Contacts of the helix formed by residues 135 - 168 (chain A) in PDB entry 3D87
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A PRO 4.7 2.0 - - - +
134A SER* 1.3 98.2 + - - +
136A PRO* 1.3 68.3 - - + +
137A TRP* 3.0 36.0 + - - -
138A GLN* 2.8 29.5 + - - +
139A ARG* 3.5 8.4 + - - +
137C TRP* 2.2 44.4 + - - +
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Residues in contact with PRO 136 (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 GLU* 3.1 17.2 - - + +
94A PRO* 4.4 0.2 - - + -
135A GLN* 1.3 94.2 - - + -
137A TRP* 1.3 78.1 + - + +
139A ARG* 3.2 21.7 - - + +
140A LEU* 2.3 39.1 + - - +
34C HIS* 3.1 38.1 - - + +
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Residues in contact with TRP 137 (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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135A GLN* 3.0 24.9 + - - +
136A PRO* 1.3 90.9 - - + +
138A GLN* 1.3 66.8 + - - +
140A LEU* 3.1 5.8 + - + +
141A LEU* 3.0 31.5 + - - +
34C HIS* 4.0 25.1 - + + -
36C ASP* 5.4 7.4 - - - -
137C TRP* 3.3 33.0 - + + +
140C LEU* 3.5 17.4 - - + +
141C LEU* 3.1 63.5 - - + +
144C PHE* 4.0 29.6 - + + -
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Residues in contact with GLN 138 (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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133A PRO* 3.5 36.6 - - + +
135A GLN* 2.8 36.6 + - - +
137A TRP* 1.3 75.0 - - - +
139A ARG* 1.3 64.3 + - - +
141A LEU* 3.4 8.7 + - - +
142A LEU* 2.9 25.8 + - - +
137C TRP* 3.0 20.9 - - + +
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Residues in contact with ARG 139 (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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88A ASP* 3.6 27.4 + - - +
89A ILE* 3.2 30.4 + - - +
92A GLY* 3.6 23.8 - - - -
93A GLU 3.4 24.0 + - - +
133A PRO* 3.7 16.0 - - + +
134A SER* 3.6 28.6 - - - +
135A GLN 3.5 5.8 + - - +
136A PRO* 3.1 28.1 - - + +
138A GLN* 1.3 79.9 - - - +
140A LEU* 1.3 65.3 + - - +
142A LEU* 2.8 7.9 + - - +
143A ARG* 2.8 29.7 + - - +
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Residues in contact with LEU 140 (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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29A HIS* 4.8 5.2 - - + +
32A VAL* 3.6 16.8 - - + -
94A PRO* 3.4 27.1 - - + -
136A PRO 2.3 30.1 + - - +
137A TRP* 3.5 9.4 - - + +
139A ARG* 1.3 67.0 - - - +
141A LEU* 1.3 67.1 + - - +
143A ARG* 3.1 30.2 - - - +
144A PHE* 3.1 45.5 - - + -
34C HIS* 5.8 0.2 - - + -
140C LEU* 4.1 12.3 - - + -
144C PHE* 3.3 37.2 - - + -
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Residues in contact with LEU 141 (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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32A VAL* 4.7 2.0 - - - -
35A MET* 2.8 47.9 - - + +
137A TRP 3.0 17.4 + - - +
138A GLN* 3.6 9.9 - - - +
140A LEU* 1.3 75.0 - - - +
142A LEU* 1.3 66.0 + - - +
144A PHE* 2.9 4.9 + - - -
145A LYS* 2.9 15.1 + - - +
94C PRO* 4.4 7.6 - - + -
136C PRO* 3.8 21.8 - - + -
137C TRP* 3.5 31.6 - - + +
140C LEU* 3.4 29.2 - - + -
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Residues in contact with LEU 142 (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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84A LEU* 6.0 0.2 - - + -
89A ILE* 3.0 41.3 - - + -
132A SER 5.4 0.4 - - - +
133A PRO* 5.2 8.1 - - + -
138A GLN 2.9 13.5 + - - +
139A ARG* 2.8 16.3 + - - +
141A LEU* 1.3 71.4 - - - +
143A ARG* 1.3 63.2 + - - +
145A LYS* 2.9 33.6 + - + +
146A ILE* 2.9 38.0 + - + +
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Residues in contact with ARG 143 (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 ILE* 2.7 31.1 + - + +
90A PHE* 3.3 46.7 + - + +
92A GLY 2.4 40.4 + - - +
93A GLU 3.6 0.6 + - - -
94A PRO* 3.1 48.4 + - - +
95A SER* 4.5 0.6 - - - +
96A LEU* 4.6 10.0 - - - +
139A ARG* 2.8 20.8 + - - +
140A LEU* 3.1 19.3 - - - +
142A LEU* 1.3 71.5 - - - +
144A PHE* 1.3 70.2 + - + +
147A LEU* 2.9 32.8 + - + +
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Residues in contact with PHE 144 (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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27A SER* 5.5 1.8 - - - -
28A ALA* 4.1 13.5 - - - -
29A HIS* 3.4 37.0 - + + -
32A VAL* 3.5 24.5 - - + -
33A GLY 5.0 3.8 - - - +
34A HIS* 5.7 5.0 - + + -
35A MET* 3.3 24.5 - - + +
102A VAL* 6.4 0.7 - - + -
140A LEU* 3.1 45.5 + - + -
141A LEU 2.9 4.4 + - - +
143A ARG* 1.3 86.8 - - + +
145A LYS* 1.3 61.2 + - - +
147A LEU* 3.5 28.9 - - + +
148A ARG* 2.8 28.8 + - - +
151A GLN* 5.4 0.3 + - - -
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Residues in contact with LYS 145 (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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35A MET* 3.0 35.6 - - + +
36A ASP 5.0 9.2 - - - -
37A LEU 5.4 4.0 - - - +
38A ARG 6.0 2.0 - - - +
141A LEU* 2.9 20.7 + - - +
142A LEU* 2.9 24.8 + - + +
144A PHE* 1.3 74.5 - - - +
146A ILE* 1.3 60.0 + - + +
148A ARG* 2.8 26.9 - - + +
149A SER* 2.9 18.7 + - - +
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Residues in contact with ILE 146 (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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49A VAL* 5.9 0.2 - - + -
81A TYR* 3.5 15.7 - - + -
84A LEU* 3.4 39.9 - - + -
85A LEU* 4.5 4.3 - - + -
89A ILE* 3.8 7.0 - - + -
90A PHE* 3.7 25.8 - - + -
142A LEU* 2.9 51.1 + - + +
143A ARG 3.7 3.1 - - - +
145A LYS* 1.3 77.4 - - + +
147A LEU* 1.3 63.6 + - - +
149A SER* 3.1 6.7 + - - -
150A LEU* 2.8 23.7 + - - +
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Residues in contact with LEU 147 (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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24A LEU 5.8 0.9 - - - +
25A ALA* 3.7 16.2 - - - +
27A SER* 5.1 10.1 - - - +
28A ALA 5.4 0.9 - - - +
85A LEU* 4.6 2.5 - - + -
90A PHE* 3.7 23.3 - - + -
102A VAL* 4.4 15.9 - - + -
105A LEU* 3.8 25.8 - - + -
143A ARG* 2.9 25.8 + - + +
144A PHE* 3.5 42.4 - - + +
146A ILE* 1.3 73.7 - - - +
148A ARG* 1.3 56.3 + - - +
150A LEU* 3.2 9.6 - - + +
151A GLN* 2.9 37.3 + - - +
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Residues in contact with ARG 148 (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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26A TRP* 3.3 23.0 - - - -
34A HIS* 3.7 26.2 - - - +
35A MET* 2.8 34.2 + - + +
36A ASP* 4.0 14.3 + - - -
37A LEU* 5.5 8.2 - - + +
144A PHE 2.8 11.5 + - - +
145A LYS* 2.8 19.1 - - + +
147A LEU* 1.3 71.4 - - - +
149A SER* 1.3 63.9 + - - +
150A LEU 3.0 1.3 - - - -
151A GLN* 2.3 60.0 + - - +
152A ALA* 3.6 5.2 + - - +
208B ARG* 5.5 2.1 + - - -
209B ASP* 3.9 19.8 + - - -
293B TYR* 3.4 11.7 + - - -
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Residues in contact with SER 149 (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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49A VAL* 4.7 14.2 - - - +
51A HIS* 5.6 2.9 - - - -
81A TYR* 2.7 27.4 + - - -
145A LYS* 2.9 22.2 + - - +
146A ILE* 3.6 6.8 - - - -
148A ARG* 1.3 75.4 - - - +
150A LEU* 1.3 62.4 + - - +
152A ALA* 3.3 8.4 + - - +
153A PHE* 3.0 17.0 + - - +
181B GLU* 3.7 5.3 - - - +
208B ARG* 5.7 3.8 - - - +
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Residues in contact with LEU 150 (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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25A ALA* 4.1 9.0 - - + -
81A TYR* 3.4 42.8 + - + -
85A LEU* 4.5 6.7 - - + -
105A LEU* 4.0 29.4 - - + -
109A LEU* 4.3 14.6 - - + -
146A ILE 2.8 13.2 + - - +
147A LEU* 3.2 13.7 - - + +
149A SER* 1.3 74.8 - - - +
151A GLN* 1.3 66.3 + - - +
153A PHE* 2.8 16.6 + - + -
154A VAL* 2.8 53.3 + - + +
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Residues in contact with GLN 151 (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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25A ALA* 2.8 32.0 + - - +
26A TRP* 3.5 33.9 + - + +
34A HIS* 2.9 35.0 + - - -
147A LEU* 2.9 21.6 + - - +
148A ARG* 2.3 49.1 + - - +
150A LEU* 1.3 73.6 - - - +
152A ALA* 1.3 56.6 + - - +
154A VAL* 3.1 10.5 - - - +
155A ALA* 3.0 27.9 + - - +
292B TYR 4.4 2.3 - - - +
293B TYR* 3.6 4.8 + - + -
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Residues in contact with ALA 152 (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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148A ARG 3.6 3.2 + - - +
149A SER 3.3 8.0 + - - +
150A LEU 3.0 0.8 - - - -
151A GLN* 1.3 76.6 - - - +
153A PHE* 1.3 71.9 + - - +
155A ALA* 3.3 3.0 + - - +
156A VAL* 3.3 23.3 + - - +
181B GLU* 4.2 9.4 - - + +
208B ARG* 3.2 49.8 - - - +
293B TYR* 3.8 8.5 - - + -
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Residues in contact with PHE 153 (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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50A PRO* 4.8 4.7 - - + -
51A HIS* 5.0 2.9 - - - -
52A ILE* 3.0 40.8 - - + -
73A ARG* 4.6 2.7 - - + -
74A ILE* 3.4 20.4 - - + -
77A GLY* 3.3 25.6 - - - -
78A LEU* 3.5 30.7 - - + -
81A TYR* 3.7 27.4 - + + -
149A SER 3.0 12.4 + - - +
150A LEU* 2.8 15.3 + - + +
152A ALA* 1.3 83.3 - - - +
154A VAL* 1.3 66.8 + - + +
156A VAL* 2.7 23.7 + - - +
157A ALA* 3.3 9.4 + - + +
181B GLU* 3.6 18.3 + - - +
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Residues in contact with VAL 154 (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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18A SER* 5.1 1.0 - - - -
21A LEU* 3.9 41.5 - - + +
22A CYS* 3.5 15.1 - - - -
25A ALA* 4.2 10.5 - - + -
78A LEU* 5.0 1.6 - - + -
109A LEU* 4.7 2.2 - - + -
150A LEU* 2.8 53.5 + - + +
151A GLN* 3.1 22.9 - - - +
153A PHE* 1.3 82.8 - - + +
155A ALA* 1.3 54.4 + - - +
157A ALA* 3.2 9.7 + - + +
158A ALA* 2.8 32.6 + - - +
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Residues in contact with ALA 155 (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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22A CYS* 4.0 2.5 - - - -
151A GLN 3.0 21.0 + - - +
152A ALA* 3.4 7.9 - - - +
153A PHE 2.8 4.6 + - - -
154A VAL* 1.3 74.3 - - - +
156A VAL* 1.3 62.3 + - - +
158A ALA* 3.4 3.3 + - - +
159A ARG* 3.1 46.0 + - - +
208B ARG* 6.1 0.2 - - - -
292B TYR* 3.5 22.8 - - - +
293B TYR* 3.9 11.9 - - + -
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Residues in contact with VAL 156 (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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52A ILE* 4.2 21.1 - - + -
58A CYS* 4.6 3.4 - - + -
152A ALA 3.3 14.8 - - - +
153A PHE 2.7 12.7 + - - +
155A ALA* 1.3 70.1 - - - +
157A ALA* 1.3 54.1 + - - +
159A ARG* 2.9 17.8 + - - +
160A VAL* 2.7 44.9 + - + +
179B ALA 3.3 26.5 - - - +
180B ALA 4.5 0.9 - - - +
181B GLU* 3.8 27.6 - - + -
246B TYR* 3.4 13.0 - - - +
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Residues in contact with ALA 157 (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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18A SER* 4.8 3.4 - - - -
21A LEU* 6.2 1.1 - - + -
52A ILE* 4.8 2.8 - - + +
74A ILE* 4.4 19.1 - - + -
78A LEU* 6.2 2.0 - - + -
112A LEU* 5.5 2.9 - - + -
153A PHE* 3.3 7.6 + - + +
154A VAL* 3.4 16.6 - - - +
156A VAL* 1.3 79.2 - - - +
158A ALA* 1.3 66.4 + - - +
160A VAL* 2.7 21.3 + - - +
161A PHE* 2.9 36.5 + - + -
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Residues in contact with ALA 158 (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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15A GLN* 3.0 5.7 + - - +
18A SER* 3.7 21.0 - - - -
19A GLN 4.4 2.5 - - - +
22A CYS* 3.5 11.0 - - - -
154A VAL 2.8 17.0 + - - +
155A ALA 3.6 0.9 - - - +
157A ALA* 1.3 76.0 - - - +
159A ARG* 1.3 62.3 + - - +
162A ALA* 2.8 25.4 + - - +
292B TYR* 3.2 37.7 - - + -
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Residues in contact with ARG 159 (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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155A ALA* 3.1 32.9 + - - +
156A VAL* 2.9 28.8 + - - +
158A ALA* 1.3 74.5 - - - +
160A VAL* 1.3 65.7 + - - +
162A ALA* 3.8 0.6 - - - -
163A HIS* 2.8 27.4 + - - +
114B TYR* 3.3 25.7 + - - -
178B PRO 5.6 1.2 + - - -
179B ALA 4.8 3.6 + - - -
208B ARG* 5.8 1.4 - - - +
246B TYR* 3.2 60.1 - - + +
247B PHE* 3.9 15.4 - - - +
290B ASP* 3.0 33.7 + - - -
292B TYR* 3.7 11.4 - - + -
293B TYR* 4.1 3.4 - - - +
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Residues in contact with VAL 160 (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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11A TRP* 3.8 3.7 - - + -
58A CYS* 3.6 29.4 - - + +
63A LEU* 3.4 31.2 - - + +
70A CYS* 3.6 18.6 - - - -
71A LEU* 4.4 12.8 - - + -
74A ILE* 4.1 11.2 - - + -
156A VAL* 2.7 32.3 + - + +
157A ALA* 2.7 11.6 + - - +
159A ARG* 1.3 72.4 - - - +
161A PHE* 1.3 60.9 + - + +
163A HIS* 3.3 2.3 - - - +
164A GLY* 2.8 25.5 + - - -
246B TYR* 4.2 1.8 - - - +
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Residues in contact with PHE 161 (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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9A PRO* 4.9 1.1 - - + -
11A TRP* 3.4 19.4 - + + -
14A CYS* 3.4 22.9 - - + -
15A GLN* 3.7 12.6 - - - +
18A SER* 3.0 28.5 - - - +
71A LEU* 3.5 26.0 - - + -
74A ILE* 4.1 7.9 - - + -
112A LEU* 4.1 17.5 - - + -
116A LEU* 3.8 31.9 - - + -
157A ALA* 2.9 44.6 + - + +
160A VAL* 1.3 73.1 - - + +
162A ALA* 1.3 55.0 + - - +
163A HIS 2.9 0.5 + - - -
164A GLY 2.9 0.5 + - - -
165A ALA* 2.5 39.5 + - - +
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Residues in contact with ALA 162 (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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15A GLN* 2.8 38.1 - - + +
158A ALA 2.8 10.7 + - - +
159A ARG 4.0 1.1 - - - +
161A PHE* 1.3 70.0 - - - +
163A HIS* 1.3 60.4 + - - +
165A ALA* 3.5 2.1 - - - +
166A ALA* 3.3 20.1 + - - +
245B SER 3.4 13.1 - - - +
248B SER* 5.2 0.4 - - - +
291B ARG* 5.7 0.4 - - - +
292B TYR* 2.8 32.5 - - + +
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Residues in contact with HIS 163 (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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60A PRO* 3.8 26.8 + - + +
63A LEU* 3.8 24.4 - - + +
64A ARG* 5.8 1.4 + - - +
159A ARG 2.8 20.4 + - - +
160A VAL 3.3 2.7 - - - +
161A PHE 2.9 0.6 + - - -
162A ALA* 1.3 75.6 - - - +
164A GLY* 1.3 65.5 + - - +
165A ALA 3.1 0.9 - - - -
166A ALA 2.9 1.9 + - - -
167A THR* 2.7 56.5 + - + +
168A LEU* 6.2 0.4 - - + -
243B PRO* 3.9 13.7 - - + -
245B SER* 2.5 38.3 + - - +
246B TYR* 3.7 12.9 + + + -
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Residues in contact with GLY 164 (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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11A TRP* 3.6 16.6 - - - -
63A LEU* 4.9 1.3 - - - +
160A VAL 2.8 14.7 + - - -
161A PHE 2.9 1.3 + - - -
163A HIS* 1.3 72.8 - - - +
165A ALA* 1.3 59.7 + - - +
166A ALA 2.9 0.5 + - - -
167A THR* 2.9 0.8 + - - -
168A LEU* 2.6 63.4 + - - +
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.2 36.6 - - + +
12A THR* 4.2 7.8 + - + +
15A GLN* 3.8 11.7 - - + -
161A PHE 2.5 22.4 + - - +
162A ALA 3.5 9.4 - - - +
164A GLY* 1.3 71.7 - - - +
166A ALA* 1.3 57.9 + - + +
168A LEU 4.3 7.6 - - - +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 3.3 14.3 + - - +
163A HIS 2.9 4.4 + - - +
165A ALA* 1.3 80.3 - - + +
167A THR* 1.3 69.0 + - + +
168A LEU 3.5 2.3 + - - +
245B SER* 4.3 13.9 - - - -
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG* 6.0 1.2 - - - +
163A HIS* 2.7 54.6 + - + +
166A ALA* 1.3 83.3 - - + +
168A LEU* 1.3 77.6 + - - +
245B SER* 4.0 5.8 - - - +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 5.3 4.5 - - - +
11A TRP* 3.3 40.5 - - + +
63A LEU* 4.9 16.6 - - + +
64A ARG* 5.1 10.3 - - + +
67A SER* 6.4 0.2 - - - -
163A HIS* 6.2 0.4 - - + -
164A GLY* 2.6 45.4 + - - +
165A ALA 4.3 8.0 - - - +
166A ALA 3.5 2.4 + - - +
167A THR* 1.3 95.6 - - - +
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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) + - + + + + + -
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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