Contacts of the helix formed by residues 97 - 123 (chain J) in PDB entry 5XVO
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 THR 97 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J ALA 3.9 9.4 - - - +
96J TRP* 1.3 74.1 - - - +
98J GLU* 1.3 65.2 + - - +
99J GLU* 3.8 6.9 + - - +
100J ARG* 3.0 29.0 + - - +
101J LYS* 3.1 21.8 + - - +
278J GLN* 3.5 19.0 + - - +
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Residues in contact with GLU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J TRP 3.9 1.2 + - - -
97J THR* 1.3 72.7 - - - +
99J GLU* 1.3 62.0 + - - +
101J LYS* 3.6 20.9 + - - +
102J GLY 3.1 17.0 + - - -
142J PHE* 3.6 29.0 - - + -
202J LEU 5.4 0.9 - - - +
203J LYS 5.7 0.7 - - - +
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Residues in contact with GLU 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J THR* 3.2 6.4 - - - +
98J GLU* 1.3 80.0 - - - +
100J ARG* 1.3 58.0 + - - +
102J GLY* 3.1 4.0 + - - -
103J GLN* 2.9 52.4 + - + +
141J LEU* 4.9 14.8 - - + +
142J PHE* 5.7 0.2 - - - -
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Residues in contact with ARG 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J TRP* 5.8 0.2 - - - -
97J THR* 3.0 25.6 + - - +
99J GLU* 1.3 76.5 - - - +
101J LYS* 1.3 63.4 + - - +
103J GLN* 3.3 22.2 + - - +
104J VAL* 3.0 31.8 + - - +
275J VAL* 3.0 31.7 + - - +
276J LEU* 3.7 28.0 - - + +
278J GLN* 3.4 34.1 + - - +
280J GLU 3.5 14.6 + - - -
281J GLU* 3.1 38.4 + - - -
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Residues in contact with LYS 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96J TRP* 4.0 33.7 + - + +
97J THR 3.1 23.0 + - - +
98J GLU* 3.8 22.5 + - - +
100J ARG* 1.3 77.1 - - - +
102J GLY* 1.3 52.1 + - - +
104J VAL* 3.7 0.7 - - - +
105J TRP* 2.8 37.8 + - - +
142J PHE* 3.9 4.0 - - + -
201J GLY 4.0 8.3 + - - -
202J LEU* 3.3 52.6 + - + +
205J ALA* 5.5 5.1 - - - +
276J LEU* 4.0 9.9 - - + -
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Residues in contact with GLY 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J GLU 3.1 7.7 + - - -
99J GLU* 3.1 7.2 + - - -
101J LYS* 1.3 73.2 - - - +
103J GLN* 1.3 64.0 + - - +
106J THR* 2.6 33.6 + - - -
141J LEU* 3.8 10.5 - - - -
142J PHE* 3.3 33.8 - - - -
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Residues in contact with GLN 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J GLU* 2.9 44.7 + - + +
100J ARG* 3.6 32.3 + - - +
102J GLY* 1.3 75.0 - - - +
104J VAL* 1.3 59.2 + - + +
106J THR* 3.9 1.4 - - - -
107J ALA* 2.9 31.3 + - - +
141J LEU* 3.8 17.2 - - + +
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Residues in contact with VAL 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100J ARG* 3.0 24.7 + - - +
101J LYS 3.9 2.0 - - - +
103J GLN* 1.3 80.6 - - + +
105J TRP* 1.3 62.9 + - - +
107J ALA* 3.3 2.1 + - - +
108J ILE* 3.0 47.4 + - + +
202J LEU* 4.0 9.6 - - + -
272J VAL* 4.0 19.1 - - + -
275J VAL* 3.4 30.7 - - + -
276J LEU* 3.9 17.0 - - + -
283J VAL* 4.0 15.0 - - + -
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Residues in contact with TRP 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J LYS 2.8 21.9 + - - +
102J GLY 4.0 1.6 - - - +
104J VAL* 1.3 73.2 - - - +
106J THR* 1.3 72.2 + - - +
108J ILE* 3.2 8.5 + - + +
109J ILE* 2.9 57.2 + - + +
142J PHE* 3.6 35.7 - + + -
143J ASP* 3.7 21.3 - - + -
148J GLU* 3.9 16.6 - - - -
202J LEU* 4.0 21.7 - - + +
203J LYS* 3.9 35.5 - - + +
216J ASP* 3.5 39.1 + - + +
219J GLU* 5.9 1.4 - - - +
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Residues in contact with THR 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102J GLY 2.6 23.7 + - - -
103J GLN* 3.9 2.0 - - - -
105J TRP* 1.3 84.0 - - + +
107J ALA* 1.3 64.1 + - - +
109J ILE* 3.4 3.7 + - + +
110J ALA* 3.0 23.7 + - - +
139J LEU* 3.8 29.8 - - + +
140J ARG 3.9 16.6 - - - +
141J LEU* 3.6 7.3 - - + -
142J PHE 3.1 22.2 + - - +
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Residues in contact with ALA 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J GLN 2.9 19.0 + - - +
104J VAL 3.5 6.1 - - - +
106J THR* 1.3 74.5 - - - +
108J ILE* 1.3 62.8 + - - +
110J ALA* 3.3 9.4 - - - +
111J GLN* 3.2 26.4 + - - +
283J VAL* 4.2 24.2 - - + -
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Residues in contact with ILE 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104J VAL* 3.0 36.2 + - + +
105J TRP* 3.4 10.5 - - + +
107J ALA* 1.3 75.9 - - - +
109J ILE* 1.3 66.9 + - + +
111J GLN* 2.9 21.5 + - - +
112J LYS* 3.1 8.7 + - - +
202J LEU* 4.8 5.4 - - + -
216J ASP* 3.6 22.2 - - + +
217J LEU* 4.1 26.5 - - + +
219J GLU* 4.1 5.4 - - + -
220J PRO* 3.7 22.0 - - + +
268J TYR* 3.9 14.1 - - - +
272J VAL* 4.3 8.3 - - + -
283J VAL* 4.5 10.1 - - + -
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Residues in contact with ILE 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J TRP* 2.9 67.5 + - + +
106J THR* 3.5 10.1 - - - +
108J ILE* 1.3 78.3 - - + +
110J ALA* 1.3 65.0 + - - +
112J LYS* 3.0 10.7 + - + +
113J ILE* 2.9 29.2 + - + +
139J LEU* 3.6 34.5 - - + -
143J ASP* 4.3 1.1 - - + -
148J GLU* 4.0 34.3 - - + +
219J GLU* 4.8 13.5 - - + +
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J THR* 3.0 13.4 + - + +
107J ALA* 3.3 14.1 - - - +
109J ILE* 1.3 78.5 - - - +
111J GLN* 1.3 57.3 + - + +
113J ILE* 3.2 2.9 + - - +
114J THR* 2.8 34.6 + - - -
136J ARG* 3.6 23.8 - - + +
139J LEU* 4.1 16.2 - - + -
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Residues in contact with GLN 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ALA* 3.4 14.5 + - - +
108J ILE* 2.9 9.4 + - - +
110J ALA* 1.3 76.2 - - + +
112J LYS* 1.3 58.8 + - - +
114J THR* 3.4 8.4 + - - -
115J ASN* 3.0 35.9 + - - -
220J PRO* 4.0 10.3 - - + +
268J TYR* 3.3 17.9 + - - -
283J VAL* 3.3 17.8 - - - +
284J PRO 2.8 22.9 + - - -
285J GLU* 3.5 22.1 - - + +
286J PHE 3.1 27.3 + - - +
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Residues in contact with LYS 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ILE 3.1 6.7 + - - +
109J ILE* 3.0 12.6 + - - +
111J GLN* 1.3 75.7 - - - +
113J ILE* 1.3 54.0 + - - +
115J ASN* 3.0 5.6 + - - +
116J GLN* 2.8 70.0 + - + +
148J GLU* 3.5 29.5 + - + +
152J ALA* 4.7 8.3 - - - +
219J GLU* 3.0 57.0 + - + +
220J PRO* 3.9 10.0 - - - +
222J ARG* 4.3 14.6 - - + +
223J PRO* 4.3 4.2 - - + +
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Residues in contact with ILE 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J ILE* 2.9 20.0 + - + +
110J ALA 3.7 6.1 - - - +
112J LYS* 1.3 80.1 - - + +
114J THR* 1.3 62.8 + - - +
116J GLN* 3.1 18.7 + - - +
117J SER* 2.9 21.8 + - - -
132J LEU* 3.6 35.9 - - + +
133J LEU* 4.9 0.7 - - - +
135J MET 5.2 0.2 - - - -
136J ARG* 4.0 17.9 - - + +
139J LEU* 4.3 22.7 - - + -
147J ARG* 4.6 2.9 - - + +
148J GLU* 4.1 27.1 - - + +
151J ALA* 4.3 16.4 - - + -
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Residues in contact with THR 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J ALA 2.8 25.0 + - - -
111J GLN* 3.5 12.7 - - - -
113J ILE* 1.3 74.8 - - - +
115J ASN* 1.3 58.8 - - - +
117J SER* 3.2 8.2 + - - -
118J LEU* 2.8 44.0 + - + +
133J LEU* 5.1 13.2 - - + +
136J ARG* 3.3 20.6 + - - +
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Residues in contact with ASN 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J GLN 3.0 19.2 + - - +
112J LYS 3.5 3.6 - - - +
114J THR* 1.3 76.6 - - - +
116J GLN* 1.3 65.9 + - - +
118J LEU* 3.9 8.5 - - - +
119J HIS* 3.0 20.8 + - - +
220J PRO* 3.0 24.0 + - - +
223J PRO* 3.7 17.6 - - + +
286J PHE* 3.0 25.3 + - - +
287J GLY* 3.2 20.2 - - - -
288J ILE* 3.3 29.8 + - + +
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Residues in contact with GLN 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J LYS* 2.8 54.7 + - + +
113J ILE* 3.4 22.1 - - - +
115J ASN* 1.3 72.7 - - - +
117J SER* 1.3 63.3 + - - +
119J HIS 3.3 1.9 + - - -
120J LEU* 3.0 17.5 + - - +
132J LEU* 3.7 6.5 - - + -
148J GLU 4.8 0.3 - - - +
151J ALA* 4.3 12.6 - - - +
152J ALA* 4.2 13.2 + - - +
155J TYR* 3.2 62.3 - - + -
156J PHE* 4.9 3.8 - - - -
222J ARG* 6.3 1.4 - - - +
223J PRO* 4.3 9.0 - - + -
226J ASP* 4.9 2.0 + - - -
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Residues in contact with SER 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J ILE 2.9 12.0 + - - -
114J THR 3.3 7.2 - - - -
116J GLN* 1.3 77.1 - - - +
118J LEU* 1.3 57.5 + - - +
120J LEU* 2.8 10.7 + - - +
121J ALA* 2.8 26.3 + - - +
129J ALA* 2.7 24.1 + - - +
132J LEU* 3.7 14.0 - - - +
133J LEU* 2.7 37.5 - - - +
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Residues in contact with LEU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLN* 5.1 1.4 + - - -
114J THR* 2.8 31.1 + - + +
115J ASN* 3.8 25.1 - - - +
117J SER* 1.3 72.7 + - - +
119J HIS* 1.3 57.7 + - - +
121J ALA* 3.4 11.3 + - + +
122J GLN* 2.9 28.3 + - - +
133J LEU* 6.5 0.2 - - + -
287J GLY* 5.1 2.5 - - - -
288J ILE* 4.1 27.6 - - + +
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Residues in contact with HIS 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115J ASN 3.0 17.9 + - - +
116J GLN 3.4 5.2 - - - +
117J SER 3.1 0.2 - - - -
118J LEU* 1.3 75.4 - - - +
120J LEU* 1.3 64.5 + - - +
122J GLN* 3.2 19.7 - - - +
123J ARG* 3.2 43.1 + - - +
155J TYR* 2.8 28.8 + - - +
159J LEU* 3.7 21.6 - - + +
223J PRO* 4.7 2.4 + - + -
226J ASP* 3.8 6.8 - - - +
227J GLN* 3.5 38.7 - - + -
230J TYR* 4.2 4.6 - - + +
288J ILE* 3.9 11.4 - - + +
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Residues in contact with LEU 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J GLN 3.0 11.0 + - - +
117J SER 2.8 6.8 + - - +
119J HIS* 1.3 73.7 - - - +
121J ALA* 1.3 65.9 + - - +
123J ARG* 2.9 14.6 + - - +
125J TYR* 3.1 27.8 + - + +
128J LYS* 4.1 17.9 - - + +
129J ALA* 4.1 8.5 - - + +
132J LEU* 3.7 39.0 - - + -
155J TYR* 3.8 16.6 - - + +
158J THR* 3.8 30.7 - - + +
159J LEU* 3.8 26.9 - - + -
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Residues in contact with ALA 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLN* 4.0 29.9 - - + +
117J SER 2.8 11.0 + - - +
118J LEU* 3.5 16.4 - - + +
120J LEU* 1.3 75.3 - - - +
122J GLN* 1.3 57.1 + - - +
124J ASP* 2.8 24.6 + - - +
125J TYR 4.5 6.1 - - - +
126J GLY* 4.8 4.6 + - - +
129J ALA* 3.8 14.8 - - + +
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Residues in contact with GLN 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E HIS* 5.1 4.3 + - - -
68F GLN* 4.2 15.6 - - - +
118J LEU 2.9 13.4 + - - +
119J HIS* 3.2 18.9 - - - +
121J ALA* 1.3 75.9 - - - +
123J ARG* 1.3 91.6 + - - +
124J ASP* 3.5 8.3 + - - +
227J GLN* 2.8 30.0 + - - +
231J GLU* 4.5 4.6 + - - -
288J ILE* 4.7 2.4 - - - +
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Residues in contact with ARG 123 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J HIS* 3.2 37.3 + - - +
120J LEU 2.9 8.7 + - - +
122J GLN* 1.3 101.4 + - - +
124J ASP* 1.3 70.2 + - - +
125J TYR* 3.3 28.3 + - + -
159J LEU* 4.2 11.7 - - + -
227J GLN* 3.5 10.9 + - - +
230J TYR* 3.2 35.2 - - + +
231J GLU* 3.1 39.8 + - - +
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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