Contacts of the helix formed by residues 83 - 106 (chain A) in PDB entry 5LN3
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 MET 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 5.6 5.6 - - + +
32A ILE* 3.9 5.5 + - - +
34A GLN* 3.7 25.6 - - - +
82A GLY* 1.4 68.8 - - - -
84A THR* 1.4 57.9 + - - +
85A ALA* 4.3 5.8 - - + +
86A ASP* 3.1 30.5 + - + +
87A SER* 2.9 27.2 + - - -
132A ARG* 5.3 9.0 - - - +
135A GLY* 3.6 7.7 + - - +
19G GLY* 4.5 5.6 - - - -
20G ARG* 3.6 61.0 - - + +
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 5.4 0.6 + - - -
82A GLY 3.6 3.5 + - - -
83A MET* 1.4 70.3 - - - +
85A ALA* 1.3 63.2 + - - +
87A SER* 3.8 7.1 - - - -
88A ARG* 3.1 58.6 + - + +
157G VAL* 4.1 18.1 - - + +
159G TYR* 3.8 24.5 + - + +
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 3.3 5.8 - - + +
84A THR* 1.3 78.7 - - - +
86A ASP* 1.4 67.9 + - - +
88A ARG* 5.2 0.2 - - - +
89A SER* 3.2 19.4 + - - -
121G HIS* 3.3 38.9 + - + -
124G THR* 6.1 1.3 - - + +
155G SER 4.7 3.8 - - - +
156G GLY* 3.3 26.0 + - - +
157G VAL* 5.1 0.2 - - - +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A MET* 3.1 34.9 + - - +
85A ALA* 1.4 82.2 - - - +
87A SER* 1.4 62.8 + - - +
89A SER* 2.8 20.9 + - - -
90A GLN* 3.3 12.5 + - - +
132A ARG* 3.5 18.4 + - - -
134A LEU* 3.9 12.7 - - + +
135A GLY* 3.2 39.8 + - - +
136A CYS* 4.9 2.4 - - + +
121G HIS* 6.0 1.4 - - - +
125G LEU* 4.2 8.7 - - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 5.7 4.3 - - - -
80A MET* 3.5 34.3 - - - +
82A GLY* 3.6 17.8 + - - -
83A MET 2.9 16.4 + - - -
84A THR* 3.8 7.9 - - - -
85A ALA 3.4 0.2 - - - -
86A ASP* 1.4 71.8 - - - +
88A ARG* 1.4 66.4 + - - +
90A GLN* 4.8 0.2 - - - -
91A VAL* 3.3 26.2 + - - +
136A CYS* 3.7 13.7 - - - -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 4.7 19.7 - - + -
84A THR* 3.1 42.9 + - + +
85A ALA 4.0 3.1 - - - +
87A SER* 1.4 76.9 - - - +
89A SER* 1.4 64.8 + - - +
91A VAL* 3.3 15.3 + - - +
92A GLN* 3.5 17.2 + - + +
114G ASP* 5.8 3.8 - - - -
117G ALA* 4.1 11.8 - - - +
118G MET* 5.0 0.7 - - - -
121G HIS* 3.7 25.7 + - + -
156G GLY 3.7 1.0 + - - -
157G VAL* 3.4 16.4 - - - +
158G SER* 3.2 54.6 + - - +
159G TYR* 5.1 1.2 - - - -
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Residues in contact with SER 89 (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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85A ALA 3.2 13.2 + - - -
86A ASP* 2.8 21.5 + - - -
88A ARG* 1.4 78.3 - - - +
90A GLN* 1.3 63.8 + - - +
91A VAL 3.4 0.2 + - - -
92A GLN* 3.4 5.4 + - - +
93A ARG* 3.1 30.8 + - - +
134A LEU* 3.3 17.3 - - - +
118G MET* 3.7 23.0 - - - +
121G HIS* 4.0 14.0 + - - +
125G LEU* 5.5 3.8 - - - +
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Residues in contact with GLN 90 (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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80A MET* 3.1 25.1 - - + +
86A ASP 3.3 12.1 + - - +
87A SER* 3.9 4.3 - - - +
89A SER* 1.3 79.9 + - - +
91A VAL* 1.4 58.3 + - - +
93A ARG* 3.2 9.7 + - - +
94A ALA* 2.9 39.5 + - - +
118A ILE* 3.9 25.2 - - + +
121A ILE* 6.3 2.7 - - + -
134A LEU* 4.1 17.7 - - + -
136A CYS* 5.7 6.1 - - + -
138A MET* 3.5 36.6 - - + +
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Residues in contact with VAL 91 (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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70A PHE* 4.3 37.2 - - + -
72A ILE* 5.5 8.5 - - + -
78A CYS* 5.8 3.1 - - + -
80A MET* 3.8 17.5 - - + -
87A SER 3.3 16.6 + - - +
88A ARG* 3.3 9.4 + - - +
89A SER 3.2 0.6 - - - -
90A GLN* 1.4 81.7 - - - +
92A GLN* 1.3 60.0 + - + +
94A ALA* 3.1 4.8 + - - +
95A ARG* 2.8 54.1 + - + +
138A MET* 5.9 0.4 - - + -
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Residues in contact with GLN 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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991 PHE* 4.4 18.1 - - + -
1031 GLU* 4.5 16.2 - - - +
88A ARG* 3.5 13.0 + - + +
89A SER 3.4 8.3 + - - +
91A VAL* 1.3 81.1 - - + +
93A ARG* 1.3 62.3 + - - +
95A ARG* 3.4 14.2 + - - +
96A TYR* 3.3 24.7 + - - +
111G HIS* 5.8 2.8 + - - -
114G ASP* 4.4 21.0 + - - +
115G ARG* 5.8 5.1 - - - +
118G MET* 3.8 37.2 - - + +
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Residues in contact with ARG 93 (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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89A SER* 3.1 17.7 + - - +
90A GLN* 3.2 13.0 + - - +
92A GLN* 1.3 76.8 - - - +
94A ALA* 1.4 62.0 + - - +
96A TYR* 3.3 9.3 + - - +
97A GLU* 3.2 21.1 + - - +
118A ILE* 5.6 2.7 - - + -
121A ILE* 4.7 20.0 - - + -
125A TYR* 3.2 26.5 + - - -
131A MET* 4.6 8.9 - - - +
134A LEU* 4.5 19.2 - - - +
118G MET* 4.8 15.3 - - + +
122G ALA* 5.8 6.5 - - - +
125G LEU* 4.8 9.8 - - - +
126G TYR* 5.3 6.5 + - - -
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Residues in contact with ALA 94 (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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72A ILE* 4.0 21.7 - - + +
90A GLN* 2.9 31.6 + - - +
91A VAL* 3.1 8.7 + - - +
93A ARG* 1.4 59.2 - - - +
95A ARG* 1.3 57.9 - - - +
97A GLU* 3.2 6.5 + - - +
98A ALA* 3.0 31.5 + - - +
114A LEU* 4.3 11.8 - - + +
118A ILE* 4.4 7.8 - - + +
138A MET* 5.0 1.1 - - + -
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Residues in contact with ARG 95 (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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991 PHE* 3.8 16.9 - - + -
1021 ILE* 3.7 41.8 + - + +
1031 GLU* 3.9 28.5 - - - +
70A PHE* 4.9 10.6 - - - -
71A LYS* 2.8 29.1 + - - +
72A ILE* 3.8 22.1 + - + +
91A VAL* 2.8 37.5 + - + +
92A GLN* 3.7 16.8 + - - +
93A ARG 3.3 0.2 - - - -
94A ALA* 1.3 74.8 - - - +
96A TYR* 1.4 62.1 - - - +
98A ALA* 3.7 5.4 + - - +
99A ALA* 3.4 22.5 + - - +
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Residues in contact with TYR 96 (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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951 TYR* 3.5 31.6 - + - -
991 PHE* 3.6 45.8 - + + -
92A GLN 3.3 8.9 + - - +
93A ARG* 3.3 10.6 + - - +
94A ALA 3.2 0.4 - - - -
95A ARG* 1.4 79.7 - - - +
97A GLU* 1.4 62.0 + - - +
99A ALA* 3.4 4.2 + - - +
100A ASN* 3.2 24.0 + - - +
115G ARG* 5.8 3.8 + - - -
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Residues in contact with GLU 97 (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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93A ARG 3.2 10.8 + - - +
94A ALA* 3.2 9.4 + - - +
96A TYR* 1.4 75.2 - - - +
98A ALA* 1.3 58.5 + - - +
100A ASN* 3.5 9.3 + - + +
101A TRP* 2.9 32.9 + - - +
114A LEU* 3.4 22.8 - - + +
117A ARG* 3.1 48.3 + - + +
118A ILE* 5.3 8.8 - - + +
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Residues in contact with ALA 98 (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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72A ILE* 5.3 8.7 - - + +
73A THR* 5.9 7.6 - - + -
76A ILE* 6.1 2.2 - - + -
94A ALA 3.0 16.8 + - - +
95A ARG* 3.9 5.8 - - - +
97A GLU* 1.3 75.4 + - - +
99A ALA* 1.3 66.1 + - - +
101A TRP* 3.0 4.7 + - - -
102A LYS* 3.0 18.4 + - - +
109A ILE* 3.4 26.2 - - + +
114A LEU* 4.1 19.3 - - + -
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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
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951 TYR* 3.8 21.4 - - + +
981 GLY 5.9 1.1 - - - -
991 PHE* 4.6 18.4 - - + +
1021 ILE* 5.9 2.5 - - + -
95A ARG 3.4 15.7 + - - +
96A TYR* 3.4 7.8 + - - +
98A ALA* 1.3 79.0 - - - +
100A ASN* 1.4 57.3 + - - +
102A LYS* 3.3 10.3 + - - +
103A TYR* 3.0 26.7 + - - +
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Residues in contact with ASN 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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951 TYR* 3.7 21.3 + - - +
96A TYR* 3.5 14.1 - - + +
97A GLU* 3.6 11.1 - - + +
99A ALA* 1.4 78.3 - - - +
101A TRP* 1.4 62.1 + - - +
103A TYR* 3.1 21.3 + - - +
104A LYS* 3.0 34.7 + - - +
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Residues in contact with TRP 101 (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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1092 HIS* 3.1 33.9 - + - -
1132 THR* 4.3 5.2 - - + -
97A GLU* 2.9 23.0 + - - +
98A ALA* 3.0 8.6 + - - +
100A ASN* 1.4 75.9 - - - +
102A LYS* 1.3 55.1 + - - +
104A LYS* 4.6 0.9 - - - -
105A TYR* 3.0 62.8 + + + +
107A TYR* 3.7 18.6 - + - -
108A GLU 3.5 18.4 - - - -
109A ILE* 3.8 28.0 - - + -
110A PRO* 4.0 11.7 - - + -
113A MET* 3.6 27.3 - - + +
117A ARG* 3.5 43.1 - - - +
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Residues in contact with LYS 102 (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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98A ALA 3.0 11.2 + - - +
99A ALA* 3.3 12.3 + - - +
101A TRP* 1.3 74.0 - - - +
103A TYR* 1.3 63.6 + - - +
106A GLY* 3.1 42.3 + - - +
107A TYR* 3.4 19.4 - - - +
108A GLU* 3.4 30.3 + - - +
109A ILE* 4.3 9.1 - - + +
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Residues in contact with TYR 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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911 ASP* 3.6 34.3 + - + -
921 ALA* 4.7 8.6 - - - +
951 TYR* 4.0 32.3 - + + -
1242 ARG* 3.0 47.7 + - - -
1282 GLN* 3.8 17.6 + - - -
99A ALA 3.0 13.2 + - - +
100A ASN* 3.1 24.9 + - - +
102A LYS* 1.3 76.5 - - - +
104A LYS* 1.3 67.0 + - + +
106A GLY* 3.7 2.1 + - - -
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Residues in contact with LYS 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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1212 THR* 4.9 1.4 - - - +
1242 ARG* 3.1 32.6 + - - +
1252 MET* 4.3 33.8 - - + +
100A ASN* 3.0 25.5 + - - +
101A TRP* 3.9 2.9 - - - +
103A TYR* 1.3 83.9 - - + +
105A TYR* 1.4 87.7 + - + +
117A ARG* 5.7 2.8 - - - +
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Residues in contact with TYR 105 (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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1052 ASN 6.0 0.2 - - - -
1082 LEU* 5.7 5.0 - - - +
1092 HIS* 3.2 53.9 + + + +
1202 VAL* 4.9 0.9 - - - +
1212 THR* 3.2 46.2 + - + +
1242 ARG* 5.1 1.1 - - - -
1252 MET* 3.8 19.5 - - + +
101A TRP* 3.0 62.8 + + + +
104A LYS* 1.4 109.4 + - + +
106A GLY* 1.4 55.3 + - - +
107A TYR* 3.1 9.9 + - + +
117A ARG* 3.9 14.8 + - - -
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Residues in contact with GLY 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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1202 VAL* 5.5 8.4 - - - +
1242 ARG* 4.8 7.6 - - - -
102A LYS* 3.1 34.8 + - - -
103A TYR 4.2 5.4 - - - -
104A LYS 3.4 2.0 - - - -
105A TYR* 1.4 74.4 - - - +
107A TYR* 1.3 58.0 + - - +
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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