Contacts of the helix formed by residues 299 - 327 (chain A) in PDB entry 1OCR
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 VAL 299 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ASP* 1.3 72.2 - - - +
300A ASP* 1.3 70.9 + - - +
302A ARG* 3.0 23.1 + - - +
303A ALA* 3.0 20.6 + - - +
84B LEU* 3.9 36.1 - - + +
85B TYR* 3.8 30.1 - - + -
88B ASP* 3.9 29.3 + - + +
22H ASN* 4.3 9.9 + - - +
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Residues in contact with ASP 300 (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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298A ASP* 3.3 4.5 - - + +
299A VAL* 1.3 87.5 - - - +
301A THR* 1.3 65.1 + - + +
303A ALA* 3.1 4.2 + - - +
304A TYR* 3.0 21.3 + - - +
85B TYR* 2.5 34.9 + - - -
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A MET* 4.2 19.0 - - + +
298A ASP* 3.7 33.9 + - + +
299A VAL 3.3 0.4 - - - -
300A ASP* 1.3 78.2 - - + +
302A ARG* 1.3 63.2 + - - +
304A TYR* 3.3 7.6 + - - +
305A PHE* 3.0 44.5 + - - -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.8 44.1 + - + +
297A MET* 2.7 58.6 + - + +
298A ASP 3.2 6.0 + - - +
299A VAL* 3.0 33.0 + - - +
301A THR* 1.3 79.5 + - - +
303A ALA* 1.3 57.9 + - - +
305A PHE* 3.5 1.3 + - - -
306A THR* 2.8 31.7 + - - +
361A SER* 4.3 11.4 - - - +
365A ILE* 5.4 4.0 - - - +
84B LEU* 3.7 27.1 + - + +
87B MET* 4.7 12.1 - - - +
88B ASP* 3.8 14.5 + - - +
23H GLN* 3.6 25.4 - - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL 3.0 7.8 + - - +
300A ASP 3.1 8.3 + - - +
302A ARG* 1.3 72.3 - - - +
304A TYR* 1.3 66.2 + - - +
306A THR* 3.5 2.3 + - - -
307A SER* 3.0 29.2 + - - -
81B LEU* 3.8 17.9 - - + +
84B LEU* 3.7 19.3 - - + +
85B TYR* 3.6 24.5 - - + +
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Residues in contact with TYR 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ILE* 3.2 47.4 + - + +
288A TRP* 6.3 0.2 - + - -
300A ASP 3.0 12.9 + - - +
301A THR* 3.6 9.6 - - - +
302A ARG 3.2 0.2 - - - -
303A ALA* 1.3 76.6 - - - +
305A PHE* 1.3 98.3 + + - +
307A SER* 3.0 8.5 + - - -
308A ALA* 2.8 41.8 + - + +
1T ALA* 5.1 4.8 - - + +
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A HIS* 6.3 0.4 - + - -
286A ILE 3.7 13.2 - - - -
287A VAL* 3.6 31.0 - - - -
288A TRP* 3.9 28.9 - + - -
289A ALA* 3.5 37.9 - - + -
290A HIS 4.6 1.6 - - - +
293A PHE* 4.0 22.3 - - + -
297A MET* 5.0 2.5 - - + -
301A THR* 3.0 42.2 + - - +
303A ALA 3.4 0.2 - - - -
304A TYR* 1.3 95.2 - + - +
306A THR* 1.3 59.5 + - - +
308A ALA* 4.0 1.7 - - - +
309A THR* 2.8 29.3 + - - -
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Residues in contact with THR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.8 3.8 - - + -
302A ARG 2.8 21.2 + - - +
303A ALA* 3.9 6.2 + - - +
305A PHE* 1.3 74.9 - - - +
307A SER* 1.3 68.7 + - - +
309A THR* 3.4 3.8 + - - -
310A MET* 3.2 31.3 + - - +
359A ALA 2.9 24.6 - - - +
360A ASN* 4.3 5.0 + - - -
361A SER* 3.0 34.5 - - - +
77B ALA* 5.7 2.6 - - - +
80B SER* 4.6 4.2 + - - +
81B LEU* 3.9 14.6 - - + +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 3.0 13.7 + - - -
304A TYR* 3.0 12.2 + - - -
306A THR* 1.3 80.1 + - - +
308A ALA* 1.3 63.8 + - - +
310A MET* 3.2 16.3 + - - +
311A ILE* 3.6 15.6 + - - +
77B ALA* 5.5 6.9 - - - +
81B LEU* 4.0 17.3 - - - +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 5.2 1.2 - - - +
286A ILE* 4.2 9.6 - - + +
287A VAL* 4.0 18.1 - - + +
304A TYR* 2.8 46.9 + - + +
305A PHE* 4.3 2.9 - - - +
307A SER* 1.3 73.8 - - - +
309A THR* 1.3 65.0 + - - +
311A ILE* 3.0 32.1 + - + +
312A ILE* 4.0 3.6 + - - +
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Residues in contact with THR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 6.0 0.4 - - - +
287A VAL* 3.5 15.6 - - + +
290A HIS* 2.7 37.6 + - + +
305A PHE 2.8 22.7 + - - -
306A THR* 3.8 4.5 - - - -
307A SER 3.3 0.2 - - - -
308A ALA* 1.3 78.8 - - - +
310A MET* 1.3 61.2 - - - +
312A ILE* 3.4 19.8 + - + +
313A ALA 4.6 0.3 + - - -
356A ILE* 4.9 0.2 - - - +
359A ALA* 3.8 16.4 - - + -
516A HEA 3.4 33.0 - - + +
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Residues in contact with MET 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A THR* 3.2 17.0 + - - +
307A SER* 3.7 9.9 - - - +
308A ALA 3.1 1.2 - - - -
309A THR* 1.3 73.7 - - - +
311A ILE* 1.3 66.2 + - + +
312A ILE 3.0 2.7 - - - -
313A ALA* 3.0 15.2 + - - +
356A ILE* 3.6 26.2 - - + +
359A ALA* 4.0 13.2 - - + -
360A ASN* 3.0 43.3 - - - +
73B LEU* 3.2 36.0 - - + +
76B ILE* 3.5 17.5 - - + -
77B ALA* 4.3 23.1 - - - +
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Residues in contact with ILE 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A LEU* 4.1 28.3 - - + -
286A ILE* 6.0 0.9 - - + -
307A SER 3.6 8.0 + - - +
308A ALA* 3.0 28.5 - - + +
310A MET* 1.3 76.7 - - + +
312A ILE* 1.3 63.8 + - - +
313A ALA 2.9 1.9 + - - -
314A ILE* 2.9 28.3 + - + +
315A PRO* 3.2 10.6 - - - +
73B LEU* 4.4 8.1 - - + -
30T LEU* 4.0 34.5 - - + -
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A HIS* 4.6 0.7 - - - +
244A TYR* 3.6 29.6 - - + +
280A ILE* 4.5 10.8 - - + +
283A LEU* 3.7 47.6 - - + +
284A GLY* 4.1 5.6 - - - +
287A VAL* 4.8 9.0 - - + -
308A ALA 4.5 4.9 - - - +
309A THR* 3.5 15.9 - - + +
310A MET 3.0 0.8 - - - -
311A ILE* 1.3 77.4 - - - +
313A ALA* 1.3 60.6 + - - +
314A ILE 3.3 0.3 + - - -
315A PRO* 3.5 4.3 - - - +
316A THR* 2.9 25.8 + - - +
516A HEA 3.6 25.6 - - + +
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR 4.6 0.6 + - - -
310A MET 3.0 13.1 + - - +
311A ILE 2.9 1.6 + - - -
312A ILE* 1.3 77.0 - - - +
314A ILE* 1.3 55.8 + - - +
316A THR* 3.7 3.4 - - - -
317A GLY* 2.7 31.9 + - - -
356A ILE* 4.0 13.4 - - + +
516A HEA 3.6 53.5 - - + +
69B PRO* 5.6 0.9 - - - -
73B LEU* 4.5 5.2 - - + -
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Residues in contact with ILE 314 (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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275A TRP* 4.7 8.7 - - + -
311A ILE* 2.9 22.4 + - + +
313A ALA* 1.3 72.9 - - - +
315A PRO* 1.3 77.1 - - + +
317A GLY* 2.8 13.0 + - - -
318A VAL* 3.1 12.2 + - + +
65B TRP 4.9 1.7 - - - +
66B THR* 4.0 34.3 - - + +
69B PRO* 4.5 9.6 - - + +
70B ALA* 3.9 34.3 - - + +
73B LEU* 3.9 20.2 - - + -
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Residues in contact with PRO 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 3.9 24.5 - - + -
276A ALA* 3.5 23.8 - - - +
279A SER* 3.8 29.8 - - - -
280A ILE* 4.1 9.4 - - + -
283A LEU* 4.4 9.0 - - + -
311A ILE 3.2 12.8 - - - +
312A ILE* 3.5 15.3 - - - +
314A ILE* 1.3 91.2 - - + +
316A THR* 1.3 60.4 + - - +
318A VAL* 3.2 9.4 + - + +
319A LYS* 3.4 8.7 + - - +
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR* 5.7 0.7 - - - -
251A PHE* 4.5 10.3 - - + -
280A ILE* 3.6 18.6 - - + +
312A ILE* 2.9 25.3 + - - +
313A ALA 3.4 3.8 + - - -
314A ILE 3.1 1.2 - - - -
315A PRO* 1.3 78.2 - - - +
317A GLY* 1.3 63.4 + - - +
319A LYS* 3.2 7.2 + - + +
320A VAL* 3.1 21.6 + - + +
348A PHE* 3.7 24.2 - - + -
516A HEA 3.7 34.2 + - + +
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Residues in contact with GLY 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ALA 2.7 16.3 + - - -
314A ILE* 2.8 5.6 + - - -
316A THR* 1.3 78.0 - - - +
318A VAL* 1.3 61.8 + - - -
320A VAL* 3.1 2.8 + - - +
321A PHE* 3.0 34.7 + - - -
516A HEA 3.5 26.7 - - - +
65B TRP 4.9 2.9 - - - -
69B PRO* 5.8 1.3 - - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A GLY 3.9 13.2 - - - +
273A MET* 5.5 0.2 - - - -
275A TRP* 3.9 19.1 - - + -
276A ALA* 3.8 17.0 - - + -
314A ILE* 3.1 14.5 + - + +
315A PRO 3.2 9.1 + - - +
317A GLY* 1.3 74.6 - - - +
319A LYS* 1.3 60.1 + - - +
321A PHE* 3.8 1.1 - - - +
322A SER* 2.7 36.8 + - - +
62B GLU* 4.3 11.7 - - - +
65B TRP* 4.0 29.6 + - + +
66B THR* 3.7 22.7 - - - +
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 5.5 0.4 - - - +
251A PHE* 3.8 47.6 - - + -
255A SER* 4.8 3.1 + - - -
273A MET* 3.3 49.7 + - - +
276A ALA* 3.6 23.6 - - + -
277A MET* 3.4 18.4 - - + +
280A ILE* 4.5 6.3 - - + -
315A PRO 3.4 3.3 + - - +
316A THR* 3.2 9.1 + - + +
317A GLY 3.2 1.0 - - - -
318A VAL* 1.3 78.9 - - - +
320A VAL* 1.3 65.3 + - + +
322A SER* 3.0 2.8 + - - -
323A TRP* 3.0 47.4 + - + -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A THR* 3.1 12.7 + - + +
317A GLY 3.1 5.6 + - - +
319A LYS* 1.3 77.8 - - + +
321A PHE* 1.3 65.2 + - + +
323A TRP* 3.3 24.5 + - + +
324A LEU* 3.3 31.3 + - + +
345A ILE* 4.3 15.0 - - + +
348A PHE* 4.6 11.7 - - + -
349A THR* 4.0 18.8 - - - +
516A HEA 4.1 33.7 - - + -
38B VAL* 4.7 7.2 - - + -
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLY* 3.0 26.3 + - - +
318A VAL 4.1 0.2 - - - +
320A VAL* 1.3 75.8 - - + +
322A SER* 1.3 59.5 + - - +
324A LEU* 3.3 20.2 + - + +
325A ALA* 2.9 28.2 + - - +
516A HEA 4.3 32.8 - - + -
34B ILE* 5.7 2.9 - - + -
37B LEU* 5.4 13.9 - - + -
38B VAL* 4.2 22.4 - - + -
41B ILE* 5.8 5.6 - - + -
65B TRP* 3.4 59.6 - + + -
69B PRO* 5.0 6.5 - - + -
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Residues in contact with SER 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 3.8 18.7 + - - +
269A GLY 5.0 1.4 + - - -
272A GLY 5.7 0.2 - - - -
273A MET* 3.4 29.2 + - - -
318A VAL* 2.7 26.3 + - - +
319A LYS 3.0 0.6 + - - -
321A PHE* 1.3 73.6 - - - +
323A TRP* 1.3 67.1 + - - +
325A ALA* 3.2 8.1 + - - +
326A THR* 2.9 26.6 + - - -
62B GLU* 4.0 16.6 + - - -
65B TRP* 4.1 3.5 + - - -
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Residues in contact with TRP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PHE* 3.6 48.2 - + - -
254A ILE* 4.2 12.6 - - + -
255A SER* 2.9 32.7 + - - +
258A VAL* 3.6 10.7 - - + +
267A PRO* 6.2 0.7 - - + -
273A MET* 3.2 19.1 - - + +
319A LYS* 3.0 36.6 + - + -
320A VAL* 3.6 30.3 - - + +
321A PHE 3.3 0.2 - - - -
322A SER* 1.3 76.5 - - - +
324A LEU* 1.3 64.0 - - - +
326A THR* 3.2 17.2 + - - -
327A LEU* 3.2 17.4 + - - +
344A PHE* 3.7 23.3 - + - -
345A ILE* 4.0 31.9 - - + -
348A PHE* 5.2 1.3 - + - -
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.3 23.2 + - + +
321A PHE* 3.5 30.1 - - + +
322A SER 3.2 0.4 - - - -
323A TRP* 1.3 79.2 - - - +
325A ALA* 1.3 64.8 + - - +
327A LEU* 3.1 22.7 + - + +
328A HIS 3.2 8.7 + - - -
345A ILE* 3.9 22.0 - - + -
38B VAL* 4.7 10.1 - - + -
41B ILE* 4.2 30.5 - - + -
42B ILE* 3.6 30.7 - - + +
45B MET* 3.6 11.8 - - + +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LYS* 4.1 3.3 + - - -
268A PHE* 3.5 37.2 - - + +
321A PHE 2.9 17.8 + - - +
322A SER 3.6 1.8 - - - +
324A LEU* 1.3 77.1 - - - +
326A THR* 1.3 61.6 + - - +
328A HIS* 3.1 24.5 - - + +
45B MET* 5.4 0.2 - - - -
56B MET* 4.3 8.2 - - - +
65B TRP* 3.9 12.8 - - + -
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Residues in contact with THR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.6 23.6 - - + +
259A THR* 3.8 26.7 - - - +
262A SER* 4.1 1.0 - - - -
264A LYS* 2.9 42.0 + - + +
266A GLU 4.9 0.4 - - - +
267A PRO* 3.8 8.5 - - + +
268A PHE* 3.0 26.7 + - - +
273A MET* 5.6 0.5 - - - +
322A SER 2.9 14.3 + - - -
323A TRP* 3.3 14.6 - - - -
324A LEU 3.1 0.2 - - - -
325A ALA* 1.3 75.6 - - - +
327A LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.9 10.5 - - + -
262A SER* 3.6 12.8 - - - +
323A TRP 3.5 13.9 - - - +
324A LEU* 3.1 26.1 + - + +
326A THR* 1.3 77.9 - - - +
328A HIS* 1.3 57.3 + - - +
329A GLY 3.1 0.9 + - - -
330A GLY* 2.8 24.1 + - - -
332A ILE* 3.9 13.2 - - + +
338A MET* 3.3 34.5 - - + -
342A LEU* 4.0 21.5 - - + -
345A ILE* 4.9 3.1 - - + -
42B ILE* 5.1 4.7 - - + -
45B MET* 4.0 22.9 - - + +
46B LEU* 4.5 10.5 - - + -
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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