Contacts of the helix formed by residues 188 - 215 (chain A) in PDB entry 4WYV
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 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 4.0 30.0 - - + +
186A LEU* 6.1 0.2 - - + -
187A LYS* 1.3 77.7 + - - +
189A ASP* 1.3 63.5 + - - +
190A SER* 2.9 24.2 + - - -
191A LEU* 3.3 22.2 + - + +
192A ARG* 3.0 26.9 + - - +
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Residues in contact with ASP 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LYS 3.2 6.8 - - - +
188A ASN* 1.3 73.7 + - - +
190A SER* 1.3 55.7 - - - +
192A ARG* 2.5 37.8 + - - +
193A LYS* 2.8 36.8 + - - +
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ASN* 2.9 12.4 + - - -
189A ASP* 1.3 76.0 - - - +
191A LEU* 1.3 58.5 + - - +
193A LYS* 3.2 8.5 - - - +
194A ARG* 3.0 37.0 + - - +
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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
----------------------------------------------------------
138A GLU* 4.0 28.9 - - + +
141A LEU* 4.0 25.6 - - + -
142A SER* 3.8 22.7 - - - +
145A LEU* 4.0 20.6 - - + +
181A PHE* 5.4 0.4 - - + -
186A LEU* 3.6 31.4 - - + -
188A ASN* 3.3 21.5 + - + +
189A ASP 3.1 0.4 - - - -
190A SER* 1.3 81.5 - - - +
192A ARG* 1.3 56.8 + - - +
194A ARG* 3.3 3.8 + - + +
195A TYR* 2.9 27.9 + - - +
14E LEU* 5.8 2.0 - - + -
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LEU* 3.5 39.9 + - + +
187A LYS* 3.7 13.3 + - - +
188A ASN 3.0 12.2 + - - +
189A ASP* 2.5 37.6 + - - +
191A LEU* 1.3 72.1 - - - +
193A LYS* 1.3 68.6 + - - +
195A TYR* 3.3 11.0 + - + +
196A ASP* 3.1 28.6 + - - +
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Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASP 2.8 13.0 + - - +
190A SER* 3.2 14.4 - - - +
192A ARG* 1.3 75.3 - - - +
194A ARG* 1.3 59.8 + - - +
196A ASP* 2.9 35.4 + - - +
197A GLY* 3.7 2.4 + - - -
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Residues in contact with ARG 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 3.5 23.4 + - - +
142A SER* 4.1 19.1 + - - -
145A LEU* 3.7 40.0 - - + +
146A ILE* 3.8 25.1 - - - +
190A SER* 3.0 19.2 + - - +
191A LEU* 3.8 4.1 - - + +
193A LYS* 1.3 77.3 - - - +
195A TYR* 1.3 66.1 + - - +
197A GLY* 3.0 15.9 + - - +
198A LEU 3.6 2.8 + - - -
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Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.9 11.8 - - + +
178A ASP* 3.3 17.1 + - - -
181A PHE* 3.2 39.7 - + + -
182A ARG* 3.8 26.7 + - - +
186A LEU* 3.8 22.0 - - + -
191A LEU 2.9 17.7 + - - +
192A ARG* 3.5 9.6 - - + +
193A LYS 3.2 0.4 - - - -
194A ARG* 1.3 76.2 - - - +
196A ASP* 1.3 70.0 + - - +
198A LEU* 3.0 33.2 + - + +
199A LYS* 4.1 1.7 + - - +
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Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 3.1 19.5 + - - +
193A LYS* 2.9 21.1 + - - +
195A TYR* 1.3 83.5 - - - +
197A GLY* 1.3 59.9 + - - +
199A LYS* 2.6 43.9 + - - +
200A TYR* 4.0 3.4 - - + -
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Residues in contact with GLY 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS 3.7 2.2 + - - -
194A ARG* 3.0 12.4 + - - -
196A ASP* 1.3 77.2 - - - +
198A LEU* 1.3 64.2 + - - +
200A TYR* 3.0 29.6 + - - +
201A ASP* 3.5 9.9 + - - +
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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
----------------------------------------------------------
145A LEU* 3.9 14.6 - - + +
148A ALA* 3.5 31.9 - - + -
174A ILE* 4.2 16.6 - - + -
177A LEU* 4.6 7.0 - - + -
178A ASP* 4.0 17.7 - - - +
181A PHE* 3.7 21.5 - - + -
194A ARG 3.6 3.8 + - - -
195A TYR* 3.0 37.7 + - + +
197A GLY* 1.3 76.3 - - - +
199A LYS* 1.3 56.6 + - - +
201A ASP* 2.9 12.3 + - + +
202A VAL* 2.9 32.7 + - + +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP* 5.8 3.4 - - - +
195A TYR 4.1 2.0 + - - +
196A ASP* 2.6 45.6 + - - +
197A GLY 3.2 1.0 + - - -
198A LEU* 1.3 78.2 - - - +
200A TYR* 1.3 91.0 + - + +
202A VAL* 3.5 10.1 + - - +
203A LYS* 3.0 26.9 + - - +
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Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ASP* 4.0 6.7 - - + -
197A GLY* 3.0 18.9 + - - +
199A LYS* 1.3 109.7 + - + +
201A ASP* 1.3 61.5 + - - +
203A LYS* 3.3 15.8 + - + +
204A LYS* 3.0 29.6 + - - +
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Residues in contact with ASP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 4.7 0.3 - - - +
148A ALA* 3.8 10.8 - - - +
149A SER* 3.1 38.7 + - - -
152A SER* 3.2 26.6 + - - -
174A ILE* 4.4 8.5 - - + -
197A GLY 3.5 6.2 + - - +
198A LEU* 2.9 23.3 + - + +
200A TYR* 1.3 76.1 - - - +
202A VAL* 1.3 65.6 + - - +
204A LYS* 3.4 2.6 + - - +
205A VAL* 3.2 27.5 + - - +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 3.6 24.5 - - + +
175A ASN* 3.7 25.1 - - - +
178A ASP* 4.0 30.1 - - + +
198A LEU* 2.9 22.2 + - + +
199A LYS* 3.6 9.6 - - - +
201A ASP* 1.3 77.2 - - - +
203A LYS* 1.3 63.3 + - - +
205A VAL* 3.3 3.0 + - - +
206A GLU* 3.1 30.4 + - + +
153D ARG* 3.8 16.6 - - - +
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Residues in contact with LYS 203 (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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199A LYS 3.0 18.0 + - - +
200A TYR* 3.6 17.9 - - + +
201A ASP 3.3 0.2 - - - -
202A VAL* 1.3 77.4 - - - +
204A LYS* 1.3 64.1 + - - +
206A GLU* 3.3 8.8 + - - +
207A GLU* 2.6 58.7 + - + +
204D LYS* 4.4 4.1 - - - +
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER* 3.8 33.9 + - - +
153A ARG* 4.6 9.3 - - - +
156A VAL* 3.9 22.2 - - + +
200A TYR 3.0 17.3 + - - +
201A ASP* 3.8 6.1 - - - +
203A LYS* 1.3 78.6 - - - +
205A VAL* 1.3 58.0 + - - +
207A GLU* 3.4 10.3 + - - +
208A VAL* 3.0 31.4 + - + +
203B LYS* 3.9 20.9 - - - +
207B GLU* 3.6 24.7 + - - +
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER* 3.6 31.4 - - - +
155A SER* 4.0 13.7 - - - +
167A PRO 4.2 4.5 - - - +
170A ILE* 4.0 10.3 - - + +
171A SER* 3.2 40.4 - - - +
174A ILE* 4.4 6.7 - - + -
201A ASP 3.2 16.6 + - - +
202A VAL* 3.9 4.7 - - - +
203A LYS 3.2 0.4 - - - -
204A LYS* 1.3 77.9 - - + +
206A GLU* 1.3 65.2 + - + +
208A VAL* 3.4 8.0 + - - +
209A VAL* 3.3 22.9 + - - +
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER* 4.0 9.9 - - - +
175A ASN* 3.4 22.0 + - - +
202A VAL* 3.1 24.6 + - - +
203A LYS* 3.8 7.6 - - - +
205A VAL* 1.3 78.7 - - + +
207A GLU* 1.3 58.8 - - + +
209A VAL* 3.4 5.4 + - - +
210A TYR* 3.1 26.0 + - - +
46D HIS* 4.6 3.1 - - - +
47D GLN* 5.0 1.4 + - - -
153D ARG* 2.9 48.0 + - - +
156D VAL* 4.4 5.5 - - + +
157D ASN* 3.3 35.6 + - - +
160D THR* 4.6 2.3 + - - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS* 2.6 57.2 + - + +
204A LYS* 3.7 8.4 - - - +
206A GLU* 1.3 78.0 - - + +
208A VAL* 1.3 64.2 + - - +
210A TYR* 3.4 9.5 + - + +
211A ASP* 3.0 31.3 + - - +
156D VAL* 4.6 12.5 - - + +
204D LYS* 2.6 29.8 + - - +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER 5.6 0.2 - - - +
155A SER* 3.7 23.8 - - - +
156A VAL* 4.0 24.9 - - + -
159A VAL* 3.9 21.1 - - + -
167A PRO* 3.8 17.3 - - + -
204A LYS* 3.0 21.3 + - + +
205A VAL* 3.7 7.2 - - - +
206A GLU 3.4 0.6 - - - -
207A GLU* 1.3 75.4 - - - +
209A VAL* 1.3 64.1 + - - +
211A ASP* 3.2 5.4 + - - +
212A LEU* 3.1 20.2 + - + +
210B TYR* 3.6 20.2 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A PRO* 3.6 31.0 - - + +
168A LEU* 4.1 21.3 - - + +
171A SER* 3.9 14.1 - - - +
205A VAL 3.3 13.6 + - - +
206A GLU* 3.7 8.3 - - - +
207A GLU 3.2 0.6 - - - -
208A VAL* 1.3 76.4 - - - +
210A TYR* 1.3 52.0 + - - +
212A LEU* 3.1 9.4 + - - +
213A SER* 2.8 39.9 + - - +
160D THR* 3.3 31.6 - - + +
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Residues in contact with TYR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLU 3.1 7.7 + - - +
207A GLU* 3.5 10.5 - - + +
209A VAL* 1.3 75.4 - - - +
211A ASP* 1.3 72.2 + - - +
213A SER* 3.0 3.0 + - - -
214A ILE* 2.8 46.9 + - + +
215A ARG* 6.1 0.2 - - - -
156D VAL* 3.5 42.4 - - + -
159D VAL* 3.8 30.3 - - + -
160D THR* 3.5 12.6 + - - +
204D LYS* 5.6 8.1 - - - -
208D VAL* 3.5 29.3 - - + -
211D ASP* 2.6 39.0 + - - +
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Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.0 19.6 + - - +
208A VAL 3.4 2.7 - - - +
210A TYR* 1.3 89.1 - - - +
212A LEU* 1.3 63.0 + - + +
214A ILE* 3.7 1.6 - - - +
215A ARG* 3.4 39.9 + - - +
210B TYR* 2.6 38.6 + - - +
214B ILE* 3.6 19.4 - - + +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A VAL* 4.0 30.7 - - + -
164A TYR* 3.6 49.1 - - + +
167A PRO* 4.0 17.9 - - + -
168A LEU* 4.0 11.0 - - + -
208A VAL* 3.1 14.0 + - + +
209A VAL* 3.1 7.2 + - - +
211A ASP* 1.3 78.3 - - + +
213A SER* 1.3 65.9 + - - +
215A ARG 3.2 2.6 + - - -
216A GLY 3.2 15.4 + - - -
217A PHE* 3.5 37.1 + - + +
210B TYR* 5.5 0.9 - - - +
214B ILE* 5.6 4.9 - - + -
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Residues in contact with SER 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL* 2.8 22.3 + - - +
210A TYR* 3.0 3.1 + - - -
212A LEU* 1.3 73.7 - - - +
214A ILE* 1.3 62.4 + - - +
215A ARG 3.1 0.2 - - - -
216A GLY* 3.1 13.4 + - - +
217A PHE 4.8 7.0 - - - +
159D VAL* 4.5 7.0 - - - -
160D THR* 3.6 40.9 + - - +
164D TYR* 4.8 9.6 + - - -
215D ARG* 6.0 0.2 - - - -
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 2.8 56.4 + - + +
211A ASP* 3.7 10.5 - - - +
213A SER* 1.3 76.8 - - - +
215A ARG* 1.3 75.9 + - + +
216A GLY 3.5 0.2 - - - -
159D VAL* 4.1 11.2 - - + -
164D TYR* 6.0 0.9 - - - -
211D ASP* 3.4 26.7 - - + +
212D LEU* 3.9 22.2 - - + +
215D ARG* 4.0 33.7 - - + +
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Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ASP* 3.4 33.4 + - - +
212A LEU* 3.2 4.1 + - - +
213A SER 3.1 0.4 - - - -
214A ILE* 1.3 89.0 - - + +
216A GLY* 1.3 65.1 + - - +
217A PHE* 4.0 18.3 - - + -
214B ILE* 3.3 55.9 + - - +
215B ARG* 4.1 30.7 - - - +
216C GLY 5.5 7.3 - - - -
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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