Contacts of the helix formed by residues 92 - 116 (chain A) in PDB entry 3CUQ
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 GLY 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 4.4 17.4 + - - -
87A TRP 3.7 0.2 + - - -
88A SER 2.9 17.4 + - - -
89A GLU 5.1 0.9 - - - -
90A MET 3.5 1.4 - - - -
91A LEU* 1.3 77.8 - - - +
93A VAL* 1.3 63.7 + - - +
94A GLY 3.1 3.2 + - - -
95A ASP* 3.7 9.5 + - - +
96A PHE* 3.4 21.3 + - - +
279B MET* 5.5 3.3 - - - +
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 4.1 26.2 - - + -
65A ARG* 5.9 0.7 - - - -
68A PHE* 4.5 15.9 - - + -
69A GLN* 6.0 2.5 - - + +
79A PRO* 4.0 28.0 - - + +
80A LEU* 3.4 14.9 - - + +
87A TRP* 3.8 20.4 - - + +
88A SER* 4.0 0.9 + - - -
91A LEU* 3.3 9.6 - - + +
92A GLY* 1.3 75.8 - - - +
94A GLY* 1.3 66.5 + - - +
96A PHE* 4.0 5.8 - - + -
97A TYR* 3.0 41.4 + - + +
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 4.7 1.6 - - - -
88A SER* 3.3 22.9 + - - -
92A GLY 3.1 1.2 - - - -
93A VAL* 1.3 76.9 - - - +
95A ASP* 1.3 53.9 + - - +
96A PHE 3.0 5.9 + - - -
97A TYR 3.1 1.9 + - - -
98A TYR* 2.7 63.0 + - - -
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Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 6.0 0.9 - - - -
88A SER* 4.3 4.8 + - - -
92A GLY* 3.7 6.9 + - - +
94A GLY* 1.3 74.7 - - - +
96A PHE* 1.3 56.7 + - - +
98A TYR* 4.5 4.5 - - - -
99A GLU* 3.1 27.2 - - - +
278B GLY 4.5 0.2 - - - +
279B MET* 3.0 42.4 - - + +
280B GLU* 2.6 31.4 + - - -
281B LEU* 3.0 34.3 + - + +
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 6.3 5.4 - - + -
65A ARG* 3.4 37.7 - - - -
92A GLY 3.4 16.6 + - - +
93A VAL* 4.0 5.2 - - + +
94A GLY 3.0 0.8 + - - -
95A ASP* 1.3 80.1 - - - +
97A TYR* 1.3 103.4 + + - +
99A GLU* 3.7 2.6 - - - +
100A LEU* 3.1 26.7 + - + +
132A ARG* 3.6 32.8 + - - +
138A ASP* 4.3 3.4 - - + -
139A VAL* 3.9 14.4 - - + -
143A ASP* 3.7 16.6 - - + -
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.5 8.1 - - - +
69A GLN* 2.7 33.1 + - - -
80A LEU* 3.6 28.9 - - + -
93A VAL* 3.0 32.5 + - + +
94A GLY 3.1 2.0 + - - +
96A PHE* 1.3 99.5 - + - +
98A TYR* 1.3 71.4 + - + +
99A GLU 3.1 1.6 - - - -
100A LEU* 2.9 8.6 + - + +
101A GLY* 2.9 21.7 + - - -
142A ASP* 5.4 0.2 + - - -
143A ASP* 2.9 37.9 + - - -
146A ARG* 3.4 32.7 - - + +
147A ALA* 4.3 14.6 - - + +
150A LYS* 6.4 0.7 - - + -
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Residues in contact with TYR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO 4.3 0.2 + - - -
80A LEU* 2.7 40.8 + - + -
82A SER 3.1 22.5 + - - -
83A GLY* 4.1 16.4 - - - -
88A SER* 4.3 0.4 - - - -
94A GLY* 2.7 45.4 + - - +
95A ASP* 4.1 3.8 - - - -
97A TYR* 1.3 75.9 - - + +
99A GLU* 1.3 57.1 + - - +
101A GLY 3.5 5.0 + - - -
102A VAL* 3.5 9.7 + - - +
150A LYS* 5.5 5.4 - - + -
270B TYR* 2.6 30.1 + - - +
274B ASN* 4.7 0.4 - - - +
281B LEU* 4.3 17.3 - - + -
282B LEU 3.6 17.0 - - - +
283B SER* 3.4 32.8 - - - -
284B PRO* 4.3 7.0 - - + -
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP 3.1 22.6 + - - +
96A PHE* 3.7 3.6 - - - +
97A TYR 3.1 0.2 - - - -
98A TYR* 1.3 75.2 - - - +
100A LEU* 1.3 64.8 + - - +
101A GLY 3.2 1.6 - - - -
102A VAL* 3.1 26.1 + - - +
103A GLN* 3.2 32.8 + - - +
132A ARG* 4.0 7.7 + - - +
274B ASN 5.2 2.8 - - - +
275B ARG* 5.5 3.1 - - - -
278B GLY 5.9 1.3 - - - +
281B LEU* 3.8 21.6 - - + +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 3.1 27.3 + - + +
97A TYR* 2.9 13.8 + - + +
99A GLU* 1.3 75.1 - - - +
101A GLY* 1.3 57.8 + - - +
103A GLN* 3.4 5.9 + - + +
104A ILE* 2.8 45.8 + - + +
128A VAL* 3.8 29.2 - - + -
132A ARG* 4.3 13.0 - - - +
139A VAL* 3.6 26.9 - - + -
143A ASP* 3.7 28.7 - - + +
144A LEU* 3.9 7.4 - - + -
147A ALA* 4.3 3.4 - - + -
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Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR 2.9 12.2 + - - -
98A TYR 3.5 4.7 + - - -
99A GLU 3.2 0.6 - - - -
100A LEU* 1.3 74.7 - - - +
102A VAL* 1.3 58.4 + - - +
104A ILE* 3.2 5.5 + - - +
105A ILE* 2.8 39.3 + - - +
147A ALA* 4.3 3.9 - - - +
151A LEU* 3.8 24.7 - - - -
270B TYR* 4.5 2.0 - - - -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TYR 3.5 14.4 + - - +
99A GLU* 3.1 21.1 + - - +
101A GLY* 1.3 75.9 - - - +
103A GLN* 1.3 59.0 + - + +
105A ILE* 3.1 10.0 + - - +
106A GLU* 2.9 50.9 + - - +
270B TYR* 3.8 17.3 - - + -
271B CYS* 4.1 16.2 - - + -
274B ASN* 3.9 22.9 - - + -
275B ARG* 4.5 18.2 - - + +
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 3.2 29.1 + - - +
100A LEU* 3.6 13.1 - - + +
102A VAL* 1.3 80.5 - - + +
104A ILE* 1.3 56.2 + - - +
106A GLU* 3.3 12.7 + - - +
107A VAL* 3.0 36.1 + - + +
128A VAL* 3.5 24.8 + - + +
131A GLY* 4.1 12.6 + - - -
132A ARG* 2.9 49.0 + - - +
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 2.8 31.0 + - + +
101A GLY* 3.2 5.6 + - - +
103A GLN* 1.3 72.3 - - - +
105A ILE* 1.3 71.5 + - - +
107A VAL* 4.2 0.7 - - - +
108A CYS* 3.2 21.2 + - - +
124A LEU* 4.1 22.4 - - + -
128A VAL* 4.3 7.2 - - + -
144A LEU* 3.7 26.2 - - + +
147A ALA* 3.6 22.4 - - + -
148A ILE* 3.3 38.4 - - + -
151A LEU* 4.7 1.6 - - + -
158A PHE* 4.0 13.7 - - + -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY 2.8 26.7 + - - +
102A VAL 3.1 3.6 + - - +
104A ILE* 1.3 80.4 - - - +
106A GLU* 1.3 64.8 + - - +
108A CYS* 3.1 10.7 + - - +
109A LEU* 3.1 29.2 + - + +
151A LEU* 3.7 33.2 - - + -
154A LEU* 4.8 2.9 - - + -
158A PHE* 4.0 19.1 - - + -
267B THR* 4.1 22.0 - - - +
270B TYR* 4.0 16.6 - - + -
271B CYS* 3.7 23.1 - - - -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 2.9 39.0 + - + +
103A GLN* 3.3 11.7 + - - +
105A ILE* 1.3 77.3 - - + +
107A VAL* 1.3 62.9 + - + +
109A LEU* 3.0 9.6 + - + +
110A ALA* 3.0 24.9 + - - +
252A GLU* 5.1 16.4 - - + +
271B CYS* 4.8 8.6 - - - +
275B ARG* 3.2 32.8 + - - -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 3.0 21.7 + - + +
104A ILE 4.2 0.2 - - - +
106A GLU* 1.3 76.2 - - - +
108A CYS* 1.3 64.7 + - - +
110A ALA* 3.5 5.6 + - - +
111A LEU* 3.1 44.0 + - + +
119A ILE* 4.2 3.1 - - + -
124A LEU* 4.0 19.7 - - + -
127A GLN* 3.7 33.2 - - + +
128A VAL* 4.0 20.0 - - + +
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Residues in contact with CYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.2 13.7 + - - +
105A ILE 3.1 10.8 + - - +
107A VAL* 1.3 79.3 - - - +
109A LEU* 1.3 58.8 + - + +
111A LEU* 3.6 4.0 - - - +
112A LYS* 2.7 30.5 + - - +
115A ASN* 5.3 0.2 - - - +
117A GLY* 5.7 0.3 - - - -
119A ILE* 4.0 26.0 - - - -
124A LEU* 4.5 10.5 - - - -
158A PHE* 3.8 14.4 - - + -
169A ILE* 5.1 2.5 - - - -
171A SER* 3.6 35.0 + - - +
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 3.1 29.6 + - + +
106A GLU* 3.0 12.5 + - + +
108A CYS* 1.3 74.1 - - + +
110A ALA* 1.3 67.5 + - - +
111A LEU 3.0 2.4 + - - -
112A LYS* 3.1 46.9 + - + +
113A HIS* 4.4 1.4 + - - +
249A THR* 4.3 6.4 - - - +
252A GLU* 4.6 38.5 - - + +
268B GLU* 6.2 3.4 - - + -
271B CYS* 6.2 0.2 - - - -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLU 3.0 15.8 + - - +
107A VAL* 3.7 7.4 - - - +
109A LEU* 1.3 75.9 - - - +
111A LEU* 1.4 64.4 + - + +
113A HIS* 3.0 25.3 + - - -
114A ARG* 4.7 0.3 + - - -
246A GLN* 4.6 16.1 - - + +
249A THR* 3.2 36.4 + - - +
250A ALA* 4.8 4.3 - - - +
252A GLU* 5.5 0.6 - - - +
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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
----------------------------------------------------------
107A VAL* 3.1 27.3 + - + +
108A CYS* 4.0 4.3 - - - +
109A LEU 3.0 0.4 - - - -
110A ALA* 1.4 81.5 - - + +
112A LYS* 1.3 65.9 + - - +
113A HIS* 2.8 6.7 + - - -
114A ARG* 2.9 39.5 + - - +
115A ASN* 3.3 23.9 + - - +
119A ILE* 3.5 29.2 - - + -
123A GLU* 4.1 15.5 - - - +
127A GLN* 4.1 15.5 - - + +
246A GLN* 4.2 24.2 - - + -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A CYS 2.7 21.1 + - - +
109A LEU* 3.1 39.9 + - + +
111A LEU* 1.3 72.1 - - - +
113A HIS* 1.3 59.2 + - + +
115A ASN* 3.7 9.0 - - - -
116A GLY* 2.8 28.5 + - - +
117A GLY* 4.5 10.3 - - - +
171A SER* 5.2 1.3 - - - +
172A VAL* 3.9 24.5 - - + -
350B VAL* 4.9 20.0 - - - +
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Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU 4.4 1.0 + - - -
110A ALA 3.0 26.6 + - - -
111A LEU 2.8 8.3 + - - -
112A LYS* 1.3 76.1 - - + +
114A ARG* 1.3 107.8 + - + +
116A GLY 4.7 0.7 + - - -
223A TRP* 6.0 1.0 - - - -
249A THR* 3.1 24.9 + - + +
9C TRP* 5.4 2.2 - - - -
28C LYS* 3.3 35.1 + - + +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 4.7 0.2 + - - -
111A LEU* 2.9 31.4 + - - +
113A HIS* 1.3 115.2 + - + +
115A ASN* 1.3 65.2 + - + +
123A GLU* 5.7 2.9 - - - -
220A GLY 5.2 0.9 - - - +
223A TRP* 4.7 5.0 + - - -
237A PRO* 3.4 21.8 - - + +
242A ASP* 5.0 7.5 + - - -
244A TYR 3.7 22.0 + - - -
245A SER* 4.2 6.9 - - - -
246A GLN* 3.7 23.1 - - - +
247A GLU 5.3 3.6 + - - -
249A THR* 4.4 4.0 + - - -
9C TRP* 3.8 56.6 - - + +
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A CYS 5.3 0.3 - - - +
111A LEU* 3.3 30.7 + - - +
112A LYS* 3.7 4.2 - - - -
114A ARG* 1.3 83.9 - - + +
116A GLY* 1.3 60.5 + - - +
117A GLY* 3.1 15.2 + - - -
118A LEU* 2.9 30.5 + - - +
119A ILE* 4.0 11.1 - - - +
123A GLU* 4.0 10.9 + - - +
220A GLY 4.0 5.9 - - - +
221A LEU* 3.5 14.0 - - - +
237A PRO* 4.0 9.9 - - - +
238A ALA* 3.9 21.8 + - - +
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Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 2.8 26.0 + - - +
113A HIS 4.6 0.8 + - - -
114A ARG 3.8 0.8 - - - -
115A ASN* 1.3 71.4 - - - +
117A GLY* 1.3 54.0 + - - +
172A VAL* 3.9 18.6 - - - +
219A GLU* 4.3 10.0 - - - +
220A GLY* 3.7 18.8 + - - -
221A LEU* 3.5 14.0 - - - +
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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