Contacts of the helix formed by residues 113 - 143 (chain M) in PDB entry 2X17
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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M LEU* 3.9 10.8 - - - +
3M SER 5.6 0.5 + - - -
6M MET* 3.7 17.7 - - + +
64M ARG* 4.6 5.9 + - - -
108M ALA* 2.8 23.8 + - - +
111M GLU* 3.1 13.6 - - + +
112M LYS* 1.3 73.2 - - - +
114M TYR* 1.3 62.7 + - - +
115M SER* 3.7 10.0 + - - -
116M THR* 2.7 35.5 + - - -
117M ARG* 3.1 21.2 + - - +
102P TYR* 5.4 0.7 + - - -
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Residues in contact with TYR 114 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112M LYS* 3.2 42.3 + - + +
113M ASP* 1.3 74.0 - - - +
115M SER* 1.3 56.8 + - - +
117M ARG* 3.4 7.8 + - + +
118M ALA* 2.9 32.9 + - - +
102P TYR* 3.6 55.1 - + + -
105P ALA* 3.8 15.9 - - + -
106P ALA* 3.5 18.6 - - + +
109P GLU* 3.0 35.8 + - - -
117P ARG* 3.5 19.6 + - - -
124P ILE* 3.5 11.6 - - + +
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Residues in contact with SER 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M TYR* 3.1 15.8 + - - -
64M ARG* 3.4 26.5 + - - -
113M ASP* 3.2 4.9 + - - -
114M TYR* 1.3 79.1 - - - +
116M THR* 1.3 56.3 + - - +
118M ALA* 3.6 2.4 + - - +
119M PHE* 3.1 23.6 + - - +
102P TYR* 2.6 30.1 + - - -
124P ILE* 3.8 11.4 + - - +
125P ASN* 5.1 0.7 - - - +
128P VAL* 3.6 19.6 - - - +
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Residues in contact with THR 116 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2M LEU* 3.6 9.5 - - - +
6M MET* 3.9 22.2 - - + -
10M LEU* 4.0 18.4 - - + -
60M TYR* 2.8 24.5 + - + -
108M ALA* 4.3 4.9 - - + -
113M ASP* 2.7 32.3 + - - -
115M SER* 1.3 74.1 - - - +
117M ARG* 1.3 60.6 + - - +
119M PHE* 3.2 2.5 + - + +
120M LEU* 3.0 44.6 + - + +
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Residues in contact with ARG 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ALA* 3.7 28.6 - - - +
108M ALA* 3.8 13.1 - - + +
109M GLU* 3.2 29.3 + - + +
113M ASP 3.1 16.7 + - - +
114M TYR* 3.7 10.1 - - + +
115M SER 3.4 0.2 - - - -
116M THR* 1.3 77.5 - - - +
118M ALA* 1.3 60.2 + - - +
120M LEU* 3.5 3.9 + - - +
121M GLU* 3.1 36.0 + - - +
124M ILE* 3.4 21.9 - - - +
114O TYR* 3.7 26.2 + - - +
117O ARG* 5.1 9.9 - - - +
118O ALA* 5.7 0.2 - - - +
117P ARG* 5.2 11.4 - - - +
121P GLU* 5.7 1.0 + - - +
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Residues in contact with ALA 118 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114M TYR 2.9 18.5 + - - +
115M SER 3.9 2.5 - - - +
117M ARG* 1.3 74.3 - - - +
119M PHE* 1.3 64.3 + - - +
121M GLU* 3.3 16.9 - - - +
122M TRP* 4.4 1.0 + - - +
117P ARG* 6.1 0.4 - - - +
121P GLU* 3.8 29.6 - - - +
124P ILE* 3.8 17.3 - - + -
125P ASN* 3.5 27.2 + - - +
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Residues in contact with PHE 119 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M LEU* 4.3 3.1 - - + -
56M ARG* 3.7 14.8 - - + -
57M PHE* 3.6 34.3 - + - -
60M TYR* 3.5 59.7 - + + -
115M SER 3.1 18.6 + - - +
116M THR* 3.5 8.7 - - + +
118M ALA* 1.3 77.6 - - - +
120M LEU* 1.3 69.3 + - + +
121M GLU 3.3 1.0 + - - -
122M TRP* 3.5 19.1 + - + +
123M PHE* 3.5 31.7 - + - -
125P ASN* 4.2 5.6 + - - +
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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
----------------------------------------------------------
10M LEU* 5.1 0.4 - - + -
57M PHE* 4.2 13.9 - - + -
101M ILE* 4.2 22.7 - - + +
104M LEU* 3.6 60.6 - - + +
105M ALA* 3.7 9.4 - - + +
108M ALA* 4.6 0.2 - - + -
116M THR* 3.0 33.6 + - + +
117M ARG* 3.9 9.9 - - - +
118M ALA 3.3 0.2 - - - -
119M PHE* 1.3 79.9 - - + +
121M GLU* 1.3 59.0 + - - +
122M TRP 3.2 2.7 - - - -
123M PHE* 2.9 11.0 + - + +
124M ILE* 2.9 35.1 + - + +
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Residues in contact with GLU 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117M ARG* 3.1 38.0 + - - +
118M ALA 3.3 16.2 - - - +
119M PHE 3.2 0.4 - - - -
120M LEU* 1.3 76.4 - - - +
122M TRP* 1.3 62.0 + - - +
124M ILE* 3.4 7.3 + - - +
125M ASN* 3.1 41.0 + - - +
117O ARG* 4.7 1.0 + - - +
118O ALA* 3.6 31.5 - - - +
121O GLU* 4.2 20.9 - - + +
121P GLU* 4.3 16.4 - - + +
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Residues in contact with TRP 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1704 MET* 4.1 21.5 - - + -
1714 GLN 4.1 6.7 + - - -
1724 GLY* 4.0 22.0 - - - -
53M HIS* 3.9 5.4 - + - -
56M ARG* 3.4 53.8 - - - +
118M ALA 4.4 0.8 + - - +
119M PHE* 3.5 13.9 + - + +
120M LEU 3.2 0.4 - - - -
121M GLU* 1.3 79.2 - - - +
123M PHE* 1.3 84.6 + + + +
125M ASN* 3.5 6.6 + - - +
126M GLU* 3.0 49.8 + - + +
1171M AG 3.9 19.3 - - - -
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Residues in contact with PHE 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M GLU* 4.3 7.2 - - - -
53M HIS* 3.7 33.9 - - + -
56M ARG* 3.7 16.2 - - + -
57M PHE* 3.5 29.2 - + - -
101M ILE* 4.0 23.1 - - + -
119M PHE* 3.5 44.0 - + - -
120M LEU* 2.9 11.9 + - + +
122M TRP* 1.3 99.0 - + + +
124M ILE* 1.3 61.0 + - - +
126M GLU* 3.7 14.1 - - - -
127M GLN* 3.0 35.8 + - + +
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Residues in contact with ILE 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M ILE* 3.9 17.3 - - + -
102M TYR* 4.5 7.2 - - + -
105M ALA* 4.4 9.9 - - + -
117M ARG* 3.4 39.0 - - - +
120M LEU* 2.9 18.8 + - + +
121M GLU* 3.7 10.1 - - - +
123M PHE* 1.3 77.4 - - - +
125M ASN* 1.3 61.1 + - - +
127M GLN* 3.7 4.2 + - - +
128M VAL* 3.3 21.1 + - - +
114O TYR* 3.4 42.4 - - + +
115O SER* 3.7 13.9 + - - +
118O ALA* 3.8 7.9 - - + -
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Residues in contact with ASN 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121M GLU* 3.1 37.7 + - - +
122M TRP* 3.8 6.1 - - - +
124M ILE* 1.3 77.1 - - - +
126M GLU* 1.3 59.9 + - - +
128M VAL* 3.4 20.8 + - - +
129M GLU* 3.7 9.2 + - - +
115O SER 4.9 1.2 - - - +
118O ALA* 3.4 31.8 + - - +
119O PHE* 4.1 3.8 + - - -
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Residues in contact with GLU 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1704 MET* 3.8 22.3 - - + +
53M HIS* 3.1 29.4 + - - -
122M TRP* 3.0 40.6 + - + +
123M PHE* 3.6 14.7 - - + +
125M ASN* 1.3 74.7 - - - +
127M GLN* 1.3 92.5 + - - +
128M VAL 3.2 0.2 - - - -
129M GLU* 3.2 10.2 + - - +
130M GLU* 2.9 31.4 + - - +
1171M AG 3.2 5.7 - - - -
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Residues in contact with GLN 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M GLU* 4.9 4.6 + - - -
50M GLU* 5.1 2.0 + - - -
53M HIS* 4.9 3.8 - - - -
94M GLU* 2.8 33.5 + - - +
97M ILE* 3.7 23.7 - - + +
98M SER* 3.0 34.8 + - - +
101M ILE* 4.7 8.3 - - + -
123M PHE* 3.0 22.9 + - + +
124M ILE* 4.1 4.7 - - - +
125M ASN 3.3 0.2 - - - -
126M GLU* 1.3 95.8 + - - +
128M VAL* 1.3 61.8 + - - +
130M GLU* 3.7 10.1 + - - +
131M GLU* 3.1 35.0 + - - +
64O ARG* 5.5 0.4 - - - -
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Residues in contact with VAL 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124M ILE 3.3 17.3 - - - +
125M ASN* 3.4 12.3 + - - +
126M GLU 3.2 0.4 - - - -
127M GLN* 1.3 77.6 - - - +
129M GLU* 1.3 62.0 + - + +
131M GLU* 4.2 1.8 - - - +
132M ALA* 3.3 23.9 + - - +
60O TYR* 4.2 14.1 - - + -
63O ASP* 4.0 22.0 - - + +
64O ARG* 3.9 30.1 - - - +
115O SER* 3.7 31.9 - - - +
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Residues in contact with GLU 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1704 MET* 3.5 25.7 - - + +
125M ASN 3.7 7.9 + - - +
126M GLU* 3.2 11.5 + - - +
128M VAL* 1.3 78.2 - - + +
130M GLU* 1.3 58.7 + - + +
132M ALA* 3.4 4.9 + - - +
133M SER* 2.9 32.1 + - - -
63O ASP* 5.4 7.4 - - - +
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Residues in contact with GLU 130 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1704 MET* 4.9 6.2 - - - +
46M GLN* 2.8 39.4 + - - +
49M GLU* 4.7 2.6 - - - +
50M GLU* 3.2 8.6 - - - +
53M HIS* 3.9 8.3 + - - -
94M GLU* 3.0 35.9 - - - +
126M GLU* 2.9 34.8 + - - +
127M GLN* 3.8 14.5 + - - +
128M VAL 3.4 0.2 - - - -
129M GLU* 1.3 76.6 - - + +
131M GLU* 1.3 61.4 + - - +
133M SER* 3.4 6.4 + - - -
134M VAL* 3.2 29.5 + - - +
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Residues in contact with GLU 131 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M TYR* 3.7 23.9 + - + -
94M GLU* 3.9 22.2 - - + +
95M LYS* 3.6 25.4 - - - +
98M SER* 2.8 32.0 + - - +
102M TYR* 4.9 1.7 + - - -
127M GLN* 3.1 18.8 + - - +
128M VAL* 4.2 4.0 - - - +
130M GLU* 1.3 75.3 - - - +
132M ALA* 1.3 58.4 + - - +
134M VAL* 3.3 1.3 + - - -
135M LYS* 2.9 31.4 + - - +
1O MET 5.3 5.4 + - - -
63O ASP 5.2 3.1 - - - +
64O ARG* 4.1 21.3 + - - +
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Residues in contact with ALA 132 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128M VAL 3.3 17.8 + - - +
129M GLU* 3.9 4.9 - - - +
131M GLU* 1.3 79.5 - - - +
133M SER* 1.3 61.4 + - - +
135M LYS* 4.2 4.9 - - - +
136M LYS* 3.1 26.9 + - - +
62O TYR 5.3 1.1 - - - +
63O ASP* 3.7 39.4 + - - +
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Residues in contact with SER 133 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M TRP* 3.7 20.6 + - - -
46M GLN* 5.2 2.8 + - - -
129M GLU 2.9 19.5 + - - -
130M GLU* 3.5 8.1 - - - -
131M GLU 3.2 0.2 - - - -
132M ALA* 1.3 78.7 - - - +
134M VAL* 1.3 61.6 + - - +
136M LYS* 3.8 7.5 - - - +
137M ILE* 3.5 26.1 + - - +
161M ARG* 5.0 2.1 + - - -
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Residues in contact with VAL 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M TYR* 5.1 4.0 - - + +
42M TRP* 4.4 17.5 - - + -
46M GLN* 5.9 2.9 - - + +
87M PHE* 3.9 25.8 - - + +
90M ALA* 4.1 8.5 - - + -
91M TYR* 3.8 37.0 - - + +
94M GLU* 4.0 18.6 - - + -
130M GLU* 3.2 18.5 + - - +
131M GLU 3.3 2.7 + - - +
133M SER* 1.3 77.1 - - - +
135M LYS* 1.3 60.0 + - - +
137M ILE* 3.2 5.9 + - - +
138M LEU* 2.9 25.3 + - + +
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Residues in contact with LYS 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91M TYR* 3.6 40.5 - - + +
131M GLU 2.9 18.7 + - - +
132M ALA* 4.2 5.4 - - - +
134M VAL* 1.3 76.6 - - - +
136M LYS* 1.3 63.0 + - - +
138M LEU* 3.2 14.2 + - + +
139M ASP* 2.8 63.2 + - - +
142M LYS* 5.5 3.6 - - - +
1O MET* 5.5 2.0 - - - -
65O ASN* 3.5 41.0 + - + +
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Residues in contact with LYS 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356 GLY 6.1 0.7 - - - +
376 GLU* 3.2 41.0 + - - +
132M ALA 3.1 20.2 + - - +
133M SER* 3.8 9.4 - - - +
135M LYS* 1.3 78.7 - - - +
137M ILE* 1.3 64.7 + - + +
139M ASP* 3.8 6.8 + - - +
140M LYS* 3.4 47.3 + - - +
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Residues in contact with ILE 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 4.4 3.1 - - + -
42M TRP* 3.6 33.7 - - + +
87M PHE* 3.8 29.4 - - + -
133M SER* 3.5 18.8 - - - +
134M VAL 3.2 5.5 + - - +
136M LYS* 1.3 79.1 - - + +
138M LEU* 1.3 65.6 + - - +
140M LYS* 3.1 10.5 + - + +
141M LEU* 3.1 29.3 + - + +
154M LEU* 4.5 12.1 - - + -
158M LEU* 3.8 31.6 - - + -
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Residues in contact with LEU 138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M LEU* 4.0 3.4 - - + +
87M PHE* 3.4 32.4 - - + +
88M GLU* 3.8 24.5 - - + -
91M TYR* 3.6 28.9 - - + -
134M VAL 2.9 15.5 + - - +
135M LYS* 3.5 14.1 - - + +
137M ILE* 1.3 76.5 - - - +
139M ASP* 1.3 64.6 + - - +
141M LEU* 3.1 13.5 + - - +
142M LYS* 3.0 52.1 + - + +
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Residues in contact with ASP 139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346 LEU 6.0 1.1 - - - +
356 GLY* 5.9 7.9 - - - -
135M LYS* 2.8 54.8 + - - +
136M LYS* 4.0 6.5 - - - +
137M ILE 3.3 0.2 - - - -
138M LEU* 1.3 82.6 - - - +
140M LYS* 1.3 58.0 + - + +
142M LYS* 3.5 16.2 + - - +
143M PHE* 3.0 26.9 + - - +
65O ASN* 4.5 3.5 - - - +
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Residues in contact with LYS 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356 GLY 4.7 14.8 - - - +
376 GLU* 6.5 0.4 - - - -
1526 PHE* 4.4 19.3 - - + -
1556 ASP* 5.4 7.9 + - - -
136M LYS* 3.4 39.0 + - + +
137M ILE* 3.1 14.5 + - + +
139M ASP* 1.3 77.3 - - + +
141M LEU* 1.3 57.4 + - - +
143M PHE* 3.3 23.5 + - + +
144M ALA* 3.6 8.3 + - - +
150M ILE* 4.9 1.4 - - - +
154M LEU* 3.7 39.0 - - + +
157M GLU* 3.6 21.0 + - - -
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Residues in contact with LEU 141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M PHE* 3.8 19.1 - - + -
83M PRO* 3.6 31.0 - - + +
84M LEU* 4.0 23.4 - - + +
87M PHE* 3.7 29.4 - - + -
137M ILE* 3.1 21.4 + - + +
138M LEU* 3.1 6.2 + - - +
140M LYS* 1.3 75.7 - - - +
142M LYS* 1.3 63.0 + - - +
143M PHE 3.1 1.6 - - - -
144M ALA* 3.3 23.6 + - + +
145M LYS* 4.0 2.9 + - - -
151M LEU* 3.8 29.4 - - + -
154M LEU* 4.1 8.7 - - + -
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Residues in contact with LYS 142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M LEU* 3.6 23.7 - - + +
88M GLU* 4.3 11.9 - - - -
135M LYS* 5.5 3.8 - - - +
138M LEU* 3.0 30.4 + - + +
139M ASP* 3.6 19.3 + - - +
141M LEU* 1.3 75.8 - - - +
143M PHE* 1.3 59.7 + - - +
145M LYS* 3.3 33.0 - - - +
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Residues in contact with PHE 143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346 LEU 5.5 8.3 - - - -
366 LEU* 5.1 9.9 - - + -
1486 PRO* 3.6 44.1 - - + +
1516 LEU* 3.8 28.9 - - + -
1526 PHE* 4.5 21.3 - + + -
139M ASP 3.0 14.8 + - - +
140M LYS* 3.3 18.8 - - + +
141M LEU 3.1 0.2 - - - -
142M LYS* 1.3 78.0 - - - +
144M ALA* 1.3 55.3 + - - +
145M LYS* 3.8 2.8 + - - +
150M ILE* 4.7 9.9 - - + +
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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
------------------------------------------------------------
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