Contacts of the helix formed by residues 113 - 143 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LEU* 4.0 11.9 - - - +
3G SER* 6.1 0.2 - - - -
6G MET* 3.6 17.4 - - + +
60G TYR* 4.5 0.3 + - - -
64G ARG* 4.6 7.3 + - - -
108G ALA* 2.8 22.2 + - - +
111G GLU* 3.1 13.2 - - + +
112G LYS* 1.3 73.4 - - - +
114G TYR* 1.3 61.3 + - - +
115G SER* 3.7 10.0 + - - -
116G THR* 2.6 33.8 + - - -
117G ARG* 3.2 21.7 + - - +
102J TYR* 5.3 1.7 + - - -
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Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LYS* 3.2 40.3 + - + +
113G ASP* 1.3 74.0 - - - +
115G SER* 1.3 56.7 + - - +
117G ARG* 3.6 8.2 - - + +
118G ALA* 2.9 31.2 + - - +
102J TYR* 3.5 55.2 - + + -
105J ALA* 3.8 19.1 - - + -
106J ALA* 3.3 21.7 - - + +
109J GLU* 2.9 37.3 + - - -
117J ARG* 3.6 20.7 + - - -
124J ILE* 3.4 13.1 - - + +
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Residues in contact with SER 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G TYR* 3.1 15.2 + - - -
64G ARG* 3.5 25.2 + - - -
113G ASP* 3.2 4.4 + - - -
114G TYR* 1.3 78.6 - - - +
116G THR* 1.3 57.6 + - - +
118G ALA* 3.5 2.8 + - - +
119G PHE* 3.0 27.4 + - - +
102J TYR* 2.7 29.0 + - - -
124J ILE* 3.8 11.1 + - - +
125J ASN* 5.0 1.0 - - - +
128J VAL* 3.7 18.3 - - - +
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Residues in contact with THR 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LEU* 5.0 2.4 - - - +
6G MET* 3.8 26.0 - - + +
10G LEU* 3.9 23.3 - - + -
60G TYR* 2.8 27.2 + - + -
108G ALA* 4.3 4.5 - - + -
113G ASP* 2.6 31.7 + - - -
115G SER* 1.3 74.1 - - - +
117G ARG* 1.3 60.1 + - - +
119G PHE* 3.4 2.5 + - + +
120G LEU* 3.0 41.7 + - + +
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Residues in contact with ARG 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ALA* 3.9 17.5 - - - +
108G ALA* 3.9 9.1 - - + +
109G GLU* 3.0 42.5 + - + +
113G ASP 3.2 17.8 + - - +
114G TYR* 3.6 11.2 - - + +
115G SER 3.3 0.2 - - - -
116G THR* 1.3 76.8 - - - +
118G ALA* 1.3 61.5 + - - +
120G LEU* 3.4 3.9 + - - +
121G GLU* 3.1 38.7 + - - +
124G ILE* 3.4 24.2 - - - +
114I TYR* 3.9 18.3 + - - +
117I ARG* 5.1 11.5 - - - +
118I ALA* 5.7 0.2 - - - +
117J ARG* 4.9 13.5 - - - +
121J GLU* 4.9 1.7 + - - +
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Residues in contact with ALA 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G TYR 2.9 17.5 + - - +
115G SER 3.9 2.2 - - - +
116G THR 3.4 0.2 - - - -
117G ARG* 1.3 76.2 - - - +
119G PHE* 1.3 62.9 + - - +
121G GLU* 3.4 15.1 - - - +
122G TRP* 4.4 1.7 + - - +
117J ARG* 5.8 0.2 - - - +
121J GLU* 3.6 29.0 + - - +
124J ILE* 3.9 15.0 - - + -
125J ASN* 3.5 32.4 + - - +
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Residues in contact with PHE 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 4.3 2.5 - - + -
56G ARG* 3.5 27.8 - - + -
57G PHE* 3.5 35.2 - + - -
60G TYR* 3.6 46.0 - + + -
115G SER 3.0 18.7 + - - +
116G THR* 3.6 9.9 - - + +
117G ARG 3.3 0.2 - - - -
118G ALA* 1.3 77.8 - - - +
120G LEU* 1.3 67.6 + - + +
121G GLU 3.4 0.3 + - - -
122G TRP* 3.6 18.1 + - + +
123G PHE* 3.5 31.4 - + - -
125J ASN* 4.1 5.1 + - - +
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Residues in contact with LEU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 5.2 0.2 - - + -
57G PHE* 4.1 31.9 - - + -
101G ILE* 4.2 13.9 - - + +
104G LEU* 3.6 51.1 - - + +
105G ALA* 3.7 11.9 - - + +
108G ALA* 4.5 1.6 - - + -
116G THR* 3.0 33.5 + - + +
117G ARG* 4.0 10.1 - - - +
118G ALA 3.4 0.2 - - - -
119G PHE* 1.3 80.5 - - + +
121G GLU* 1.3 64.5 + - - +
122G TRP 3.2 1.1 - - - -
123G PHE* 3.0 18.4 + - + +
124G ILE* 3.0 18.3 + - + +
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Residues in contact with GLU 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ARG* 3.1 41.3 + - - +
118G ALA 3.4 15.5 - - - +
119G PHE 3.2 0.2 - - - -
120G LEU* 1.3 77.1 - - - +
122G TRP* 1.3 63.1 + - - +
124G ILE* 3.3 11.0 + - - +
125G ASN* 3.0 38.5 + - - +
117I ARG* 4.9 0.7 + - - +
118I ALA* 3.7 27.3 - - - +
121I GLU* 4.1 23.7 - - + +
121J GLU* 4.2 14.6 - - + +
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Residues in contact with TRP 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G HIS* 3.5 32.8 - + - -
56G ARG* 3.4 52.9 - - - +
118G ALA 4.4 1.2 + - - +
119G PHE* 3.6 13.5 + - + +
121G GLU* 1.3 81.2 - - - +
123G PHE* 1.3 79.3 + + + +
125G ASN* 3.5 7.1 + - - +
126G GLU* 2.9 46.6 + - + +
1172G AG 4.3 0.4 - - - -
170Y MET* 4.3 23.1 - - + -
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Residues in contact with PHE 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 4.2 8.5 - - - -
53G HIS* 3.7 24.2 - + + -
56G ARG* 3.6 30.3 - - + -
57G PHE* 3.5 32.5 - + - -
101G ILE* 4.2 20.4 - - + -
119G PHE* 3.5 43.1 - + - -
120G LEU* 3.0 12.3 + - + +
122G TRP* 1.3 97.0 - + + +
124G ILE* 1.3 60.5 + - - +
126G GLU* 3.4 11.7 - - - +
127G GLN* 2.8 35.6 + - + +
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Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ILE* 4.0 18.2 - - + -
102G TYR* 4.7 6.5 - - + -
105G ALA* 4.5 9.4 - - + -
117G ARG* 3.4 36.1 - - - +
120G LEU 3.0 14.2 + - - +
121G GLU* 3.3 15.2 + - - +
123G PHE* 1.3 78.0 - - - +
125G ASN* 1.3 61.8 + - - +
127G GLN* 3.3 5.1 + - - +
128G VAL* 3.3 25.2 + - + +
114I TYR* 3.4 43.3 - - + +
115I SER* 3.8 13.4 + - - +
118I ALA* 3.8 7.9 - - + -
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Residues in contact with ASN 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLU* 3.0 33.7 + - - +
122G TRP* 3.8 7.0 - - - +
124G ILE* 1.3 75.8 - - - +
126G GLU* 1.3 62.3 + - - +
128G VAL* 3.5 21.3 + - - +
129G GLU* 3.6 11.3 + - - +
115I SER 5.0 1.0 - - - +
118I ALA* 3.4 31.5 + - - +
119I PHE* 4.2 3.3 + - - +
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Residues in contact with GLU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 5.5 0.2 - - - +
53G HIS* 2.9 38.2 - - - +
122G TRP* 2.9 42.9 + - + +
123G PHE* 3.4 16.1 - - - +
124G ILE 3.3 0.4 - - - -
125G ASN* 1.3 77.7 - - - +
127G GLN* 1.3 81.4 + - - +
129G GLU* 3.2 8.1 + - - +
130G GLU* 3.0 43.1 + - - +
170Y MET* 3.7 21.9 - - + +
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Residues in contact with GLN 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 4.8 6.9 + - - -
50G GLU* 5.3 3.6 + - - -
94G GLU* 2.8 31.7 + - - +
97G ILE* 3.6 23.9 - - + +
98G SER* 2.9 38.4 + - - +
101G ILE* 4.6 9.8 - - + +
123G PHE* 2.8 25.3 + - + +
124G ILE* 3.3 6.9 + - - +
126G GLU* 1.3 93.9 + - - +
128G VAL* 1.3 60.0 + - - +
130G GLU* 3.8 4.2 - - - +
131G GLU* 3.0 35.2 + - - +
64I ARG* 5.3 0.4 - - - -
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Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ILE 3.3 18.2 + - - +
125G ASN* 3.5 13.2 - - - +
126G GLU 3.3 0.4 - - - -
127G GLN* 1.3 76.2 - - - +
129G GLU* 1.3 63.1 + - + +
131G GLU* 4.1 1.7 - - - +
132G ALA* 3.3 23.0 + - - +
60I TYR* 4.2 15.0 - - + -
63I ASP* 4.3 18.9 - - + +
64I ARG* 3.8 29.6 + - - +
115I SER* 3.6 33.2 - - - +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G ASN 3.6 8.6 + - - +
126G GLU* 3.2 9.5 + - - +
127G GLN 3.2 0.6 - - - -
128G VAL* 1.3 79.8 - - + +
130G GLU* 1.3 54.4 + - - +
132G ALA* 3.4 4.3 + - - +
133G SER* 2.8 37.7 + - - -
63I ASP* 6.0 3.4 - - - +
170Y MET* 3.4 25.1 - - + +
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLN* 2.8 38.8 + - - +
49G GLU* 4.5 1.4 - - - +
50G GLU* 3.3 5.2 - - - +
53G HIS* 3.6 9.2 - - - -
94G GLU* 3.3 34.6 - - - +
126G GLU* 3.0 43.7 + - + +
127G GLN* 3.4 9.1 + - - +
129G GLU* 1.3 73.8 - - - +
131G GLU* 1.3 63.2 + - - +
133G SER* 3.4 6.6 + - - -
134G VAL* 3.1 31.4 + - - +
1172G AG 4.0 4.5 - - - -
170Y MET* 4.9 4.6 - - + +
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Residues in contact with GLU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G TYR* 3.8 21.5 + - + -
94G GLU* 3.8 23.2 - - + +
95G LYS* 4.0 20.2 - - - +
98G SER* 2.8 32.6 + - - +
102G TYR* 5.1 0.5 + - - -
127G GLN* 3.0 18.4 + - - +
128G VAL 4.1 3.6 - - - +
130G GLU* 1.3 76.1 - - - +
132G ALA* 1.3 51.6 + - - +
134G VAL* 3.2 2.5 + - - -
135G LYS* 2.8 37.8 + - - +
1I MET 5.7 2.4 + - - -
63I ASP 5.4 2.2 - - - +
64I ARG* 3.2 30.5 + - - +
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Residues in contact with ALA 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G VAL 3.3 14.0 + - - +
129G GLU* 3.9 4.0 - - - +
131G GLU* 1.3 79.7 - - - +
133G SER* 1.3 57.3 + - - +
135G LYS* 3.9 6.2 - - - +
136G LYS* 3.0 30.5 + - - +
62I TYR 5.3 0.9 - - - +
63I ASP* 3.5 46.1 + - + +
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Residues in contact with SER 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G TRP* 3.9 16.0 + - - -
46G GLN* 5.2 3.7 + - - -
129G GLU 2.8 19.6 + - - -
130G GLU* 3.6 7.9 - - - -
131G GLU 3.2 0.2 - - - -
132G ALA* 1.3 79.1 - - - +
134G VAL* 1.3 61.5 + - - +
136G LYS* 3.9 7.9 - - - +
137G ILE* 3.4 26.7 + - - +
161G ARG* 5.1 2.4 + - - -
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Residues in contact with VAL 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G TYR* 4.9 6.7 - - + +
42G TRP* 4.1 19.5 - - + -
46G GLN* 5.7 2.2 - - - +
87G PHE* 3.8 25.5 - - + +
90G ALA* 4.1 6.7 - - + -
91G TYR* 3.9 34.5 - - + +
94G GLU* 4.2 16.6 - - + -
130G GLU* 3.1 21.0 + - - +
131G GLU 3.9 2.7 - - - +
133G SER* 1.3 75.5 - - - +
135G LYS* 1.3 60.1 + - - +
136G LYS 3.3 0.2 - - - -
137G ILE* 3.3 4.7 + - - +
138G LEU* 2.9 26.0 + - - +
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Residues in contact with LYS 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G TYR* 3.6 42.1 - - + +
131G GLU 2.8 17.7 + - - +
132G ALA* 3.9 8.5 - - - +
134G VAL* 1.3 73.7 - - - +
136G LYS* 1.3 63.7 + - - +
138G LEU* 3.6 12.4 - - + +
139G ASP* 2.8 65.2 + - - +
142G LYS* 5.4 5.0 - - - +
1I MET* 5.4 0.7 - - - -
65I ASN* 3.5 40.5 + - + +
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Residues in contact with LYS 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350 GLY 6.1 0.9 - - - +
370 GLU* 3.2 42.5 + - - +
132G ALA 3.0 19.9 + - - +
133G SER* 3.9 9.6 - - - +
135G LYS* 1.3 77.4 - - - +
137G ILE* 1.3 65.1 + - + +
139G ASP* 3.6 7.9 + - - +
140G LYS* 3.4 51.0 + - - +
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Residues in contact with ILE 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G PHE* 4.5 1.1 - - + -
42G TRP* 3.5 34.8 - - + +
87G PHE* 3.7 34.3 - - + -
133G SER* 3.4 18.8 + - - +
134G VAL 3.3 3.2 + - - +
136G LYS* 1.3 79.7 - - + +
138G LEU* 1.3 66.5 + - - +
140G LYS* 3.3 11.1 + - + +
141G LEU* 3.2 25.9 + - + +
154G LEU* 4.3 11.9 - - + -
158G LEU* 3.8 31.9 - - + -
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LEU* 4.0 3.5 - - + +
87G PHE* 3.4 34.2 - - + +
88G GLU* 3.8 22.2 - - + -
91G TYR* 3.6 27.8 - - + -
134G VAL 2.9 16.3 + - - +
135G LYS* 3.6 13.0 - - + +
137G ILE* 1.3 76.8 - - - +
139G ASP* 1.3 66.5 + - - +
141G LEU* 3.0 22.2 + - - +
142G LYS* 3.1 42.3 + - + +
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Residues in contact with ASP 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350 GLY* 5.9 7.9 - - - -
135G LYS* 2.8 55.2 + - - +
136G LYS* 3.8 8.4 - - - +
137G ILE 3.3 0.2 - - - -
138G LEU* 1.3 81.7 - - - +
140G LYS* 1.3 57.5 - - + +
142G LYS* 3.3 16.2 + - - +
143G PHE* 2.9 26.9 + - - +
65I ASN* 4.9 1.9 - - - +
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Residues in contact with LYS 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350 GLY 4.9 13.0 - - - +
1520 PHE* 4.5 21.3 - - + -
1550 ASP* 5.8 3.4 + - - -
136G LYS* 3.4 42.4 + - - +
137G ILE* 3.3 13.4 + - + +
138G LEU 3.2 0.6 - - - -
139G ASP* 1.3 78.1 - - + +
141G LEU* 1.3 56.7 + - - +
143G PHE* 3.4 15.0 - - + +
144G ALA* 3.2 24.4 + - - +
150G ILE* 5.0 2.0 - - + +
154G LEU* 3.8 31.9 - - + +
157G GLU* 3.6 20.6 + - - -
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Residues in contact with LEU 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G PHE* 4.2 13.7 - - + -
83G PRO* 3.4 32.1 - - + +
84G LEU* 3.8 26.6 - - + +
87G PHE* 3.6 30.7 - - + -
137G ILE* 3.2 18.5 + - + +
138G LEU* 3.0 8.1 + - - +
140G LYS* 1.3 76.9 - - - +
142G LYS* 1.3 62.5 + - - +
143G PHE 3.2 0.2 - - - -
144G ALA* 3.3 25.1 - - + +
145G LYS* 3.8 2.6 + - - -
151G LEU* 3.8 28.7 - - + -
154G LEU* 4.3 8.5 - - + -
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Residues in contact with LYS 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G LEU* 3.7 19.3 - - + -
88G GLU* 4.6 10.3 - - - -
135G LYS* 5.4 4.0 - - - +
138G LEU* 3.1 32.2 + - + +
139G ASP* 3.5 19.5 + - - +
141G LEU* 1.3 74.8 - - - +
143G PHE* 1.3 60.4 + - - +
144G ALA 3.1 2.5 + - - -
145G LYS* 3.4 34.5 - - - +
----------------------------------------------------------
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Residues in contact with PHE 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340 LEU* 5.2 11.9 - - + -
360 LEU* 4.8 11.7 - - + -
1480 PRO* 3.9 38.0 - - + +
1510 LEU* 4.0 28.0 - - + -
1520 PHE* 4.6 22.0 - + + -
139G ASP 2.9 18.4 + - - +
140G LYS* 3.4 17.7 - - + +
141G LEU 3.2 0.4 - - - -
142G LYS* 1.3 75.1 - - - +
144G ALA* 1.3 56.8 + - - +
145G LYS 3.8 0.8 + - - -
150G ILE* 4.3 12.8 - - + +
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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