Contacts of the helix formed by residues 91 - 123 (chain A) in PDB entry 1JQO
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 ALA 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLY 3.6 2.3 + - - -
90A LEU* 1.3 75.0 - - - +
92A PRO* 1.3 77.9 - - + +
93A ALA* 3.3 3.1 - - + +
94A ASP* 2.8 33.3 + - - +
95A ALA* 2.9 9.7 + - - -
922A GLN 4.6 13.2 + - - +
924A PRO* 4.9 12.8 - - + -
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Residues in contact with PRO 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 4.0 1.0 - - - +
91A ALA* 1.3 87.7 - - + +
93A ALA* 1.3 61.0 + - - +
95A ALA* 3.3 6.6 + - + +
96A ILE* 2.9 32.3 + - - +
939A VAL* 4.1 15.3 - - + -
949A PRO* 3.8 23.3 - - + -
950A GLY* 4.0 18.8 - - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ALA* 3.0 3.9 + - + +
92A PRO* 1.3 78.8 - - - +
94A ASP* 1.3 66.6 + - - +
96A ILE* 3.3 3.7 + - - +
97A LEU* 2.9 29.8 + - + +
926A SER* 5.9 2.7 - - - -
928A GLU 5.8 6.3 - - - -
936A ALA* 4.2 24.7 - - + -
938A LEU* 3.7 12.4 - - + +
939A VAL* 4.1 8.9 - - + +
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.8 1.6 - - + +
90A LEU* 4.0 18.8 - - + -
91A ALA* 2.8 22.4 + - - +
93A ALA* 1.3 75.1 - - - +
95A ALA* 1.3 53.7 + - - +
97A LEU* 3.0 7.6 + - - +
98A VAL* 2.5 44.8 + - + +
923A PRO 3.9 0.2 - - - +
924A PRO* 3.3 11.4 - - - +
925A LEU* 2.9 38.9 + - + +
926A SER* 3.1 30.0 + - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU 5.7 0.2 - - - +
90A LEU* 4.0 22.3 - - + +
91A ALA 2.9 12.7 + - - +
92A PRO* 3.4 11.0 - - + +
94A ASP* 1.3 77.5 - - - +
96A ILE* 1.3 57.2 + - - +
99A ALA* 2.9 32.4 + - - +
904A PHE* 3.8 18.4 - - + -
950A GLY* 5.7 1.1 - - - -
951A LEU* 6.5 0.7 - - + -
954A THR* 4.0 15.0 - - + +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PRO 2.9 19.4 + - - +
93A ALA* 3.6 7.2 - - - +
95A ALA* 1.3 75.3 - - - +
97A LEU* 1.3 57.9 + - + +
99A ALA* 4.6 0.2 - - - -
100A SER* 3.0 30.8 + - - -
230A ILE* 5.8 0.2 - - + -
938A LEU* 3.8 31.0 - - + +
939A VAL* 5.0 7.6 - - + -
950A GLY* 3.4 26.2 - - - +
953A ASP* 3.3 35.2 - - + +
954A THR* 3.4 8.3 - - - +
957A LEU* 3.8 19.0 - - + +
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A HIS* 3.5 28.5 - - + +
57A LEU* 3.6 18.6 - - + -
93A ALA* 2.9 17.7 + - + +
94A ASP* 3.3 9.9 - - - +
96A ILE* 1.3 74.3 - - - +
98A VAL* 1.3 55.4 + - - +
100A SER* 3.1 7.1 + - - -
101A SER* 2.6 41.4 + - - +
225A PHE* 4.4 14.6 - - + -
926A SER* 3.4 36.8 - - - +
938A LEU* 4.0 19.3 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.0 17.0 - - + +
60A PHE* 3.8 30.3 - - + -
61A VAL* 4.9 9.0 - - + -
64A CYS* 4.9 3.8 - - - -
87A LEU* 4.5 5.8 - - + -
90A LEU* 3.4 25.6 - - + -
94A ASP 2.5 24.6 + - - +
95A ALA 3.8 3.1 - - - +
97A LEU* 1.3 72.5 - - - +
99A ALA* 1.3 67.0 + - - +
101A SER* 3.2 13.8 + - - -
102A ILE* 3.2 26.4 + - + +
904A PHE* 4.4 9.2 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ALA 2.9 18.6 + - - +
96A ILE 3.9 3.4 - - - +
98A VAL* 1.3 78.7 - - - +
100A SER* 1.3 62.3 + - - +
102A ILE* 3.2 4.2 + - - +
103A LEU* 3.2 19.2 + - - +
901A LEU* 4.4 9.1 - - + +
904A PHE* 3.8 21.0 - - + -
954A THR* 4.2 10.3 - - + +
957A LEU* 3.8 26.5 - - + +
958A THR* 5.0 3.6 - - + +
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.0 19.2 + - - -
97A LEU* 3.4 8.3 - - - -
99A ALA* 1.3 79.7 - - - +
101A SER* 1.3 58.2 + - - +
103A LEU* 3.1 9.2 + - - +
104A HIS* 3.0 47.2 + - - -
225A PHE* 4.0 10.6 + - - -
229A GLU* 3.5 14.5 + - - -
957A LEU* 4.2 14.5 - - - +
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Residues in contact with SER 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PHE* 3.7 24.2 - - - -
49A LEU* 3.8 17.6 - - - +
57A LEU* 5.2 1.2 - - - +
61A VAL* 4.1 22.8 - - - +
97A LEU* 2.6 30.0 + - - +
98A VAL* 3.3 9.9 - - - -
100A SER* 1.3 72.7 - - - +
102A ILE* 1.3 61.3 + - - +
104A HIS 3.4 0.9 + - - -
105A MET* 3.0 29.6 + - - +
225A PHE* 4.3 4.4 - - - -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 4.6 15.0 - - + -
64A CYS* 5.1 5.4 - - + -
98A VAL* 3.2 23.4 + - + +
99A ALA* 3.8 1.6 - - - +
101A SER* 1.3 73.2 - - - +
103A LEU* 1.3 60.2 + - - +
105A MET* 3.4 8.1 + - - +
106A LEU* 2.9 30.7 + - + +
897A TYR* 3.7 32.1 - - + +
900A THR* 3.6 34.1 - - + +
901A LEU* 3.6 39.9 - - + -
904A PHE* 5.9 1.1 - - + -
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ALA 3.2 10.7 + - - +
100A SER* 3.1 13.4 + - - +
102A ILE* 1.3 78.0 - - - +
104A HIS* 1.3 64.3 + - + +
106A LEU* 3.3 3.5 + - - +
107A ASN* 3.0 29.5 + - + +
186A LEU* 5.3 8.7 - - + -
229A GLU* 4.1 35.7 - - + -
901A LEU* 4.8 1.9 - - + +
957A LEU* 4.6 13.2 - - + +
960A LYS* 4.1 19.5 - - + +
961A GLY* 3.6 35.9 - - - +
964A ALA* 4.4 7.9 - - + -
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Residues in contact with HIS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.8 21.1 - + + -
100A SER* 3.0 36.3 + - - +
101A SER 3.9 0.7 - - - +
103A LEU* 1.3 79.1 - - + +
105A MET* 1.3 65.6 + - - +
107A ASN* 3.2 8.1 + - - +
108A LEU* 2.9 29.9 + - + +
186A LEU* 4.5 21.8 - - + +
221A ILE 5.7 0.2 + - - -
224A ALA* 3.5 30.8 + - - +
225A PHE* 3.6 19.8 - + - -
229A GLU* 2.7 36.3 + - + +
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Residues in contact with MET 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.4 31.9 - - + +
45A PHE* 3.5 30.1 - - + -
46A LEU* 4.0 18.6 - - + -
61A VAL* 3.9 23.8 - - + +
62A GLN* 5.9 1.1 - - - +
101A SER 3.0 19.4 + - - +
102A ILE* 3.7 5.6 - - - +
104A HIS* 1.3 75.0 - - - +
106A LEU* 1.3 63.4 + - - +
108A LEU* 3.3 12.2 - - + +
109A ALA* 3.0 20.7 + - - +
897A TYR* 2.9 49.5 - - + +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 2.9 16.6 + - + +
103A LEU* 3.4 4.7 - - - +
105A MET* 1.3 74.2 - - - +
107A ASN* 1.3 67.4 + - - +
109A ALA* 2.9 22.8 + - + +
110A ASN* 3.1 11.1 + - - -
894A ARG* 4.5 16.1 + - + +
897A TYR* 3.3 41.7 - - + -
898A ILE* 4.2 14.4 - - + +
901A LEU* 4.4 11.4 - - + -
961A GLY* 3.4 28.3 - - - +
964A ALA* 4.7 2.9 - - + -
965A GLY* 3.7 23.6 - - - +
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Residues in contact with ASN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 3.0 18.6 + - + +
104A HIS* 3.4 14.3 + - - +
106A LEU* 1.3 74.4 - - - +
108A LEU* 1.3 68.4 + - - +
110A ASN* 3.0 27.5 + - - +
111A LEU* 3.0 19.6 + - - +
186A LEU* 3.7 21.5 - - + +
190A ASN* 3.0 42.6 - - - +
193A ILE* 5.7 1.0 - - - +
964A ALA* 4.9 4.8 - - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.6 54.0 - - + +
42A VAL* 4.6 4.7 - - + +
45A PHE* 3.8 24.0 - - + -
104A HIS* 2.9 19.7 + - + +
105A MET* 3.3 15.3 - - - +
107A ASN* 1.3 78.7 - - - +
109A ALA* 1.3 63.9 + - - +
111A LEU* 2.9 22.0 + - + +
112A ALA* 2.8 24.0 + - - +
193A ILE* 4.7 6.7 - - + -
221A ILE* 4.3 20.9 - - + -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 4.2 13.3 - - - +
42A VAL* 5.6 4.4 - - + +
105A MET 3.0 11.6 + - - +
106A LEU* 2.9 17.6 + - + +
108A LEU* 1.3 74.2 - - - +
110A ASN* 1.3 64.5 + - - +
112A ALA* 2.9 7.6 + - - +
113A GLU* 2.9 22.6 + - - +
893A LEU* 4.1 24.9 - - + -
894A ARG* 4.4 14.8 - - + +
897A TYR* 6.1 2.5 - - + -
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU 3.6 11.9 + - - -
107A ASN* 3.0 17.5 + - - +
109A ALA* 1.3 76.8 - - - +
111A LEU* 1.3 64.0 + - + +
113A GLU* 3.3 3.9 + - - +
114A GLU* 3.1 35.6 + - - +
894A ARG* 2.9 37.6 + - - +
964A ALA* 3.1 30.6 + - - +
965A GLY* 4.8 0.2 - - - -
967A GLN* 3.5 16.5 + - + +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.4 7.0 - - + -
107A ASN* 3.0 22.5 + - - +
108A LEU* 2.9 21.1 + - + +
110A ASN* 1.3 77.2 - - + +
112A ALA* 1.3 62.1 + - - +
114A GLU* 3.3 11.9 + - - +
115A VAL* 3.2 27.5 + - + +
190A ASN* 3.7 37.7 - - + +
193A ILE* 4.2 29.2 - - + -
194A ARG* 3.6 41.3 - - + +
197A LEU* 5.3 1.6 - - + -
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Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.8 28.1 - - + -
38A ASP* 3.9 23.8 - - - +
41A LEU* 3.8 13.8 - - + +
108A LEU 2.8 13.8 + - - +
109A ALA* 3.3 8.7 - - - +
111A LEU* 1.3 72.7 - - - +
113A GLU* 1.3 64.3 + - - +
115A VAL* 3.3 7.8 + - - +
116A GLN* 2.9 27.1 + - - +
197A LEU* 4.7 0.2 - - - -
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Residues in contact with GLU 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 5.3 1.1 + - - +
109A ALA 2.9 11.4 + - - +
110A ASN* 3.4 11.1 - - - +
112A ALA* 1.3 77.7 - - - +
114A GLU* 1.3 65.1 + - + +
116A GLN* 3.1 11.5 + - - +
117A ILE* 2.8 40.7 + - + +
886A PHE* 4.1 22.6 - - + +
890A GLY* 4.5 8.5 - - - -
894A ARG* 3.1 32.1 + - - +
967A GLN* 3.3 12.3 - - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN* 3.1 29.4 + - - +
111A LEU* 3.3 10.8 + - - +
113A GLU* 1.3 81.1 - - + +
115A VAL* 1.3 64.4 + - + +
117A ILE* 3.1 7.1 + - - +
118A ALA* 2.9 24.2 + - - +
194A ARG* 3.1 40.7 + - - -
679A PHE* 6.2 0.3 - - - -
685A HIS* 5.0 7.5 - - + -
686A LEU* 4.3 26.8 - - + +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.6 22.9 - - + -
111A LEU 3.2 17.2 + - - +
112A ALA 3.6 5.4 - - - +
114A GLU* 1.3 76.3 - - + +
116A GLN* 1.3 64.6 + - - +
118A ALA* 3.1 6.9 + - - +
119A HIS* 3.0 53.9 + - + +
194A ARG* 4.5 19.1 - - + +
197A LEU* 4.3 24.9 - - + -
198A THR* 4.3 10.3 - - - +
201A ASN* 4.7 0.4 - - - +
685A HIS* 5.8 1.6 - - - -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 2.3 40.1 + - - +
36A GLU* 3.9 3.3 + - - +
37A TYR* 3.8 30.0 - - + +
38A ASP* 3.7 10.5 + - - -
112A ALA 2.9 16.9 + - - +
113A GLU* 3.5 7.6 - - - +
115A VAL* 1.3 76.4 - - - +
117A ILE* 1.3 62.6 + - - +
119A HIS* 3.6 1.5 + - + +
120A ARG* 2.9 70.6 + - + +
886A PHE* 4.5 10.8 - - + -
889A GLN* 5.1 0.2 - - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLU* 2.8 29.0 + - + +
114A GLU* 3.4 9.9 - - - +
116A GLN* 1.3 77.0 - - - +
118A ALA* 1.3 64.6 + - - +
120A ARG* 4.7 6.1 - - - +
121A ARG* 3.2 64.5 + - - +
886A PHE* 3.3 34.8 - - + -
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU 2.9 12.7 + - - +
115A VAL* 3.5 9.4 - - - +
117A ILE* 1.3 80.4 - - - +
119A HIS* 1.3 69.6 + - + +
121A ARG* 4.7 0.8 - - - +
122A ARG* 3.3 21.8 + - - +
685A HIS* 4.1 33.0 - - + +
----------------------------------------------------------
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A TYR* 3.8 16.6 + - - +
115A VAL* 3.0 51.5 + - + +
116A GLN* 4.0 3.4 - - + +
118A ALA* 1.3 78.9 - - + +
120A ARG* 1.3 68.9 + - + +
122A ARG* 3.9 2.6 - - - +
123A ASN* 3.0 38.7 + - - +
198A THR* 4.4 24.4 + - + +
201A ASN* 3.6 27.9 + - + +
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.1 6.1 - - - +
116A GLN* 2.9 59.5 + - + +
117A ILE* 3.8 6.7 - - - +
119A HIS* 1.3 82.8 - - + +
121A ARG* 1.3 63.9 + - + +
123A ASN* 2.8 29.1 + - - +
886A PHE* 3.0 51.5 - - - +
889A GLN* 4.3 7.0 + - - +
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.2 50.4 + - - +
118A ALA* 4.7 1.6 - - - +
120A ARG* 1.3 82.0 - - + +
122A ARG* 1.3 60.0 + - - +
123A ASN 4.7 1.1 - - - -
693A ARG* 4.9 12.1 - - - +
886A PHE* 5.4 4.6 - - - -
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA 3.3 17.1 + - - +
119A HIS* 3.3 4.1 + - - +
120A ARG 2.9 2.8 + - - -
121A ARG* 1.3 74.9 - - - +
123A ASN* 1.3 66.5 + - - +
262A ARG* 4.3 7.3 - - - +
204B ASP 5.0 11.7 + - - +
205B ILE* 6.0 0.2 - - - -
206B THR* 4.1 17.4 - - + +
209B ASP* 2.9 37.7 + - - -
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Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 3.0 40.4 + - - +
120A ARG* 2.8 14.0 + - - +
121A ARG 4.7 1.3 - - - -
122A ARG* 1.3 82.8 - - - +
204B ASP* 6.1 1.4 - - - +
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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