Contacts of the helix formed by residues 201 - 223 (chain A) in PDB entry 4RWN
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 PRO 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASN 3.7 2.2 - - - +
200A ARG* 1.3 94.1 - - + +
202A THR* 1.3 66.2 + - - +
203A LYS 4.5 1.6 - - - +
204A LEU* 3.1 25.2 + - + +
205A LYS* 3.3 9.9 + - - +
240A TRP* 3.6 37.0 - - + +
246A LYS 4.8 0.7 - - - +
247A THR* 4.2 33.9 - - + -
249A PHE* 5.7 0.2 - - + -
14C A 4.8 2.9 - - - +
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Residues in contact with THR 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG 3.5 3.2 + - - -
201A PRO* 1.3 71.8 - - - +
203A LYS* 1.3 62.0 + - - +
205A LYS* 3.2 10.4 + - - +
206A SER* 3.1 25.2 + - - +
6B U 4.0 12.8 - - - +
7B U 3.3 24.8 + - - +
14C A 2.8 43.4 + - + -
15C A 3.8 27.4 - - - +
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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
----------------------------------------------------------
12A ASP* 3.8 15.7 + - - +
201A PRO* 3.2 1.6 - - - +
202A THR* 1.3 76.4 - - - +
204A LEU* 1.3 66.7 + - - +
206A SER* 3.2 9.6 + - - -
207A LEU* 3.0 18.9 + - - +
247A THR 3.6 20.6 + - - +
248A ASP* 3.3 11.3 + - - +
249A PHE* 2.5 49.6 + - + +
250A SER* 4.7 0.4 - - - +
251A THR* 3.3 24.4 + - - +
15C A 3.6 30.1 + - - +
16C A 3.0 26.8 + - - -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ARG* 3.8 31.2 - - + +
201A PRO* 3.1 20.3 + - + +
203A LYS* 1.3 77.9 - - - +
205A LYS* 1.3 58.1 + - - +
207A LEU* 3.2 6.7 + - + +
208A ILE* 2.9 39.1 + - + +
236A THR* 4.1 22.7 - - + +
237A VAL* 4.7 12.3 - - + -
240A TRP* 3.6 53.2 - - + -
249A PHE* 3.7 13.6 - - + -
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS 2.9 19.9 + - - +
66A GLY 3.4 18.8 - - - +
67A THR* 4.0 14.1 - - + +
197A LEU* 3.3 22.0 - - + +
198A ARG 2.7 24.5 + - - -
200A ARG* 3.7 16.6 - - + +
201A PRO 3.3 9.6 + - - +
202A THR* 3.2 9.2 + - - +
204A LEU* 1.3 76.5 - - - +
206A SER* 1.3 57.0 + - - +
208A ILE* 3.3 13.7 + - + +
209A ARG* 2.9 38.2 + - - +
7B U 2.9 29.6 + - - +
8B G 3.2 8.9 + - - -
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Residues in contact with SER 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 5.6 2.0 - - - -
15A ILE* 3.7 30.9 - - - +
20A LEU* 4.0 17.0 - - - +
202A THR* 3.1 19.2 + - - +
203A LYS* 3.2 17.5 + - - -
205A LYS* 1.3 75.6 - - - +
207A LEU* 1.3 60.7 + - - +
209A ARG* 3.2 13.9 + - - +
210A LEU 3.0 22.3 + - - -
251A THR* 5.9 0.4 - - - -
15C A 5.0 2.9 + - - -
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.8 2.2 - - - +
203A LYS 3.0 13.4 + - - +
204A LEU* 3.5 13.2 - - + +
206A SER* 1.3 72.9 - - - +
208A ILE* 1.3 65.9 + - - +
210A LEU* 3.1 8.7 + - + +
211A VAL* 2.9 29.8 + - + +
236A THR* 3.7 24.0 - - + +
249A PHE* 4.1 18.8 - - + -
251A THR* 3.8 20.4 + - + +
254A GLY* 3.9 22.7 - - - +
255A PHE* 3.7 30.1 - - + +
258A VAL* 5.0 0.7 - - + -
343A TRP* 4.2 9.9 - - + -
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Residues in contact with ILE 208 (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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67A THR* 4.4 9.6 - - + -
197A LEU* 3.6 31.4 - - + -
204A LEU* 2.9 26.4 + - + +
205A LYS* 3.5 15.5 - - + +
206A SER 3.2 0.2 - - - -
207A LEU* 1.3 76.9 - - - +
209A ARG* 1.3 56.8 + - - +
211A VAL* 3.2 5.3 + - + +
212A LYS* 2.9 42.3 + - + +
233A GLU* 3.6 33.2 - - + +
236A THR* 3.8 22.7 - - + -
237A VAL* 4.3 12.8 - - + -
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 5.0 0.9 - - + -
19A LEU* 3.9 19.3 - - + -
20A LEU* 3.3 30.4 - - - +
21A PRO* 3.6 12.4 - - - +
66A GLY 2.8 24.6 + - - -
67A THR* 3.9 10.3 - - - +
68A THR* 2.5 56.9 + - - +
69A LEU* 3.6 16.8 - - + +
202A THR 5.8 0.2 + - - -
205A LYS* 2.9 26.8 + - - +
206A SER* 3.2 9.9 + - - +
208A ILE* 1.3 75.9 - - - +
210A LEU* 1.3 55.8 + - - +
212A LYS* 3.4 6.2 + - - +
213A HIS* 2.9 28.4 + - - +
6B U 4.0 4.8 + - - -
7B U 3.3 25.1 - - - -
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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
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3A LEU* 3.8 32.3 - - + +
11A LEU* 4.2 13.0 - - + -
14A PHE* 4.4 4.3 - - + -
15A ILE* 4.2 13.0 - - + -
19A LEU* 3.9 18.1 - - + +
206A SER 3.0 13.3 + - - +
207A LEU* 3.1 10.7 + - + +
209A ARG* 1.3 77.6 - - - +
211A VAL* 1.3 58.1 + - - +
213A HIS* 3.1 4.2 + - - +
214A TRP* 2.9 27.4 + - - +
251A THR* 3.9 26.0 - - + -
255A PHE* 3.9 35.2 - - + -
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 2.9 23.9 + - + +
208A ILE* 3.7 4.3 - - - +
210A LEU* 1.3 75.1 - - - +
212A LYS* 1.3 59.3 + - + +
214A TRP* 3.2 18.5 + - + +
215A TYR* 2.8 27.9 + - - +
232A LEU* 3.9 27.1 - - + +
233A GLU* 5.9 0.7 - - - -
236A THR* 3.5 27.4 - - + +
255A PHE* 4.3 16.2 - - + -
258A VAL* 4.2 26.5 - - + -
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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
----------------------------------------------------------
62A SER* 3.4 5.7 - - - -
67A THR* 2.8 27.1 + - - +
68A THR* 4.4 0.2 - - - +
69A LEU* 4.3 15.1 - - + +
73A SER* 4.4 1.0 + - - -
208A ILE* 2.9 38.8 + - + +
209A ARG* 3.6 5.6 - - - +
211A VAL* 1.3 78.9 - - + +
213A HIS* 1.3 56.9 + - - +
215A TYR* 3.4 7.6 + - - +
216A GLN* 3.0 32.9 + - - +
229A GLN* 3.6 28.6 - - + +
232A LEU* 6.3 1.1 - - + -
233A GLU* 4.5 14.1 + - + +
401A APC 2.9 43.1 + - - -
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Residues in contact with HIS 213 (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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3A LEU* 3.6 29.2 + - + +
14A PHE* 3.7 25.5 - + - -
18A HIS* 6.3 0.7 - - + -
19A LEU* 3.9 19.3 - - + +
69A LEU* 4.2 6.2 - - + +
72A ARG* 2.9 37.3 + - - +
209A ARG 2.9 14.2 + - - +
210A LEU* 3.5 7.0 - - - +
212A LYS* 1.3 73.0 - - - +
214A TRP* 1.3 65.2 + - - +
216A GLN* 3.3 4.0 + - - +
217A THR* 2.8 42.3 + - - -
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Residues in contact with TRP 214 (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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3A LEU* 4.5 8.5 - - + -
210A LEU 2.9 13.8 + - - +
211A VAL* 3.2 20.4 + - + +
213A HIS* 1.3 77.1 - - - +
215A TYR* 1.3 72.8 + - + +
217A THR* 3.1 7.6 + - - -
218A CYS* 3.0 38.1 + - - -
232A LEU* 4.0 24.5 - - + -
255A PHE* 4.0 20.2 - + + -
258A VAL* 5.4 2.2 - - + -
259A LEU* 3.5 27.6 - - + -
262A VAL* 4.4 9.2 - - + -
319A LEU* 3.7 30.5 - - + -
323A ALA* 3.9 17.7 - - + -
326A TRP* 3.4 55.0 - + - +
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Residues in contact with TYR 215 (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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211A VAL 2.8 20.4 + - - +
212A LYS* 3.5 7.0 - - - +
213A HIS 3.3 0.2 - - - -
214A TRP* 1.3 83.4 - - + +
216A GLN* 1.3 68.6 + - - +
218A CYS* 3.1 9.0 + - - +
219A LYS* 3.0 42.5 + - + +
226A LEU* 3.9 29.1 + - + +
227A PRO* 2.6 32.3 + - + -
228A PRO* 4.2 0.9 - - - +
229A GLN* 3.5 47.5 + - + -
232A LEU* 4.1 25.8 - - + -
319A LEU* 4.6 6.3 - - + -
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Residues in contact with GLN 216 (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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69A LEU* 4.9 6.1 - - + -
72A ARG* 4.4 20.2 - - - +
212A LYS 3.0 22.7 + - - +
213A HIS* 3.7 4.9 - - + +
214A TRP 3.3 0.2 - - - -
215A TYR* 1.3 86.9 - - - +
217A THR* 1.3 61.1 + - - +
219A LYS* 3.1 42.5 + - - +
220A LYS* 3.5 9.8 + - - +
229A GLN* 2.9 26.0 + - - +
401A APC 4.7 4.4 + - - -
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Residues in contact with THR 217 (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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3A LEU* 5.8 0.2 - - - +
4A ARG* 5.2 11.2 - - - +
213A HIS* 2.8 34.7 + - - -
214A TRP* 3.1 10.6 + - - -
216A GLN* 1.3 74.7 - - - +
218A CYS* 1.3 63.9 + - - +
220A LYS* 3.1 40.3 + - + +
221A THR* 4.0 3.6 + - - -
326A TRP* 4.0 27.0 - - + -
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Residues in contact with CYS 218 (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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214A TRP* 3.0 51.3 + - - -
215A TYR* 3.1 8.9 + - - +
217A THR* 1.3 76.7 - - - +
219A LYS* 1.3 61.8 + - - +
221A THR* 3.1 5.9 + - - +
222A HIS* 3.1 27.5 + - + +
226A LEU* 3.9 14.1 - - + -
319A LEU* 4.4 5.8 - - + -
322A GLU* 3.6 33.4 - - + -
326A TRP* 4.5 6.5 - - - -
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Residues in contact with LYS 219 (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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215A TYR* 3.0 26.7 + - + +
216A GLN* 3.2 40.8 + - - +
217A THR 3.1 0.4 - - - -
218A CYS* 1.3 73.5 - - - +
220A LYS* 1.3 60.5 + - - +
223A GLY* 3.0 47.7 + - - +
224A ASN* 3.5 35.7 + - - +
226A LEU* 3.8 11.0 - - + +
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Residues in contact with LYS 220 (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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2A GLU* 5.3 6.7 + - - -
216A GLN 4.1 7.4 - - - +
217A THR* 3.1 30.1 + - + +
218A CYS 3.1 0.2 - - - -
219A LYS* 1.3 81.4 - - - +
221A THR* 1.3 62.5 + - - +
223A GLY* 4.5 1.0 + - - -
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Residues in contact with THR 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A THR 4.7 3.8 + - - -
218A CYS* 3.1 5.2 + - - -
220A LYS* 1.3 82.7 - - - +
222A HIS* 1.3 88.3 + - + +
223A GLY 3.4 2.0 + - - -
225A LYS* 5.6 0.3 + - - -
318A ARG* 5.2 2.5 + - - +
322A GLU* 4.2 10.6 + - - +
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Residues in contact with HIS 222 (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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218A CYS 3.1 13.9 + - - +
221A THR* 1.3 92.4 - - + +
223A GLY* 1.3 64.8 + - - +
224A ASN 3.3 0.2 + - - -
225A LYS* 3.1 31.0 + - - +
226A LEU* 3.8 25.8 - - + -
318A ARG* 3.0 57.1 + - + +
321A GLN* 4.2 13.0 - - - -
322A GLU* 2.6 42.0 + - + +
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Residues in contact with GLY 223 (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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219A LYS* 3.0 41.8 + - - +
220A LYS 4.5 1.2 + - - -
221A THR 3.4 3.2 + - - -
222A HIS* 1.3 77.2 - - - +
224A ASN* 1.3 62.3 + - - -
225A LYS* 3.6 4.9 + - - -
226A LEU* 4.4 4.3 - - - +
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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) + - + + + + + -
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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