 + - - +
122M LYS* 2.7 50.3 + - - +
73N PHE* 4.0 21.4 - - - +
74N ILE* 3.6 11.4 + - + +
75N ASP* 2.8 44.3 + - - +
76N THR* 4.4 6.3 - - - +
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Residues in contact with THR 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE* 3.4 41.9 - - + -
68M VAL* 3.0 30.5 + - + +
115M TYR* 3.2 39.9 - - + +
116M VAL 2.6 16.8 + - - -
118M GLN* 1.3 77.4 - - + +
120M LEU* 1.3 60.0 + - - +
122M LYS* 3.1 6.9 + - - +
123M GLN* 3.0 23.7 + - - +
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Residues in contact with LEU 120 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE* 6.4 0.9 - - + -
68M VAL* 5.4 5.2 - - + +
70M MET* 4.6 20.0 - - + +
116M VAL* 3.1 8.4 + - + +
117M PHE* 3.5 9.2 - - - +
119M THR* 1.3 86.9 + - - +
121M GLN* 1.3 61.2 + - - +
123M GLN* 3.4 13.5 + - - +
124M VAL* 3.4 27.7 + - - +
117N PHE* 3.6 31.9 - - + +
120N LEU* 4.3 12.5 - - + +
121N GLN* 3.5 35.0 - - + +
124N VAL* 4.1 18.3 - - + +
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Residues in contact with GLN 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M PHE* 2.9 38.9 + - - +
118M GLN* 3.5 5.2 - - - +
120M LEU* 1.3 75.0 - - - +
122M LYS* 1.3 59.2 + - - +
123M GLN 3.2 0.4 - - - -
124M VAL* 3.2 26.1 - - + +
125M SER* 3.7 6.2 + - - -
70N MET* 3.3 29.0 - - + +
72N GLY 2.3 35.9 + - - -
73N PHE* 3.7 23.6 - - + -
74N ILE* 3.4 16.5 + - - +
80N VAL* 4.1 5.6 - - + +
120N LEU* 4.3 13.6 - - + +
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Residues in contact with LYS 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M PHE* 4.1 16.2 - - + -
118M GLN* 2.7 28.6 + - + +
119M THR* 3.1 11.0 + - - +
121M GLN* 1.3 77.8 - - - +
123M GLN* 1.3 60.8 + - - +
125M SER 4.1 1.1 - - - -
126M TYR* 3.4 14.9 + - - +
224M TRP* 3.6 23.8 + - + -
228M ALA* 3.9 33.6 + - + +
229M CYS* 4.3 3.8 - - - -
301M GSH 3.0 44.5 + - - +
73N PHE* 3.9 12.8 - - + -
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Residues in contact with GLN 123 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M GLN* 2.9 27.9 + - - +
63M TYR* 2.7 34.2 + - - -
67M PHE* 4.7 5.6 - - + -
68M VAL 5.3 2.3 - - - +
69M ILE* 6.0 0.9 - - - -
119M THR 3.0 14.6 + - - +
120M LEU* 3.6 15.9 - - - +
121M GLN 3.2 0.4 - - - -
122M LYS* 1.3 76.2 - - - +
124M VAL* 1.3 59.9 + - - +
125M SER 3.1 2.2 - - - -
126M TYR* 3.1 2.6 + - - +
127M SER* 2.9 40.1 + - - +
301M GSH 4.2 12.7 - - - -
124N VAL* 3.5 36.7 - - + +
128N LEU* 4.8 3.0 - - - +
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Residues in contact with VAL 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M LEU 3.4 11.4 + - - +
121M GLN* 3.2 27.6 - - + +
123M GLN* 1.3 76.7 - - - +
125M SER* 1.3 63.6 + - - +
127M SER* 4.2 5.0 - - - -
128M LEU* 3.2 34.5 + - + +
70N MET* 6.2 2.7 - - + -
80N VAL* 6.3 2.2 - - + -
120N LEU* 4.1 15.9 - - + +
123N GLN* 3.6 31.6 - - + -
124N VAL* 3.6 21.8 - - + +
127N SER* 5.2 2.3 + - - -
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Residues in contact with SER 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M GLN 3.8 13.9 - - - -
122M LYS 4.0 2.2 - - - -
123M GLN 3.1 0.4 - - - -
124M VAL* 1.3 81.7 - - - +
126M TYR* 1.3 64.3 + - - +
128M LEU* 3.5 6.4 + - - +
129M ALA* 3.2 25.1 + - - +
224M TRP* 3.0 24.8 - - - -
73N PHE* 4.6 4.4 - - - -
80N VAL* 2.4 41.6 + - - +
83N TYR* 4.6 5.2 + - - -
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Residues in contact with TYR 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M GLN* 3.0 35.4 - - + -
122M LYS 3.4 5.3 + - - +
123M GLN 3.1 8.2 + - - +
125M SER* 1.3 80.5 - - - +
127M SER* 1.3 63.0 - - - +
129M ALA* 3.9 1.8 - - - +
130M LYS* 2.9 68.7 + - + +
149M ILE* 3.2 23.2 - - + +
221M LEU* 4.6 5.3 - - + +
224M TRP* 3.4 49.8 - + + +
301M GSH 2.3 48.0 + - + -
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Residues in contact with SER 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M GLN* 4.5 0.2 + - - -
123M GLN* 2.9 35.7 + - - +
124M VAL* 4.2 4.0 - - - -
126M TYR* 1.3 83.6 - - - +
128M LEU* 1.3 54.1 + - - +
130M LYS* 3.7 3.8 - - - +
131M PHE* 2.7 35.9 + - - +
124N VAL* 5.2 1.6 + - - +
127N SER* 3.7 31.2 - - - -
128N LEU* 4.4 13.3 - - - +
131N PHE* 6.1 0.5 - - - +
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Residues in contact with LEU 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M VAL* 3.2 26.2 + - + +
125M SER* 3.8 6.5 - - - +
127M SER* 1.3 75.0 - - - +
129M ALA* 1.3 54.9 + - - +
131M PHE* 3.0 10.0 + - + +
132M ASN* 2.7 34.7 + - - +
48N LEU* 3.8 24.5 - - + -
60N LEU* 3.8 40.4 - - + +
61N GLN* 4.6 14.4 - - - +
63N TYR* 5.0 4.7 - - - +
83N TYR* 4.1 21.1 - - + +
123N GLN* 5.6 3.8 - - + +
127N SER* 5.0 9.2 - - - +
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Residues in contact with ALA 129 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125M SER 3.2 14.4 + - - +
126M TYR* 4.0 3.1 - - - +
128M LEU* 1.3 78.8 - - - +
130M LYS* 1.3 60.9 + - - +
132M ASN* 3.1 20.8 + - - +
133M ASP* 3.3 7.4 + - - +
220M LYS* 3.8 29.6 - - + +
221M LEU* 3.5 18.0 - - + +
224M TRP* 4.2 8.5 - - + -
83N TYR* 3.7 14.9 + - - +
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Residues in contact with LYS 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M LEU 3.0 26.4 + - - -
61M GLN* 3.6 6.2 - - + +
126M TYR* 2.9 55.0 + - + +
127M SER* 3.8 4.9 - - - +
129M ALA* 1.3 73.1 - - - +
131M PHE* 1.3 65.6 + - - +
132M ASN 3.3 0.5 + - - -
134M PHE* 3.1 63.9 + - + +
146M GLN* 3.5 16.3 + - - -
149M ILE* 3.9 8.3 - - - -
177M SER* 4.7 1.0 + - - -
221M LEU* 3.9 19.0 - - + +
301M GSH 4.1 0.4 + - - -
131N PHE* 4.3 19.0 - - + -
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Residues in contact with PHE 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127M SER 2.7 23.7 + - - +
128M LEU* 3.5 8.3 - - + +
130M LYS* 1.3 71.5 - - - +
132M ASN* 1.3 69.4 + - - +
134M PHE* 4.8 2.5 - - + -
135M SER* 3.3 27.7 + - - -
58N MET* 4.1 10.1 - - + +
59N ASN 4.5 1.3 - - - -
60N LEU* 3.6 44.0 - - + -
127N SER* 5.5 4.0 - - - +
130N LYS* 3.8 23.1 - - + -
131N PHE* 4.6 29.1 - + + -
134N PHE* 3.3 46.4 - + + -
177N SER 4.3 4.7 - - - -
178N SER 6.2 0.2 - - - -
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Residues in contact with ASN 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M LEU 2.7 11.0 + - - +
129M ALA* 3.2 15.5 - - - +
130M LYS 3.1 0.4 - - - -
131M PHE* 1.3 83.8 - - - +
133M ASP* 1.3 79.1 + - - +
135M SER 3.0 13.9 + - - -
136M ILE* 3.4 24.6 + - - +
219M PRO* 5.7 0.4 - - - +
220M LYS* 3.5 19.1 - - + +
50N SER* 3.6 21.9 + - - -
52N SER* 6.2 1.6 - - - -
58N MET* 3.5 20.7 - - - +
60N LEU* 3.2 24.2 - - - +
83N TYR* 4.7 0.6 - - - +
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Residues in contact with ASP 133 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M ALA 3.3 6.1 + - - -
132M ASN* 1.3 93.2 + - - +
134M PHE* 1.3 65.0 + - + +
135M SER 3.1 3.2 + - - -
136M ILE* 3.5 22.6 - - - +
137M ASN* 3.8 8.0 + - - +
141M GLY* 4.4 11.2 - - - +
217M TYR 4.2 4.4 - - - +
218M ALA* 3.3 15.2 - - + -
219M PRO* 3.5 16.3 - - - +
220M LYS* 3.0 29.6 + - - +
221M LEU* 3.2 31.6 + - + +
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Residues in contact with PHE 134 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M LYS* 3.1 53.4 + - + +
131M PHE* 4.6 3.4 - - + +
132M ASN 3.3 0.4 - - - -
133M ASP* 1.3 79.2 - - - +
135M SER* 1.3 59.8 + - - +
137M ASN 2.9 15.5 - - - +
138M GLY 4.1 1.0 - - - +
139M LYS* 6.0 1.2 - - - -
141M GLY 4.7 1.1 - - - -
142M SER* 3.2 63.2 + - - +
145M GLY* 4.1 8.7 - - - -
146M GLN* 4.0 18.8 - - + -
177M SER 4.3 1.1 - - - -
178M SER* 4.1 16.4 - - - -
221M LEU* 4.8 5.6 - - + -
131N PHE* 3.8 33.2 - + + -
135N SER* 5.5 0.7 - - - -
139N LYS* 5.1 1.4 + - - -
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Residues in contact with SER 135 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131M PHE* 3.3 26.7 + - - -
132M ASN 3.0 10.3 + - - -
134M PHE* 1.3 79.1 - - - +
136M ILE* 1.3 65.6 + - - +
137M ASN 3.1 6.2 + - - +
58N MET* 3.7 20.5 - - - +
134N PHE* 4.9 6.2 - - - +
139N LYS* 3.3 23.6 + - - +
179N GLY* 3.8 19.1 + - - +
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Residues in contact with ILE 136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132M ASN* 3.4 18.8 + - - +
133M ASP* 3.5 38.1 - - + +
135M SER* 1.3 75.8 - - - +
137M ASN* 1.3 81.1 + - - +
217M TYR 4.8 3.4 - - - +
219M PRO* 4.9 7.6 - - + -
52N SER* 5.8 7.4 - - - -
54N ASN* 6.1 1.1 - - - +
56N THR* 4.9 25.7 - - + +
57N ILE 5.3 0.7 - - - +
58N MET* 4.1 22.9 - - + -
179N GLY* 4.8 9.1 - - - +
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Residues in contact with ASN 137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133M ASP 3.8 2.7 + - - +
134M PHE 2.9 19.1 - - - +
135M SER 3.4 6.2 - - - +
136M ILE* 1.3 101.1 - - - +
138M GLY* 1.3 66.2 + - - +
140M LEU* 6.0 0.2 - - + -
141M GLY* 3.9 17.3 - - - +
216M ARG 5.5 0.6 + - - -
217M TYR* 3.3 48.3 + - + +
139N LYS* 4.9 1.7 + - - -
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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