Contacts of the helix formed by residues 153 - 183 (chain A) in PDB entry 4IKV
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 ARG 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 2.6 43.8 + - - +
16A ARG* 4.7 2.8 - - - +
20A GLY 2.8 27.2 + - - +
21A HIS* 3.4 19.9 - - + +
22A PRO* 3.3 18.3 - - - +
147A TYR* 3.9 11.6 - - + -
151A ASP* 2.9 37.5 + - - +
152A ASP* 1.3 79.4 - - + +
154A ARG* 1.3 66.0 + - - +
155A ASP 3.4 1.6 - - - -
156A ALA* 3.1 8.3 + - - +
157A GLY* 2.9 20.4 + - - -
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Residues in contact with ARG 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY* 2.9 43.9 + - - -
147A TYR* 3.5 36.3 + - + +
148A LYS 5.1 2.4 + - - -
149A PRO* 6.1 0.8 - - - +
151A ASP 3.3 15.0 + - - +
152A ASP 3.3 0.6 - - - -
153A ARG* 1.3 75.8 - - - +
155A ASP* 1.3 72.0 + - - +
157A GLY* 3.1 11.3 + - - -
158A PHE* 3.1 39.9 + - + -
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP 4.9 3.4 + - - +
153A ARG 3.4 0.4 - - - -
154A ARG* 1.3 85.0 - - - +
156A ALA* 1.3 63.4 + - - +
158A PHE* 3.2 10.1 + - - +
159A SER* 3.0 21.7 + - - -
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Residues in contact with ALA 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 3.9 15.3 - - + +
152A ASP 5.3 1.9 + - - +
153A ARG* 3.1 12.7 + - - +
155A ASP* 1.3 78.6 - - - +
157A GLY* 1.3 58.2 + - - +
159A SER* 3.1 9.2 + - - -
160A ILE* 2.9 34.5 + - + +
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Residues in contact with GLY 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 3.4 8.5 - - - -
25A LEU* 3.7 14.0 - - - +
143A VAL* 4.7 3.6 - - - -
147A TYR* 3.5 25.8 - - - -
153A ARG 2.9 10.1 + - - -
154A ARG 3.1 3.1 + - - -
156A ALA* 1.3 77.6 - - - +
158A PHE* 1.3 55.4 + - - +
160A ILE* 3.4 1.4 + - - +
161A PHE* 2.9 28.9 + - - +
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 3.4 22.2 - - - -
141A SER* 5.7 0.2 - - - -
143A VAL* 3.9 15.3 - - + -
144A GLY* 3.6 28.7 - - - -
147A TYR* 5.4 0.7 - + - -
154A ARG* 3.1 55.4 + - + -
155A ASP* 3.6 10.5 - - - +
157A GLY* 1.3 75.6 - - - +
159A SER* 1.3 57.6 + - - +
161A PHE* 3.3 5.0 + + - +
162A TYR* 2.9 70.9 + + + -
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP 3.0 13.0 + - - -
156A ALA* 3.1 13.9 + - - -
158A PHE* 1.3 75.0 - - - +
160A ILE* 1.3 65.9 + - - +
162A TYR* 3.5 5.3 + - - +
163A MET* 3.1 30.4 + - - +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.2 13.5 - - + +
19A PHE* 5.0 15.3 - - + -
21A HIS* 3.5 37.5 - - + +
25A LEU* 4.2 14.1 - - + -
29A PHE* 3.3 27.3 - - + -
156A ALA* 2.9 16.7 + - + +
157A GLY 3.7 4.5 - - - +
159A SER* 1.3 74.7 - - - +
161A PHE* 1.3 65.2 + - - +
163A MET* 3.2 32.0 + - + +
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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
----------------------------------------------------------
25A LEU* 4.1 11.4 - - + +
28A LEU* 3.4 43.3 - - + -
29A PHE* 4.1 13.5 - - - +
32A GLU* 3.5 33.6 - - + +
139A VAL* 3.8 24.0 - - + -
140A SER* 3.4 24.5 - - - -
143A VAL* 4.1 19.1 - - + -
157A GLY 2.9 17.6 + - - +
158A PHE* 3.4 7.6 - + - +
160A ILE* 1.3 76.8 - - - +
162A TYR* 1.3 86.4 + + - +
164A GLY* 3.2 15.1 + - - -
165A ILE 4.4 0.5 + - - -
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A SER* 2.9 35.8 + - - -
158A PHE* 2.9 55.3 + + + +
159A SER* 4.2 4.9 - - - +
161A PHE* 1.3 81.4 - + - +
163A MET* 1.3 59.7 + - - +
164A GLY 3.0 2.2 - - - -
165A ILE* 2.9 52.8 + - + +
166A ASN* 4.0 2.6 + - - +
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Residues in contact with MET 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 4.4 7.0 - - + -
159A SER* 3.1 23.3 + - - +
160A ILE* 3.2 26.9 + - + +
162A TYR* 1.3 76.0 - - - +
164A GLY* 1.3 59.7 + - - +
166A ASN* 3.6 7.3 + - + +
167A LEU* 3.2 25.6 + - + +
347A ILE* 5.8 4.9 - - + +
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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
----------------------------------------------------------
29A PHE* 3.6 24.7 - - - -
32A GLU* 5.2 0.9 - - - -
33A PHE* 3.7 25.7 - - - -
36A ARG* 4.5 1.1 - - - +
161A PHE 3.2 11.5 + - - -
162A TYR 3.0 1.4 - - - -
163A MET* 1.3 77.4 - - - +
165A ILE* 1.3 57.8 + - - +
167A LEU* 3.8 3.8 - - - -
168A GLY* 2.9 24.3 + - - -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.4 25.6 - - + +
36A ARG* 4.0 24.8 - - + +
40A TYR* 4.3 14.5 - - + +
161A PHE 4.4 0.4 + - - -
162A TYR* 2.9 45.3 + - + +
164A GLY* 1.3 76.2 - - - +
166A ASN* 1.3 66.5 + - - +
168A GLY* 3.1 3.3 + - - -
169A ALA* 2.8 26.8 + - + +
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Residues in contact with ASN 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR 4.0 2.2 + - - +
163A MET* 3.6 7.6 + - + +
165A ILE* 1.3 87.9 - - - +
167A LEU* 1.3 58.3 + - - +
169A ALA* 3.7 6.4 - - - +
170A PHE* 2.9 30.3 + - - +
342A ASN* 5.1 1.4 - - - +
343A PRO* 3.5 23.8 - - + +
346A ILE* 3.3 35.4 - - - +
347A ILE* 3.9 23.8 - - + +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 5.4 6.7 - - + -
33A PHE* 3.5 19.1 - - + -
163A MET* 3.2 22.6 + - + +
164A GLY* 3.8 7.0 - - - +
165A ILE 3.2 0.8 - - - -
166A ASN* 1.3 76.2 - - - +
168A GLY* 1.3 57.9 + - - +
170A PHE* 3.3 8.0 + - + +
171A LEU* 3.0 69.5 + - + +
347A ILE* 4.5 14.1 - - + +
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Residues in contact with GLY 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.7 17.0 - - - -
36A ARG* 4.6 0.4 - - - -
37A PHE* 4.1 22.2 - - - -
40A TYR* 4.4 2.2 - - - -
164A GLY 2.9 15.1 + - - -
165A ILE 3.6 2.5 - - - -
167A LEU* 1.3 75.2 - - - +
169A ALA* 1.3 63.2 + - - +
171A LEU 4.7 0.2 - - - -
172A ALA* 3.0 31.4 + - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 3.5 37.7 - - + +
165A ILE* 2.8 17.2 + - + +
166A ASN* 4.1 5.4 - - - +
168A GLY* 1.3 75.6 - - - +
170A PHE* 1.3 58.1 + - - +
173A PRO* 3.1 24.6 - - - +
339A GLN 4.0 2.8 - - - +
340A SER* 4.3 0.2 - - - -
343A PRO* 3.6 28.7 - - + +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASN 2.9 18.2 + - - +
167A LEU* 3.7 11.2 - - + +
169A ALA* 1.3 77.8 - - - +
171A LEU* 1.3 89.0 + - + +
172A ALA 3.7 0.2 + - - -
174A LEU* 3.7 25.4 - - + +
340A SER* 2.7 45.5 + - - -
343A PRO* 3.7 10.8 - - + -
344A LEU* 3.9 35.9 - - + -
347A ILE* 4.6 8.1 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.2 12.1 - - + -
37A PHE* 4.1 13.2 - - + -
167A LEU* 3.0 43.2 + - + +
170A PHE* 1.3 102.5 - - + +
172A ALA* 1.3 66.3 + - - +
174A LEU* 3.1 11.8 + - + +
175A VAL* 3.0 29.8 + - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.0 46.8 - - + +
40A TYR 4.0 1.6 - - - -
41A GLY* 3.3 17.3 - - - +
168A GLY 3.0 18.9 + - - +
171A LEU* 1.3 77.2 - - - +
173A PRO* 1.4 60.6 - - + +
176A VAL* 2.6 36.4 + - - +
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 4.5 6.3 - - + +
44A ALA* 4.0 16.2 - - + -
169A ALA 3.1 26.2 - - - +
170A PHE 3.7 4.9 - - - +
172A ALA* 1.4 90.3 - - + +
174A LEU* 1.3 56.2 + - - +
177A GLY* 2.9 28.9 - - - +
336A ALA* 3.5 21.9 - - - +
337A TRP* 3.4 12.5 - - - -
339A GLN* 3.7 21.1 - - + -
340A SER* 3.4 15.3 - - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PHE* 3.7 41.5 - - + +
171A LEU* 3.1 12.7 + - + +
173A PRO* 1.3 76.7 - - - +
175A VAL* 1.3 62.3 + - + +
178A THR* 2.6 25.9 + - - -
337A TRP* 4.0 32.3 - - + +
340A SER* 3.5 16.8 - - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.9 27.1 - - + -
171A LEU* 3.0 23.5 + - + +
174A LEU* 1.3 81.9 - - + +
176A VAL* 1.3 69.7 + - + +
177A GLY 3.3 0.2 - - - -
178A THR* 3.4 3.0 + - - -
179A ALA* 3.1 23.0 + - - +
191A LEU* 4.6 13.9 - - + +
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Residues in contact with VAL 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.8 29.2 - - + -
41A GLY* 3.3 36.1 - - - +
42A MET* 4.3 1.1 - - - +
45A ILE* 4.0 7.2 - - + +
172A ALA 2.6 16.6 + - - +
175A VAL* 1.3 74.3 - - + +
177A GLY* 1.3 57.9 + - - +
179A ALA* 3.4 5.3 + - - +
180A GLY* 2.8 28.4 + - - -
188A GLY* 3.3 31.1 - - - +
191A LEU* 4.1 12.3 - - + -
192A ALA* 4.2 8.1 - - + +
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Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 5.0 0.6 + - - -
44A ALA* 5.1 0.9 - - - -
45A ILE* 3.7 17.7 - - - -
172A ALA 3.4 2.0 + - - -
173A PRO* 2.9 21.7 + - - +
176A VAL* 1.3 80.3 - - - +
178A THR* 1.3 60.7 + - - +
181A MET* 3.0 31.3 + - - +
334A SER* 3.9 1.9 + - - -
336A ALA* 3.9 8.5 - - - -
337A TRP* 4.4 4.3 - - - -
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PRO 3.5 3.8 + - - -
174A LEU 2.6 24.5 + - - -
175A VAL* 3.4 3.9 + - - -
176A VAL 3.3 0.4 - - - -
177A GLY* 1.3 75.7 - - - +
179A ALA* 1.3 58.3 + - - +
182A LYS* 2.8 52.0 + - + +
183A TYR* 3.7 13.4 - - + -
334A SER* 5.2 0.4 - - - -
337A TRP* 3.1 28.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL 3.1 10.0 + - - +
176A VAL 3.8 3.1 - - - +
178A THR* 1.3 81.4 - - - +
180A GLY* 1.3 62.2 + - - +
183A TYR* 3.1 22.0 + - - +
184A ASN 3.0 22.1 + - - +
187A LEU* 4.2 15.8 - - + +
188A GLY* 4.2 2.5 - - - -
191A LEU* 3.5 31.4 - - + -
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.1 7.9 - - - -
176A VAL 2.8 20.6 + - - -
179A ALA* 1.3 73.2 - - - +
181A MET* 1.3 65.1 + - - +
184A ASN* 3.2 31.3 + - - -
185A PHE* 3.2 17.4 + - - -
188A GLY* 3.8 10.7 - - - -
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.8 14.1 - - + -
48A TYR* 3.6 30.7 - - + -
52A TYR* 3.5 37.7 - - + +
177A GLY 3.0 20.3 + - - +
178A THR 4.6 0.2 - - - +
180A GLY* 1.3 79.2 - - - +
182A LYS* 1.3 65.2 + - + +
183A TYR 3.6 0.9 + - - -
185A PHE* 3.5 25.4 - - + -
334A SER* 3.4 22.9 - - - +
335A PRO* 4.6 9.0 - - + -
336A ALA* 4.0 7.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 2.8 36.6 + - + +
181A MET* 1.3 75.5 - - + +
183A TYR* 1.3 81.6 + - + +
332A HIS* 2.6 43.9 + - + +
334A SER* 3.7 25.6 - - - +
337A TRP* 3.7 17.7 - - - -
----------------------------------------------------------
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 3.7 21.5 - - + +
179A ALA* 3.1 14.3 + - - +
180A GLY 4.4 0.4 - - - -
181A MET 5.0 0.9 - - - -
182A LYS* 1.3 102.5 - - + +
184A ASN* 1.3 67.2 + - + +
187A LEU* 4.1 16.4 - - + -
----------------------------------------------------------
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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