Contacts of the helix formed by residues 183 - 212 (chain A) in PDB entry 2YPA
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 HIS 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 1.3 87.7 - - + +
184A THR* 1.3 63.6 + - - +
185A LYS* 3.2 14.2 + - + +
186A VAL* 3.4 26.6 + - + +
187A VAL* 3.4 15.1 + - - +
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO 5.1 3.1 - - - +
183A HIS* 1.3 69.1 - - - +
185A LYS* 1.3 77.2 + - - +
186A VAL 3.1 2.8 + - - -
187A VAL* 3.9 11.1 - - + +
188A ARG* 3.2 44.9 + - - +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A HIS* 3.2 9.6 - - + -
184A THR* 1.3 86.1 + - - +
186A VAL* 1.3 65.4 + - + +
188A ARG* 3.8 32.2 - - - +
189A ARG* 3.5 22.7 + - - +
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 5.7 6.1 - - + -
183A HIS* 3.8 27.4 - - + +
184A THR 3.1 0.6 - - - -
185A LYS* 1.3 79.4 - - + +
187A VAL* 1.3 67.2 + - + +
188A ARG 3.0 2.0 - - - -
189A ARG* 2.9 20.2 + - + +
190A ILE* 2.9 32.6 + - + +
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PRO* 5.1 15.5 - - + +
183A HIS 3.4 17.3 - - - +
184A THR* 3.5 11.6 + - + +
186A VAL* 1.3 76.9 - - + +
188A ARG* 1.3 62.8 + - - +
190A ILE* 3.6 9.9 + - + +
191A PHE* 3.1 26.4 + - + +
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 3.2 46.2 + - - +
185A LYS* 3.8 30.7 - - - +
187A VAL* 1.3 75.8 - - - +
189A ARG* 1.3 56.6 + - + +
191A PHE* 3.0 8.3 + - - +
192A THR* 2.8 42.1 + - - +
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Residues in contact with ARG 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LYS 3.5 15.5 - - - +
186A VAL* 2.9 16.2 + - + +
188A ARG* 1.3 74.6 - - + +
190A ILE* 1.3 55.2 + - + +
192A THR* 3.1 34.0 + - - +
193A ASN* 2.7 65.2 + - - +
10E T 3.6 45.7 + - - +
11E G 3.5 37.1 + - - -
12E T 6.2 0.2 - - - +
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Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 2.9 35.9 + - + +
187A VAL* 3.9 8.7 - - + +
189A ARG* 1.3 77.5 - - + +
191A PHE* 1.3 62.8 + - - +
193A ASN* 3.5 13.2 + - - +
194A SER* 3.1 22.8 + - - -
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Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.1 18.2 + - + +
188A ARG* 3.0 11.1 + - - +
190A ILE* 1.3 78.5 - - - +
192A THR* 1.3 62.7 + - - +
194A SER* 3.3 9.0 + - - -
195A ARG* 3.2 42.4 + - + +
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Residues in contact with THR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ARG* 2.8 21.2 + - - +
189A ARG* 3.4 32.5 + - - +
191A PHE* 1.3 74.8 - - - +
193A ASN* 1.3 65.8 + - - +
195A ARG* 3.1 28.4 + - - +
196A GLU* 3.1 24.1 + - + +
10E T 5.3 3.6 - - + -
11E G 5.8 2.5 - - - +
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Residues in contact with ASN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ARG* 2.7 49.8 + - - +
190A ILE* 3.7 12.5 - - - +
192A THR* 1.3 72.5 - - - +
194A SER* 1.3 63.0 + - - +
196A GLU* 3.4 2.6 + - - +
197A ARG* 3.0 24.3 + - - +
9E C 3.7 38.0 + - - +
10E T 2.9 43.1 + - + +
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Residues in contact with SER 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ILE* 3.1 11.6 + - - -
191A PHE* 3.5 11.4 - - - -
192A THR 3.1 0.8 - - - -
193A ASN* 1.3 79.6 - - - +
195A ARG* 1.3 58.8 + - - +
197A ARG* 3.4 8.2 + - - +
198A TRP* 3.0 27.4 + - - +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 3.2 33.4 + - + +
192A THR* 3.1 34.5 + - - +
194A SER* 1.3 74.9 - - - +
196A GLU* 1.3 58.7 + - - +
198A TRP* 3.1 16.0 + - + +
199A ARG* 2.8 30.3 + - - +
22F G 3.9 40.4 + - - -
23F A 3.0 35.2 + - - -
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A THR* 3.1 14.0 + - + +
193A ASN 3.7 4.0 - - - +
195A ARG* 1.3 79.3 - - - +
197A ARG* 1.3 58.0 + - - +
199A ARG* 3.0 32.6 + - - +
200A GLN* 2.9 53.1 + - + +
9E C 5.0 7.1 + - + +
10E T 3.4 32.1 - - + +
11E G 5.9 0.2 - - - +
24F A 4.1 3.8 - - - +
25F C 3.4 25.0 + - - +
26F A 4.5 1.3 + - - +
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Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASN 3.0 17.2 + - - +
194A SER* 3.7 8.3 - - - +
195A ARG 3.2 0.2 - - - -
196A GLU* 1.3 74.0 - - - +
198A TRP* 1.3 66.7 + - - +
200A GLN* 3.2 7.6 + - + +
201A GLN* 2.9 53.5 + - + +
8E T 2.8 54.4 + - + +
9E C 4.4 12.6 - - - +
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Residues in contact with TRP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A SER 3.0 14.3 + - - +
195A ARG* 3.3 19.7 - - + +
197A ARG* 1.3 76.7 - - - +
199A ARG* 1.3 75.1 + - + +
201A GLN* 3.5 18.5 + - - +
202A ASN* 3.1 49.9 + - - +
23F A 6.0 3.1 - - - -
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Residues in contact with ARG 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ARG* 2.8 14.4 + - - +
196A GLU* 3.0 40.9 + - - +
197A ARG 3.1 0.2 - - - -
198A TRP* 1.3 89.7 - - + +
200A GLN* 1.3 76.6 + - - +
202A ASN* 3.1 16.8 + - + +
203A VAL* 3.2 29.4 + - + +
585B LYS* 6.0 2.0 - - - +
586B LEU* 5.7 5.4 - - + +
23F A 4.2 7.6 - - + -
24F A 3.7 64.7 + - - +
25F C 3.9 23.8 + - - -
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Residues in contact with GLN 200 (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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196A GLU* 2.9 36.8 + - + +
197A ARG* 3.2 11.6 + - + +
199A ARG* 1.3 86.9 - - - +
201A GLN* 1.3 67.0 + - - +
203A VAL* 2.9 23.6 + - - +
204A ASN* 3.0 24.7 - - - +
7E A 6.6 0.2 - - + -
8E T 4.5 29.1 + - + +
9E C 5.5 1.4 - - - +
25F C 5.6 0.4 - - - -
26F A 4.9 10.5 + - - +
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Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 2.9 57.7 + - + +
198A TRP* 3.5 22.1 - - + +
199A ARG 3.4 0.2 - - - -
200A GLN* 1.3 74.0 - - - +
202A ASN* 1.3 60.2 + - - +
204A ASN* 2.9 13.1 + - - +
205A GLY* 2.8 26.0 + - - -
8E T 5.5 3.1 - - - +
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Residues in contact with ASN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 3.1 56.0 + - - +
199A ARG* 3.1 11.7 + - + +
200A GLN 3.1 0.6 - - - -
201A GLN* 1.3 83.4 - - - +
203A VAL* 1.3 61.9 + - - +
205A GLY* 3.4 3.9 + - - +
206A ALA* 3.1 20.1 + - - +
586B LEU* 3.9 18.2 - - + +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ARG* 3.2 27.1 + - + +
200A GLN* 2.9 20.7 + - - +
202A ASN* 1.3 76.6 - - - +
204A ASN* 1.3 61.1 + - - +
206A ALA* 3.0 5.4 + - - +
207A PHE* 2.9 39.7 + - + -
566B PHE* 5.3 1.1 - - + -
585B LYS* 5.1 15.0 - - + -
586B LEU* 4.2 27.1 - - + +
589B LEU* 3.7 19.5 - - + -
25F C 5.9 0.4 - - - +
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Residues in contact with ASN 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLN* 3.0 20.5 - - - +
201A GLN* 2.9 11.3 + - - +
203A VAL* 1.3 78.0 - - - +
205A GLY* 1.3 66.8 + - - +
206A ALA 3.0 1.5 + - - -
207A PHE* 3.0 10.0 + - + +
208A ALA* 2.9 25.4 + - - +
225A LYS* 3.5 22.5 + - - +
7E A 2.9 32.3 + - - -
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Residues in contact with GLY 205 (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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201A GLN 2.8 13.1 + - - -
202A ASN* 3.7 6.3 - - - -
203A VAL 3.4 0.2 - - - -
204A ASN* 1.3 75.3 - - - +
206A ALA* 1.3 55.7 + - - +
208A ALA* 3.4 6.8 + - - +
209A GLU* 3.1 30.7 + - - +
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Residues in contact with ALA 206 (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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202A ASN 3.1 11.6 + - - +
203A VAL 3.0 11.1 + - - +
204A ASN 3.0 0.6 - - - -
205A GLY* 1.3 74.0 - - - +
207A PHE* 1.3 65.0 + - - +
209A GLU* 3.3 9.6 + - - +
210A LEU* 3.1 22.0 + - - +
586B LEU* 4.1 14.8 - - + +
589B LEU* 3.8 32.1 - - + +
590B GLN* 5.2 4.3 - - + -
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A VAL* 2.9 42.0 + - + -
204A ASN* 3.0 8.7 + - + +
206A ALA* 1.3 75.9 - - - +
208A ALA* 1.3 57.1 + - - +
210A LEU* 3.2 7.0 + - - +
211A ARG* 2.8 28.5 + - - +
225A LYS* 3.7 63.0 - - + +
228A ILE* 3.9 33.6 - - + +
229A LEU* 3.8 15.0 - - + -
562B ILE* 5.6 0.4 - - + -
566B PHE* 3.7 27.4 - + - -
589B LEU* 4.0 12.1 - - + +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASN 2.9 15.5 + - - +
205A GLY* 3.6 7.6 - - - +
207A PHE* 1.3 74.1 - - - +
209A GLU* 1.3 66.1 + - - +
211A ARG* 3.3 9.1 + - - +
212A LYS* 3.0 35.9 + - + +
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Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY 3.1 16.9 + - - +
206A ALA* 3.4 12.3 - - - +
208A ALA* 1.3 78.8 - - - +
210A LEU* 1.3 62.7 + - - +
212A LYS* 3.5 36.8 + - - +
213A LEU* 3.7 11.3 - - - +
593B VAL* 4.2 26.6 - - + +
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Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ALA 3.1 10.2 + - - +
207A PHE* 3.4 8.5 - - - +
209A GLU* 1.3 77.3 - - - +
211A ARG* 1.3 67.5 + - - +
213A LEU* 2.8 22.3 + - + +
214A ILE* 3.6 6.0 + - + +
228A ILE* 3.9 22.9 - - + -
229A LEU* 4.9 0.9 - - + -
232A ALA* 4.0 19.5 - - + -
569B LEU* 4.7 5.6 - - + -
589B LEU* 4.0 22.9 - - + +
592B ALA* 4.0 25.1 - - + -
593B VAL* 3.8 15.2 - - + +
596B ILE* 3.8 28.7 - - + -
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE 2.8 17.4 + - - +
208A ALA* 3.4 13.0 - - - +
210A LEU* 1.3 72.8 - - - +
212A LYS* 1.3 59.0 + - + +
213A LEU 2.7 12.1 + - - -
214A ILE* 2.8 36.7 + - - +
216A THR* 3.1 16.9 + - - +
219A PRO 2.7 28.8 + - - -
220A ASP 4.2 0.8 - - - -
221A LYS 3.2 22.6 + - - -
223A LEU* 3.5 35.6 - - - +
228A ILE* 4.3 15.4 - - + +
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Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 3.0 21.4 + - - +
209A GLU* 3.5 43.0 + - - +
210A LEU 3.2 0.2 + - - -
211A ARG* 1.3 79.0 - - + +
213A LEU* 1.3 64.1 + - + +
214A ILE 5.0 0.7 - - - +
86C ARG* 4.2 10.2 + - - -
102C ARG* 4.9 1.0 + - - -
104C TYR* 4.5 6.4 + - - -
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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