Contacts of the helix formed by residues 135 - 168 (chain B) in PDB entry 3QWR
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 GLN 135 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 1.4 78.4 + - - +
136B PRO* 1.3 74.3 - - + +
137B TRP* 4.5 6.5 - - + +
138B GLN* 2.9 26.6 + - + +
139B ARG* 3.3 9.6 + - - +
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Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLU* 4.8 9.4 - - + +
94B PRO* 3.7 29.9 - - + +
134B SER 3.7 5.4 - - - +
135B GLN* 1.3 84.6 - - + +
137B TRP* 1.4 61.2 + - - +
139B ARG* 3.1 15.6 + - + +
140B LEU* 3.2 18.3 + - + +
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Residues in contact with TRP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B HIS* 3.1 34.5 + + - -
35B MET 5.7 1.2 + - - -
36B ASP* 5.4 9.9 - - + -
135B GLN* 3.3 5.1 + - + +
136B PRO* 1.4 76.6 - - - +
138B GLN* 1.3 70.3 + - + +
140B LEU* 3.7 10.2 + - + +
141B LEU* 3.3 49.6 + - + +
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Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PRO* 5.8 2.5 - - + -
134B SER* 5.3 4.9 - - - +
135B GLN* 2.9 23.9 + - + +
137B TRP* 1.3 90.5 - - + +
139B ARG* 1.4 56.9 + - - +
141B LEU* 3.6 4.1 + - - +
142B LEU* 3.0 30.1 + - - +
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP 5.5 0.9 - - - +
89B ILE* 4.0 18.8 - - - +
93B GLU 4.4 15.9 - - - +
94B PRO* 4.5 2.0 - - + -
133B PRO* 4.4 20.3 - - + +
134B SER 6.1 0.4 - - - +
135B GLN 3.3 7.1 + - - +
136B PRO* 3.1 9.6 + - + +
138B GLN* 1.4 73.1 - - - +
140B LEU* 1.3 59.6 + - - +
142B LEU* 3.2 6.6 + - - +
143B ARG* 2.8 41.0 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO 6.1 0.7 - - - -
31B LEU* 4.7 4.9 - - + +
32B VAL* 4.1 27.4 - - + -
34B HIS* 3.6 33.2 - - + +
94B PRO* 3.9 24.2 - - + -
136B PRO* 3.2 16.1 + - + +
137B TRP* 3.9 9.2 - - + +
139B ARG* 1.3 74.7 - - - +
141B LEU* 1.3 61.8 + - - +
143B ARG* 3.5 30.4 + - - +
144B PHE* 3.2 20.8 + - - +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.1 7.0 - - + -
34B HIS* 4.2 15.6 - - + +
36B ASP* 3.8 31.6 - - - +
38B ARG 6.0 2.0 - - - +
137B TRP* 3.3 38.9 + - + +
138B GLN* 3.9 5.4 - - - +
139B ARG 3.3 0.4 - - - -
140B LEU* 1.3 74.9 - - - +
142B LEU* 1.3 65.8 + - - +
144B PHE* 3.2 10.3 + - + +
145B LYS* 3.0 52.5 + - + +
79D TYR* 6.0 3.6 - - + -
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 3.6 33.0 - - + -
131B LEU* 5.7 7.2 - - - -
132B SER 5.6 2.0 - - - -
133B PRO* 5.2 11.7 - - + -
138B GLN 3.0 19.1 + - - +
139B ARG* 3.7 5.4 - - - +
141B LEU* 1.3 75.3 - - - +
143B ARG* 1.3 57.1 + - - +
145B LYS* 3.2 18.1 + - + +
146B ILE* 2.9 50.8 + - + +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PRO* 4.9 2.5 - - + -
89B ILE* 2.7 37.4 + - + +
90B PHE* 3.8 30.7 + - + +
92B GLY 3.0 18.4 + - - -
93B GLU 3.9 9.3 + - - -
94B PRO* 2.8 34.1 + - - +
95B SER 4.6 0.4 + - - -
96B LEU* 3.6 33.3 - - - +
139B ARG* 2.8 27.9 + - - +
140B LEU* 3.7 24.9 - - - +
142B LEU* 1.3 75.3 - - - +
144B PHE* 1.4 63.4 + - - +
146B ILE 3.5 0.3 + - - -
147B LEU* 3.0 35.4 + - + +
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 3.8 16.8 - + - -
30B PRO* 3.7 28.6 - - + +
31B LEU* 3.9 28.7 - - + +
140B LEU 3.2 10.0 + - - +
141B LEU* 3.2 15.3 + - + +
143B ARG* 1.4 79.3 - - - +
145B LYS* 1.3 72.8 + - + +
147B LEU* 3.3 1.9 + - - +
148B ARG* 3.0 47.1 + - + +
28D TYR* 4.0 7.4 - - - -
77D SER* 4.7 2.0 - - - -
79D TYR* 3.6 32.5 - + + -
82D ASP* 3.6 36.8 - - + -
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.0 40.8 + - + +
142B LEU* 3.2 23.1 + - + +
144B PHE* 1.3 87.0 - - + +
146B ILE* 1.3 62.5 + - + +
148B ARG* 3.3 6.6 + - - +
149B SER* 3.1 23.4 + - - -
79D TYR* 3.4 27.7 + - + +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.8 16.6 - - + -
84B LEU* 4.3 20.4 - - + -
85B LEU* 4.0 26.7 - - + -
89B ILE* 3.9 16.2 - - + -
90B PHE* 3.7 20.6 - - + -
142B LEU* 2.9 43.6 + - + +
143B ARG 4.0 3.4 - - - +
145B LYS* 1.3 75.5 - - + +
147B LEU* 1.3 59.3 + - + +
149B SER* 2.7 21.0 + - - -
150B LEU* 2.9 15.3 + - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 5.4 2.5 - - - +
30B PRO* 3.9 29.6 - - + -
85B LEU* 4.3 9.0 - - + -
90B PHE* 3.9 22.9 - - + -
101B PRO* 6.0 4.0 - - + -
102B VAL* 4.1 19.3 - - + -
105B LEU* 4.2 15.5 - - + -
143B ARG* 3.0 22.9 + - + +
144B PHE 3.9 2.9 - - - +
146B ILE* 1.3 75.0 - - - +
148B ARG* 1.3 63.2 + - - +
150B LEU* 3.4 24.3 + - + +
151B GLN* 3.0 31.6 + - - +
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ARG* 4.9 7.3 + - - +
209A ASP* 2.9 23.6 + - - -
293A TYR* 3.0 20.6 + - - -
26B TRP* 3.5 15.0 - - - -
30B PRO* 5.4 1.6 - - + -
144B PHE* 3.0 41.9 + - + +
145B LYS* 3.6 6.5 - - - +
146B ILE 3.3 0.2 - - - -
147B LEU* 1.3 76.3 - - - +
149B SER* 1.3 63.1 + - - +
151B GLN* 2.7 50.7 + - - +
152B ALA* 3.4 7.8 + - - +
28D TYR* 3.3 18.8 + - - -
81D TYR 2.6 30.3 + - - -
82D ASP* 3.6 9.2 + - - +
83D MET 3.1 15.4 - - - +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.4 14.3 - - - +
208A ARG* 5.3 4.5 - - - +
51B HIS* 5.5 6.5 - - - -
81B TYR* 3.3 22.0 + - - -
145B LYS 3.1 11.0 + - - -
146B ILE* 2.7 23.7 + - - -
148B ARG* 1.3 77.7 - - - +
150B LEU* 1.3 61.3 + - - +
152B ALA* 3.2 6.4 + - - +
153B PHE 3.1 17.3 + - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA* 5.1 3.8 - - + -
81B TYR* 3.5 42.0 - - + -
85B LEU* 4.5 12.6 - - + -
105B LEU* 3.9 35.0 - - + -
109B LEU* 4.2 12.6 - - + -
146B ILE 2.9 18.8 + - - +
147B LEU* 3.5 18.6 - - + +
149B SER* 1.3 77.2 + - - +
151B GLN* 1.4 55.7 + - - +
153B PHE* 3.3 1.4 + - + -
154B VAL* 2.9 51.0 + - + +
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TYR 4.8 0.3 - - - +
293A TYR* 3.9 14.7 - - + -
25B ALA* 2.9 34.7 + - + +
26B TRP* 3.6 26.4 + - - +
30B PRO* 5.6 3.4 - - - +
147B LEU* 3.0 20.9 + - - +
148B ARG* 2.7 44.8 + - - +
150B LEU* 1.4 75.7 - - - +
152B ALA* 1.3 60.5 + - - +
154B VAL* 3.5 10.5 - - - +
155B ALA* 3.3 23.4 + - - +
28D TYR* 3.4 26.7 + - - -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.7 17.3 - - + +
208A ARG* 3.6 42.6 - - - +
293A TYR* 3.9 9.8 - - - -
148B ARG 3.4 3.2 + - - +
149B SER* 3.2 9.7 + - - +
151B GLN* 1.3 76.0 - - - +
153B PHE* 1.3 65.7 + - - +
155B ALA* 3.4 4.4 + - - +
156B VAL* 3.2 26.7 + - - +
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Residues in contact with PHE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.8 23.5 + - - +
50B PRO 4.8 5.4 - - - -
52B ILE* 4.1 27.8 - - + -
74B ILE* 3.4 33.7 - - + -
77B GLY* 3.6 18.8 - - - -
78B LEU* 3.8 31.4 - - + -
81B TYR* 3.8 27.1 - + + -
149B SER 3.1 10.0 + - - +
150B LEU* 3.6 6.7 - - + +
152B ALA* 1.3 79.3 - - - +
154B VAL* 1.3 74.0 + - + +
156B VAL* 3.1 15.8 + - - +
157B ALA* 3.1 15.0 + - + +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR 5.4 0.4 - - - +
18B SER* 4.6 2.0 - - - +
21B LEU* 4.2 34.5 - - + +
22B CYS* 3.6 29.9 - - - +
25B ALA* 4.3 5.2 - - + -
26B TRP* 6.0 0.2 - - - +
78B LEU* 5.3 0.9 - - + -
105B LEU* 6.3 0.2 - - + -
109B LEU* 4.6 4.0 - - + -
150B LEU* 2.9 43.0 + - + +
151B GLN* 3.5 12.8 - - - +
153B PHE* 1.3 84.7 - - + +
155B ALA* 1.4 54.9 + - - +
157B ALA* 3.3 7.4 + - + +
158B ALA* 2.8 35.2 + - - +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A TYR* 3.9 32.7 - - + +
293A TYR* 4.3 9.6 - - + +
22B CYS* 3.9 0.7 - - - -
151B GLN 3.3 17.8 + - - +
152B ALA* 3.6 6.1 - - - +
153B PHE 3.2 0.8 - - - -
154B VAL* 1.4 72.7 - - - +
156B VAL* 1.4 65.4 + - - +
158B ALA* 3.2 2.8 + - - +
159B ARG* 3.1 45.2 + - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA 3.4 21.3 - - - +
180A ALA 4.4 1.3 - - - +
181A GLU* 4.2 21.5 - - + +
246A TYR* 3.6 17.3 - - - +
52B ILE* 4.0 32.1 - - + -
58B CYS* 4.7 1.3 - - + -
74B ILE* 6.1 1.3 - - + -
152B ALA 3.2 12.7 + - - +
153B PHE* 3.1 9.2 + - - +
155B ALA* 1.4 76.3 - - - +
157B ALA* 1.3 61.7 + - - +
159B ARG* 3.2 17.4 + - - +
160B VAL* 3.1 28.2 + - + +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 4.1 11.2 - - - +
74B ILE* 4.1 36.6 - - + -
78B LEU* 5.7 1.1 - - + -
112B LEU* 5.3 2.9 - - + -
153B PHE* 3.1 18.6 + - + +
154B VAL* 3.6 11.7 - - + +
155B ALA 3.3 0.2 - - - -
156B VAL* 1.3 77.3 - - - +
158B ALA* 1.3 62.4 + - - +
160B VAL* 3.3 3.1 + - - +
161B PHE* 3.0 32.2 + - + -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TYR* 3.3 39.2 - - + -
15B GLN* 5.0 2.6 - - - +
18B SER* 3.7 21.3 - - - +
19B GLN 4.6 0.2 - - - +
22B CYS* 3.7 8.7 - - - -
154B VAL 2.8 20.1 + - - +
155B ALA 3.2 1.5 + - - +
157B ALA* 1.3 74.2 - - - +
159B ARG* 1.4 56.3 + - - +
161B PHE* 3.5 1.6 + - - +
162B ALA* 2.9 29.8 + - - +
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 3.2 22.1 + - - -
179A ALA* 5.3 2.2 + - - +
246A TYR* 2.9 74.9 + - + +
247A PHE* 3.8 19.8 - - - +
248A SER 4.9 0.2 - - - +
290A ASP* 3.2 34.1 + - - -
292A TYR* 3.7 14.3 - - + -
293A TYR* 4.4 3.2 - - - +
155B ALA* 3.1 39.4 + - - +
156B VAL* 3.2 16.2 + - - +
158B ALA* 1.4 72.4 - - - +
160B VAL* 1.3 60.5 + - - +
162B ALA* 4.5 0.9 - - - -
163B HIS* 2.9 25.8 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TYR* 3.7 10.3 - - + +
11B TRP* 3.8 6.4 - - + -
58B CYS* 3.4 28.7 - - + +
63B LEU* 5.8 7.2 - - + -
70B CYS* 3.7 22.2 - - - -
71B LEU* 4.2 13.7 - - + -
74B ILE* 3.7 23.1 - - + -
156B VAL* 3.1 18.1 + - + +
157B ALA 3.5 8.1 - - - +
159B ARG* 1.3 77.3 - - - +
161B PHE* 1.3 59.9 + - + +
163B HIS* 3.8 2.0 - - - +
164B GLY* 2.9 27.2 + - - -
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 5.7 3.6 - - + -
11B TRP* 3.7 21.9 - + - +
14B CYS* 3.5 33.4 - - + -
15B GLN* 3.7 23.6 - - - +
18B SER* 3.1 28.7 - - - +
71B LEU* 3.7 23.6 - - + -
74B ILE* 4.1 28.5 - - + -
78B LEU* 5.8 0.4 - - + -
112B LEU* 4.0 16.8 - - + -
116B LEU* 5.9 6.7 - - + -
157B ALA* 3.0 22.5 + - + +
158B ALA 4.1 2.2 - - - +
160B VAL* 1.3 72.8 - - + +
162B ALA* 1.3 60.4 + - - +
165B ALA* 2.9 31.4 + - - +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER 3.4 14.5 - - - +
248A SER* 4.3 2.7 - - - +
291A ARG* 5.6 2.0 - - - +
292A TYR* 3.4 20.9 - - + +
15B GLN* 3.8 19.2 - - + +
158B ALA 2.9 18.5 + - - +
159B ARG* 3.9 2.7 - - - +
160B VAL 3.3 0.2 - - - -
161B PHE* 1.3 76.6 - - - +
163B HIS* 1.3 56.9 + - - +
165B ALA* 3.4 3.1 + - - +
166B ALA* 3.0 28.8 + - - +
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Residues in contact with HIS 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PRO* 4.0 18.1 - - + +
245A SER* 2.3 45.0 + - - +
246A TYR* 4.0 13.8 + + + -
60B PRO* 3.5 36.3 + - + +
63B LEU* 4.8 11.0 - - + -
64B ARG* 6.2 0.2 - - - +
159B ARG 2.9 17.9 + - - +
160B VAL* 3.8 2.9 - - - +
162B ALA* 1.3 71.4 - - - +
164B GLY* 1.3 55.4 + - - +
166B ALA 3.1 1.7 + - - -
167B THR* 2.7 64.7 + - + +
168B LEU* 5.9 0.7 - - + -
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Residues in contact with GLY 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 3.6 27.9 - - - -
63B LEU* 6.3 0.7 - - - -
160B VAL 2.9 12.9 + - - -
163B HIS* 1.3 75.9 - - - +
165B ALA* 1.3 56.1 + - - +
168B LEU* 2.7 54.9 + - - +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 3.6 28.8 - - + +
12B THR* 4.4 11.8 - - + +
15B GLN* 4.4 9.2 - - + +
161B PHE 2.9 19.7 + - - +
162B ALA* 3.6 7.4 - - - +
163B HIS 3.3 0.2 - - - -
164B GLY* 1.3 76.1 - - - +
166B ALA* 1.3 60.5 + - - +
168B LEU 4.4 7.2 - - - +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 4.1 20.0 - - - -
162B ALA 3.0 16.8 + - - +
163B HIS 3.1 2.4 + - - +
165B ALA* 1.3 78.2 - - - +
167B THR* 1.3 62.5 + - + +
168B LEU 3.8 0.2 - - - -
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A SER* 4.2 5.8 - - - +
163B HIS* 2.7 59.6 + - + +
166B ALA* 1.3 82.2 - - + +
168B LEU* 1.4 77.3 + - - +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B TRP* 4.2 36.0 - - + +
63B LEU* 4.0 29.2 - - + +
64B ARG* 4.9 13.5 - - - +
67B SER* 4.9 4.0 - - - -
163B HIS* 5.9 0.9 - - + -
164B GLY* 2.7 38.5 + - - +
165B ALA* 4.4 6.4 - - - +
166B ALA 3.8 0.6 - - - -
167B THR* 1.4 94.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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