Contacts of the helix formed by residues 122 - 147 (chain D) in PDB entry 3O2Q
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 ASN 122 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ILE* 3.3 51.2 - - + +
89D ARG* 4.0 2.9 - - - +
120D ASP* 2.9 14.7 + - - +
121D GLU* 1.3 80.7 - - + +
123D VAL* 1.3 67.2 + - - +
124D ASN* 3.1 23.1 + - - +
125D VAL* 3.1 8.4 + - + +
126D VAL* 3.1 20.5 + - - +
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Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLU 3.9 3.9 + - - +
122D ASN* 1.3 73.6 + - - +
124D ASN* 1.3 67.4 + - - +
126D VAL* 3.1 10.0 + - + +
127D LYS* 2.8 44.9 + - - +
176D ASN* 3.6 30.3 - - + +
179D ILE* 3.9 16.8 - - + -
166E GLU 5.8 0.2 - - - +
167E ASP* 3.2 30.1 - - + +
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Residues in contact with ASN 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ILE* 4.1 14.4 - - + +
90D LYS* 4.0 17.3 - - + +
122D ASN* 3.1 19.7 + - - +
123D VAL* 1.3 81.0 - - - +
125D VAL* 1.3 60.7 + - - +
127D LYS* 3.3 28.9 + - - +
128D LYS* 3.0 29.6 + - - +
166E GLU 5.0 8.9 + - - -
167E ASP* 5.4 2.6 - - - +
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Residues in contact with VAL 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D ILE* 3.7 32.3 - - + +
89D ARG* 3.9 20.9 - - + +
90D LYS* 4.1 7.4 - - + -
93D ILE* 3.5 20.6 - - + +
117D LEU* 3.8 15.5 - - + +
120D ASP* 3.4 37.9 - - + +
122D ASN* 3.1 10.4 + - - +
124D ASN* 1.3 75.5 - - - +
126D VAL* 1.3 65.3 + - - +
128D LYS 3.3 1.2 + - - -
129D ALA* 3.0 19.1 + - - +
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU 4.2 5.6 - - - -
118D LEU* 3.6 28.9 - - + +
119D ARG 4.6 0.2 - - - -
120D ASP 3.2 31.0 - - - +
122D ASN 3.1 9.6 + - - +
123D VAL* 3.1 10.9 + - + +
125D VAL* 1.3 76.2 - - - +
127D LYS* 1.3 64.3 + - - +
129D ALA* 3.1 5.8 + - - +
130D ILE* 3.0 30.9 + - + +
171D LEU* 4.7 8.7 - - + -
179D ILE* 3.8 25.8 - - + -
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Residues in contact with LYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D VAL* 2.8 28.4 + - - +
124D ASN* 3.3 29.7 + - - +
126D VAL* 1.3 70.5 - - - +
128D LYS* 1.3 64.1 + - - +
130D ILE* 3.1 10.1 + - - +
131D LEU* 3.1 19.2 + - - +
176D ASN* 4.8 1.5 + - - +
178D GLY* 3.5 16.7 - - - +
179D ILE* 3.9 17.0 - - + +
182D HIS* 3.5 38.7 - - + +
167E ASP* 4.2 9.9 + - - -
169E GLU* 2.8 48.7 + - - +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LYS* 3.7 43.1 - - + +
93D ILE* 3.9 17.5 - - + -
94D GLY* 4.0 18.0 - - - +
97D GLU* 4.0 17.2 + - - -
124D ASN 3.0 18.9 + - - +
125D VAL 3.6 4.5 - - - +
127D LYS* 1.3 76.9 - - - +
129D ALA* 1.3 62.7 + - - +
131D LEU* 3.2 18.8 + - + +
132D THR* 2.9 27.8 + - - -
132E GLN* 6.1 1.3 - - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.7 19.7 - - + +
114D LEU* 4.6 8.8 - - + +
117D LEU* 4.1 0.9 - - + -
118D LEU* 3.7 38.8 - - + +
125D VAL 3.0 12.1 + - - +
126D VAL 3.1 9.2 + - - +
128D LYS* 1.3 74.6 - - - +
130D ILE* 1.3 57.7 + - - +
132D THR* 3.3 3.3 + - - +
133D MET* 3.0 31.9 + - - +
164D MET* 5.1 0.7 - - + -
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D LEU* 3.7 14.8 - - + -
126D VAL* 3.0 22.2 + - + +
127D LYS* 3.1 8.5 + - - +
129D ALA* 1.3 76.5 - - - +
131D LEU* 1.3 57.7 + - + +
133D MET* 3.4 3.5 + - - +
134D THR* 2.8 30.3 + - - +
168D ILE* 3.9 19.5 - - + -
171D LEU* 4.1 20.6 - - + -
179D ILE* 4.1 15.7 - - + +
182D HIS* 3.5 44.2 - - + +
183D ALA* 4.2 2.7 - - - +
186D PHE* 3.8 15.2 - - + -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLU* 4.7 1.5 - - - +
127D LYS 3.1 16.5 + - - +
128D LYS* 3.2 19.9 + - + +
130D ILE* 1.3 73.2 - - - +
132D THR* 1.3 66.0 + - - +
134D THR* 3.2 16.2 + - - +
135D GLN* 3.5 15.8 + - - +
182D HIS* 3.7 31.2 - - + +
185D LYS* 5.3 4.9 - - + -
130E THR* 3.4 25.8 - - + +
131E CYS* 3.6 21.5 - - + +
132E GLN* 4.0 32.5 - - + +
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Residues in contact with THR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ILE* 3.2 26.7 + - + +
97D GLU* 2.9 41.1 + - + +
114D LEU* 4.0 18.4 - - + -
128D LYS* 2.9 14.6 + - - -
129D ALA 3.3 7.4 + - - -
131D LEU* 1.3 77.7 - - - +
133D MET* 1.3 57.7 + - - +
135D GLN* 3.2 5.2 + - - +
136D LEU* 3.0 41.8 + - + +
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Residues in contact with MET 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 6.4 0.2 - - - -
111D ILE* 5.0 2.7 - - - -
114D LEU* 4.3 19.1 - - + -
129D ALA 3.0 17.4 + - - +
130D ILE 3.7 5.8 - - - +
131D LEU 3.3 0.2 - - - -
132D THR* 1.3 74.5 - - - +
134D THR* 1.3 60.3 + - - +
135D GLN 3.2 0.2 - - - -
136D LEU* 3.8 8.3 - - - +
137D TYR* 3.0 43.6 + - + +
161D VAL* 3.9 37.9 - - + +
164D MET* 3.5 44.2 - - + +
165D ALA 4.8 2.7 - - - +
168D ILE* 3.8 18.8 - - + -
186D PHE* 3.4 8.6 - - + -
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Residues in contact with THR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ILE* 2.8 19.3 + - - +
131D LEU* 3.5 16.7 - - - +
132D THR 3.1 0.6 - - - -
133D MET* 1.3 78.8 - - - +
135D GLN* 1.3 67.7 + - - +
137D TYR* 4.8 1.4 + - - +
138D LYS* 4.1 18.8 + - - +
182D HIS 5.1 0.3 + - - -
185D LYS* 4.3 16.7 - - + +
186D PHE* 3.2 29.4 + - + +
189D GLY* 5.2 8.5 - - - -
130E THR 5.4 0.2 - - - -
131E CYS* 4.3 22.7 - - + -
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Residues in contact with GLN 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLU* 3.2 29.4 - - + +
101D LYS* 3.5 26.8 + - - +
131D LEU 3.5 7.0 + - - +
132D THR 3.2 8.1 + - - +
134D THR* 1.3 89.4 + - - +
136D LEU* 1.3 62.5 + - - +
137D TYR 3.5 0.2 - - - -
138D LYS* 3.4 32.3 + - - +
139D VAL* 3.3 20.5 - - - +
206D ARG* 5.2 4.7 + - - -
129E GLU 3.1 27.6 + - - +
130E THR* 4.3 11.4 + - - +
131E CYS* 5.5 2.0 - - - -
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ILE* 4.4 0.7 - - + -
97D GLU* 3.8 29.2 - - + +
100D CYS* 3.9 31.2 - - + -
101D LYS* 4.3 14.8 - - + +
104D ILE* 5.1 2.5 - - + +
107D LEU* 4.5 12.1 - - + -
114D LEU* 3.7 28.7 - - + -
132D THR* 3.0 31.8 + - + +
133D MET* 3.6 9.6 + - + -
135D GLN* 1.3 73.9 - - - +
137D TYR* 1.3 56.6 + - - +
139D VAL* 2.9 10.0 + - + +
140D ALA* 2.7 36.4 + - - +
161D VAL* 5.5 1.1 - - + -
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D MET* 3.0 25.3 + - + +
134D THR 5.1 1.8 - - - +
136D LEU* 1.3 76.4 - - - +
138D LYS* 1.3 66.3 + - + +
140D ALA* 3.3 3.6 + - - +
141D LEU* 3.0 39.9 + - + +
158D TRP* 3.8 26.8 - + - -
161D VAL* 3.7 25.4 - - + -
162D SER* 4.4 7.8 + - - -
165D ALA* 3.8 30.1 - - + -
186D PHE* 4.2 9.6 - + + -
190D LEU* 3.4 24.1 - - + +
193D THR* 4.5 7.0 - - + -
194D LEU* 3.7 27.6 - - + +
228D LEU* 4.3 4.2 - - - +
231D GLU* 4.7 3.6 + - - -
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Residues in contact with LYS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 4.1 15.2 + - - +
135D GLN* 3.4 37.3 + - - +
137D TYR* 1.3 81.2 - - + +
139D VAL* 1.3 66.6 + - + +
141D LEU* 4.3 4.5 - - - +
142D GLN* 3.1 24.3 + - - +
193D THR* 4.3 22.2 - - + +
207D GLN* 4.6 8.5 + - - +
210D ASP* 2.9 38.2 + - + +
211D ILE* 3.7 20.0 + - + +
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D CYS 4.8 5.8 - - - +
101D LYS* 4.7 24.5 - - + +
104D ILE* 3.8 24.9 - - + -
135D GLN 3.3 18.8 - - - +
136D LEU* 2.9 12.1 + - + +
138D LYS* 1.3 80.0 - - + +
140D ALA* 1.3 67.1 + - - +
142D GLN* 3.4 13.7 + - - +
143D TRP* 3.1 21.1 + - - +
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ILE* 4.2 11.7 - - - +
107D LEU* 3.9 24.0 - - + -
136D LEU 2.7 19.0 + - - +
137D TYR 3.6 4.0 - - - +
139D VAL* 1.3 74.3 - - - +
141D LEU* 1.3 62.3 + - - +
143D TRP* 3.3 7.0 + - + +
144D MET* 2.9 27.1 + - + +
157D CYS* 6.1 0.2 - - - -
158D TRP* 4.0 17.9 - - + -
161D VAL* 4.1 9.6 - - + -
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Residues in contact with LEU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D TYR* 3.0 21.0 + - + +
138D LYS* 4.0 5.6 - - - +
139D VAL 3.3 0.4 - - - -
140D ALA* 1.3 75.6 - - - +
142D GLN* 1.3 57.7 + - - +
144D MET* 3.3 2.2 + - - -
145D VAL* 2.9 50.4 + - + +
158D TRP* 3.7 30.5 - - + -
193D THR* 4.0 17.5 - - + +
194D LEU* 3.9 26.9 - - + -
211D ILE* 4.2 8.5 - - + -
212D SER 6.2 0.2 - - - -
216D ILE* 4.5 7.6 - - + -
223D ILE* 4.0 22.7 - - + -
228D LEU* 4.1 9.2 - - + -
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Residues in contact with GLN 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LYS 3.1 17.8 + - - +
139D VAL* 3.6 13.0 - - - +
141D LEU* 1.3 77.3 - - - +
143D TRP* 1.3 62.1 + - - +
145D VAL* 3.3 1.2 + - - +
146D LYS* 3.0 56.1 + - + +
209D HIS 3.4 22.9 + - - +
210D ASP* 5.5 1.6 - - - +
211D ILE* 4.2 32.0 + - + +
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Residues in contact with TRP 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ILE* 3.5 47.8 - - + +
105D GLU* 3.5 35.4 - - + +
107D LEU* 5.1 0.9 - - + -
108D LEU* 3.9 23.8 - - + -
139D VAL 3.1 13.5 + - - +
140D ALA* 3.3 14.3 + - + +
142D GLN* 1.3 77.5 - - - +
144D MET* 1.3 61.2 + - - +
146D LYS* 3.9 5.3 - - + +
147D SER* 2.6 43.9 + - - -
154D GLN* 3.1 45.8 + - + +
157D CYS* 4.7 11.4 - - - -
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Residues in contact with MET 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D ALA* 2.9 21.6 + - + +
141D LEU* 3.5 7.9 - - - +
143D TRP* 1.3 75.6 - - + +
145D VAL* 1.3 61.6 + - - +
147D SER 3.3 17.3 + - - +
150D ILE* 3.8 30.9 - - + +
154D GLN* 3.4 35.0 - - - +
155D GLU* 4.3 10.8 - - + -
158D TRP* 3.5 50.5 - - + -
220D HIS* 3.3 9.8 + - - -
222D TYR* 4.7 4.7 - - + -
223D ILE* 3.7 22.4 - - + -
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Residues in contact with VAL 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D LEU* 2.9 37.3 + - + +
142D GLN 4.0 2.7 - - - +
144D MET* 1.3 74.5 - - - +
146D LYS* 1.3 62.8 - - + +
147D SER 3.8 0.2 - - - +
148D ARG* 6.0 0.5 - - - +
211D ILE* 4.2 17.5 - - + -
215D ARG 3.9 22.2 - - - +
216D ILE* 3.9 21.8 - - + -
217D PRO* 4.1 16.1 - - + +
220D HIS* 3.2 23.6 + - - +
223D ILE* 4.4 9.6 - - + -
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D GLN* 3.0 46.1 + - + +
143D TRP* 4.1 4.9 - - + +
145D VAL* 1.3 79.9 - - + +
147D SER* 1.3 58.7 + - - +
148D ARG* 3.5 19.5 + - - +
211D ILE* 6.0 2.5 - - + -
----------------------------------------------------------
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D TRP* 2.6 33.6 + - - -
144D MET 3.3 1.0 - - - +
145D VAL 3.3 0.8 - - - -
146D LYS* 1.3 76.6 - - - +
148D ARG* 1.3 68.2 + - - +
149D VAL 4.4 5.6 - - - -
150D ILE* 3.6 28.3 - - - +
154D GLN* 3.5 11.8 + - - -
220D HIS* 3.2 27.0 + - - -
----------------------------------------------------------
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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