Contacts of the helix formed by residues 184 - 212 (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 ASN 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLY* 6.2 1.6 - - - -
179A ALA 3.0 4.9 + - - -
180A GLY* 3.2 11.6 + - - -
183A TYR* 1.3 81.8 + - + +
185A PHE* 1.3 65.9 + - - +
186A HIS* 2.9 33.6 + - - +
187A LEU* 3.0 22.0 + - + +
188A GLY 3.2 15.9 + - - -
607A OLA 3.2 35.4 + - + +
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Residues in contact with PHE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.8 18.5 - - + +
48A TYR 3.9 1.3 - - - -
49A TYR* 3.5 56.3 - + + -
52A TYR* 3.8 24.5 - + + -
56A LYS 3.8 18.6 - - - -
57A GLY* 3.4 26.9 - - - +
58A GLY 4.1 2.2 - - - -
180A GLY* 3.2 12.8 + - - -
181A MET* 3.5 29.6 - - + -
184A ASN* 1.3 73.8 - - - +
186A HIS* 1.3 60.0 + - + +
188A GLY* 2.9 5.2 + - - -
189A PHE* 2.9 33.9 + + + -
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Residues in contact with HIS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.3 33.4 + + - -
57A GLY* 5.0 4.2 + - - -
112A LEU 2.7 28.0 + - - -
113A ALA* 3.3 18.3 - - - +
114A ILE 3.4 17.3 + - - -
115A PRO* 4.2 9.8 - - + +
116A GLY 4.2 7.2 + - - -
184A ASN* 2.9 11.4 + - - +
185A PHE* 1.3 78.3 - - + +
187A LEU* 1.3 57.8 + - - +
189A PHE* 3.4 2.2 + - - -
190A GLY* 2.8 27.0 + - - -
607A OLA 3.6 41.7 - - + +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ALA* 4.2 17.3 - - + -
183A TYR* 4.1 24.9 - - + -
184A ASN* 3.0 25.2 + - + +
186A HIS* 1.3 76.3 - - - +
188A GLY* 1.3 62.4 + - - +
190A GLY* 3.1 1.4 + - - -
191A LEU* 3.0 34.3 + - + +
607A OLA 3.7 35.7 - - + +
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Residues in contact with GLY 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 4.0 5.4 - - - -
176A VAL* 3.3 23.5 - - - +
179A ALA* 4.2 4.3 - - - -
180A GLY* 3.8 21.9 - - - -
184A ASN 3.2 4.4 + - - -
185A PHE 2.9 8.0 + - - -
187A LEU* 1.3 79.0 - - - +
189A PHE* 1.3 60.6 + - - +
191A LEU* 3.2 12.3 + - - +
192A ALA 3.2 8.8 + - - -
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 4.0 19.1 - - + -
45A ILE* 3.7 25.5 - - + +
46A LEU* 4.0 12.8 - - + -
49A TYR* 3.6 53.6 - + + -
109A HIS* 4.0 7.6 - - - +
112A LEU* 3.6 59.0 - - + -
113A ALA* 3.9 3.1 - - - +
176A VAL* 5.2 0.2 - - - -
185A PHE* 2.9 30.4 + - + -
186A HIS* 3.9 2.7 - - - +
188A GLY* 1.3 75.1 - - - +
190A GLY* 1.3 62.4 + - - +
192A ALA* 3.3 8.8 + - + +
193A ALA* 3.0 20.6 + - - +
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 3.6 16.4 - - - +
186A HIS 2.8 18.1 + - - -
187A LEU 3.1 2.7 + - - -
189A PHE* 1.3 77.5 - - - +
191A LEU* 1.3 55.2 + - - +
193A ALA* 3.1 6.9 + - - +
194A VAL* 2.9 33.8 + - - +
606A OLA 4.4 1.8 - - - +
607A OLA 4.1 16.6 - - - -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.4 5.9 - - + -
175A VAL* 4.6 18.2 - - + +
176A VAL* 4.1 12.6 - - + -
179A ALA* 3.5 31.9 - - + -
187A LEU* 3.0 28.4 + - + +
188A GLY* 3.2 6.9 + - - +
190A GLY* 1.3 75.6 - - - +
192A ALA* 1.3 58.8 + - - +
194A VAL* 3.3 13.4 + - + +
195A GLY* 2.9 25.6 + - - -
607A OLA 5.2 4.3 - - + -
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Residues in contact with ALA 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 5.0 1.3 - - - -
38A SER* 2.2 57.4 + - - +
42A MET* 4.5 10.8 - - + +
109A HIS* 3.7 14.8 - - + +
176A VAL* 4.2 8.3 - - + +
188A GLY 3.2 11.2 + - - +
189A PHE* 3.5 12.3 - - - +
191A LEU* 1.3 78.0 - - - +
193A ALA* 1.3 61.4 + - - +
195A GLY 3.3 0.2 + - - -
196A MET* 3.0 6.4 + - - +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 3.9 6.7 - - - +
109A HIS* 3.6 25.7 - - + +
110A ILE* 4.1 13.9 - - + +
189A PHE 3.0 10.0 + - - +
190A GLY* 3.3 11.2 - - - +
192A ALA* 1.3 74.3 - - - +
194A VAL* 1.3 60.5 + - - +
196A MET* 3.3 4.5 + - - +
197A PHE* 2.9 27.5 + - - +
606A OLA 3.8 24.2 - - + -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A GLY 2.9 21.2 + - - +
191A LEU* 3.3 16.1 + - + +
193A ALA* 1.3 72.1 - - - +
195A GLY* 1.3 61.4 + - - +
197A PHE* 3.2 13.4 + - + +
198A LEU* 2.9 50.7 + - + +
606A OLA 3.7 22.0 - - + -
607A OLA 5.4 5.2 - - + -
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.2 38.9 - - - +
37A PHE* 4.7 2.2 - - - -
38A SER* 3.5 7.6 - - - -
191A LEU 2.9 14.7 + - - -
192A ALA 3.6 4.0 - - - -
193A ALA 3.2 0.4 - - - -
194A VAL* 1.3 76.9 - - - +
196A MET* 1.3 61.0 + - - +
198A LEU* 3.1 5.6 + - - +
199A GLY 3.1 16.3 + - - -
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Residues in contact with MET 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 4.7 5.6 - - + +
34A TRP* 4.4 2.5 - - - -
35A GLU* 3.7 36.3 - - + -
38A SER* 3.0 14.6 + - - +
102A GLY* 3.8 34.1 - - - +
105A ILE* 3.8 18.6 - - + -
106A MET* 3.8 20.4 - - + +
109A HIS* 4.3 3.8 - - + -
135A LEU* 4.4 7.0 - - + -
192A ALA 3.0 8.3 + - - +
193A ALA 3.8 6.7 - - - +
195A GLY* 1.3 74.0 - - - +
197A PHE* 1.3 56.9 + - - +
199A GLY* 3.2 7.8 + - - -
200A LEU* 2.9 41.1 + - + +
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Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 3.9 27.0 - - + +
193A ALA 2.9 15.3 + - - +
194A VAL* 3.3 18.8 - - + +
196A MET* 1.3 76.6 - - - +
198A LEU* 1.3 68.8 + - + +
200A LEU* 3.2 6.5 + - + +
201A VAL* 2.9 58.0 + - + +
606A OLA 4.1 18.6 - - + -
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.7 46.4 - - + +
194A VAL* 2.9 33.0 + - + +
195A GLY* 3.1 6.3 + - - +
197A PHE* 1.3 87.3 - - + +
199A GLY* 1.3 64.2 + - - +
201A VAL* 3.3 7.4 + - + +
202A VAL* 3.1 30.6 + - + +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE 5.0 0.2 - - - -
31A THR* 3.7 18.6 + - - -
34A TRP* 3.8 24.1 - - - +
195A GLY 3.1 10.5 + - - -
196A MET* 3.2 11.4 + - - -
198A LEU* 1.3 77.2 - - - +
200A LEU* 1.3 61.4 + - - +
202A VAL* 3.9 2.1 - - - +
203A PHE* 3.0 23.8 + - - +
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 5.8 0.4 - - + -
98A VAL 5.0 0.9 - - - +
99A PHE* 3.9 41.7 - - + +
102A GLY* 3.6 30.7 - - - +
103A LEU* 3.6 24.0 - - + +
106A MET* 4.0 22.0 - - + -
196A MET* 2.9 18.1 + - + +
197A PHE* 3.6 9.9 - - + +
199A GLY* 1.3 74.1 - - - +
201A VAL* 1.3 56.0 + - + +
203A PHE* 3.3 8.6 + - + +
204A VAL* 2.8 42.1 + - + +
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 2.9 56.6 + - + +
198A LEU* 3.6 9.6 - - + +
200A LEU* 1.3 76.1 - - + +
202A VAL* 1.3 61.0 + - + +
204A VAL* 4.1 3.7 - - - +
205A ALA* 2.8 42.1 + - + +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.8 32.3 - - + -
27A THR* 4.4 14.8 - - - +
30A PHE* 4.7 14.4 - - + -
31A THR* 5.0 1.3 - - - +
34A TRP* 5.5 4.5 - - + +
198A LEU* 3.1 18.8 + - + +
199A GLY* 3.9 4.3 - - - +
201A VAL* 1.3 76.3 - - + +
203A PHE* 1.3 62.0 + - - +
205A ALA* 4.7 2.9 - - - -
206A THR* 2.5 44.9 + - + +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 4.1 13.7 - - + -
28A LEU* 4.3 10.1 - - + -
31A THR* 3.5 32.7 + - + +
95A SER* 3.6 39.9 - - - -
98A VAL* 3.9 18.2 - - + -
99A PHE* 4.1 24.9 - + + -
142A ILE* 4.5 3.1 - - + -
199A GLY 3.0 13.4 + - - +
200A LEU* 3.5 9.6 - - + +
202A VAL* 1.3 77.2 - - - +
204A VAL* 1.3 60.8 + - + +
207A ARG* 2.9 55.8 + - + +
211A LEU* 4.2 18.6 - - + -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 3.5 38.4 - - + -
200A LEU* 2.8 27.4 + - + +
201A VAL* 4.1 3.8 - - - +
203A PHE* 1.3 74.7 - - + +
205A ALA* 1.3 64.1 + - - +
206A THR 3.3 0.5 + - - -
207A ARG* 4.0 27.4 + - - +
208A LYS* 5.0 2.6 + - - +
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Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A VAL* 2.8 30.2 + - + +
202A VAL* 4.7 1.1 - - - -
204A VAL* 1.3 76.3 - - + +
206A THR* 1.3 68.7 + - + +
208A LYS* 5.3 2.2 + - - +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 5.2 6.1 - - + -
27A THR* 2.8 21.7 + - - +
202A VAL* 2.5 33.5 + - + +
205A ALA* 1.3 88.0 - - + +
207A ARG* 1.3 67.0 + - - +
208A LYS 3.2 3.7 + - - -
209A LYS* 3.5 4.9 + - - +
210A ASN* 3.0 41.9 + - - +
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 4.7 0.4 - - - -
95A SER* 3.9 20.7 + - - +
96A ARG* 4.9 9.1 - - - +
99A PHE* 3.8 33.3 - - - +
203A PHE* 2.9 43.5 + - + +
204A VAL* 4.0 29.8 + - - +
205A ALA 3.8 0.6 - - - -
206A THR* 1.3 78.9 + - - +
208A LYS* 1.3 66.6 + - - +
211A LEU* 2.9 55.0 + - + +
212A GLY 3.5 3.2 + - - +
216A THR* 6.1 4.0 - - + -
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL 5.0 3.2 + - - +
205A ALA 5.3 1.8 + - - +
206A THR 3.2 1.0 + - - -
207A ARG* 1.3 87.7 - - + +
209A LYS* 1.3 61.7 + - - +
212A GLY* 3.3 22.8 + - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER 4.6 1.7 - - - +
14A PRO* 3.2 27.6 - - + +
23A LYS* 3.1 31.9 - - - +
206A THR* 3.5 5.8 + - - +
208A LYS* 1.3 80.5 - - - +
210A ASN* 1.3 75.5 + - - +
212A GLY* 4.3 1.6 + - - -
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Residues in contact with ASN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.3 23.2 - - - +
14A PRO* 3.5 9.5 - - - +
23A LYS* 3.6 30.9 + - - +
24A GLY* 3.8 18.0 + - - +
26A PHE* 4.6 6.7 - - - -
27A THR* 2.9 26.1 + - - +
206A THR* 3.0 28.3 + - - +
209A LYS* 1.3 97.1 + - - +
211A LEU* 1.3 60.8 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.4 11.3 - - - +
24A GLY* 3.7 26.0 - - - -
27A THR* 4.0 14.4 - - + -
28A LEU* 3.8 32.8 - - + -
95A SER* 5.5 2.2 - - - +
142A ILE* 4.0 13.5 - - + -
146A MET* 3.8 22.4 - - + -
203A PHE* 4.2 7.0 - - + -
207A ARG* 2.9 31.4 + - + +
210A ASN* 1.3 80.0 - - + +
212A GLY* 1.3 67.2 + - - +
213A LEU 3.1 0.5 + - - -
214A ALA* 2.9 31.0 + - + +
216A THR* 6.3 0.2 - - + -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 3.7 20.7 + - - -
207A ARG* 3.5 3.6 + - - +
208A LYS* 3.3 21.7 + - - +
209A LYS 4.3 1.3 + - - -
210A ASN 3.7 1.4 - - - -
211A LEU* 1.3 75.1 - - - +
213A LEU* 1.3 62.8 + - - +
216A THR* 3.4 15.2 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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