Contacts of the helix formed by residues 325 - 350 (chain A) in PDB entry 4OGB
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 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 5.1 5.8 - - + +
103A GLY* 4.0 25.6 - - - +
323A THR 4.5 1.6 - - - +
324A LYS* 1.3 89.9 - - + +
326A LEU* 1.3 56.3 - - - +
327A GLN* 3.1 6.3 - - + +
328A LEU* 2.7 36.1 + - + +
329A TYR 3.1 4.2 + - - -
398A THR* 4.2 10.3 - - + -
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LYS 3.3 4.3 + - - -
325A PRO* 1.3 72.0 - - - +
327A GLN* 1.3 56.1 + - - +
329A TYR* 3.8 19.3 - - + -
330A ARG* 2.8 54.9 + - + +
402A ASN* 3.8 25.1 + - + +
405A TRP* 3.6 56.3 - - + +
406A TYR* 4.5 0.4 - - + -
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A HIS* 5.5 2.8 - - - -
325A PRO* 3.0 6.3 + - + +
326A LEU* 1.3 78.7 - - - +
328A LEU* 1.3 62.9 + - + +
330A ARG* 4.3 3.8 - - - +
331A GLN* 3.4 31.1 + - + +
513A DMS 3.6 26.0 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 3.7 26.0 - - - +
104A LEU 3.5 24.9 - - - +
105A HIS* 5.3 1.8 - - - +
106A VAL* 4.6 5.4 - - + -
107A PHE* 3.8 29.3 - - + -
324A LYS* 4.0 15.0 - - + +
325A PRO* 2.7 26.9 + - + +
327A GLN* 1.3 73.7 - - + +
329A TYR* 1.3 66.6 + - - +
331A GLN* 3.0 16.0 + - - +
332A TRP* 3.1 23.0 + - + +
513A DMS 4.0 21.8 - - + +
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Residues in contact with TYR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN* 3.3 33.1 + - + +
322A PRO* 3.5 26.6 - - + +
324A LYS 3.8 10.1 - - - +
325A PRO 3.1 2.4 + - - -
326A LEU* 3.8 11.4 - - + +
328A LEU* 1.3 76.9 - - - +
330A ARG* 1.3 56.9 + - - +
332A TRP* 3.1 7.1 + - - +
333A THR* 2.8 46.0 + - - -
369A GLN* 2.3 39.3 + - - +
373A ILE* 3.6 14.8 - - + +
402A ASN* 3.7 29.6 - - + -
406A TYR* 3.4 29.4 - + - -
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Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 2.8 41.1 + - + +
327A GLN* 4.3 4.7 - - - +
329A TYR* 1.3 69.9 - - - +
331A GLN* 1.3 61.4 + - + +
333A THR* 3.8 6.4 - - - -
334A ASP* 2.9 45.1 + - - +
405A TRP* 3.4 43.6 - - - -
406A TYR* 4.0 10.5 - - - +
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.5 47.1 - - + +
327A GLN* 3.4 23.0 + - + +
328A LEU* 3.0 10.2 + - - +
330A ARG* 1.3 77.9 - - + +
332A TRP* 1.3 63.8 + - - +
334A ASP* 3.4 10.6 + - - +
335A ARG* 3.1 32.5 + - - +
513A DMS 3.6 27.2 - - - +
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Residues in contact with TRP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.0 9.4 - - + +
107A PHE* 3.4 35.6 - + - -
159A TYR* 3.5 27.8 - + + -
161A ASN* 5.2 0.7 - - - -
163A ILE* 3.9 10.8 - - + -
164A HIS* 3.7 40.4 - - + -
167A ASP* 3.6 31.1 + - + -
321A ASN* 3.4 43.7 - - + +
324A LYS* 5.4 3.9 - - + +
328A LEU* 3.1 32.6 + - + +
329A TYR* 3.4 6.7 - - - +
331A GLN* 1.3 77.0 - - - +
333A THR* 1.3 57.4 + - - +
335A ARG* 3.1 13.1 + - - +
336A ILE* 2.9 30.9 + - - +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A TYR* 2.8 45.1 + - - -
330A ARG 3.8 3.8 - - - -
331A GLN 3.3 0.2 - - - -
332A TRP* 1.3 73.5 - - - +
334A ASP* 1.3 66.3 + - - +
336A ILE* 3.3 6.9 - - + +
337A MET* 2.9 33.2 + - + +
365A VAL* 3.9 17.7 - - + -
369A GLN* 3.9 26.5 + - + +
406A TYR* 3.4 23.6 + - - +
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Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG* 2.9 30.6 + - - +
331A GLN* 3.6 9.6 - - - +
333A THR* 1.3 78.6 - - - +
335A ARG* 1.3 57.8 + - + +
337A MET* 3.8 4.8 - - - +
338A GLU* 2.9 31.1 + - - +
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.2 41.7 - - - -
158A ALA* 2.8 59.0 + - + +
159A TYR* 3.9 8.5 - - + -
161A ASN* 3.8 10.7 - - - +
163A ILE* 4.0 14.9 - - - +
331A GLN* 3.1 23.5 + - - +
332A TRP* 3.7 14.3 - - - +
334A ASP* 1.3 77.2 - - + +
336A ILE* 1.3 61.5 + - - +
338A GLU* 3.2 7.9 + - - +
339A GLU* 2.9 28.6 + - - +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 3.7 41.8 - - + -
160A HIS* 4.0 13.0 - - + +
332A TRP 2.9 13.7 + - - +
333A THR* 3.3 19.1 - - + +
335A ARG* 1.3 76.0 - - - +
337A MET* 1.3 63.7 + - + +
339A GLU* 3.2 5.4 + - + +
340A PHE* 2.7 73.7 + - + -
369A GLN* 5.0 0.7 - - - +
501A 2SR 3.9 28.9 - - + +
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Residues in contact with MET 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 2.9 32.8 + - + +
334A ASP* 3.8 5.6 - - - +
336A ILE* 1.3 81.2 - - + +
338A GLU* 1.3 57.3 - - - +
340A PHE* 3.7 14.2 - - + +
341A PHE* 2.9 79.4 + - + -
357A MET* 3.7 24.5 - - + +
363A ALA* 4.9 4.0 - - + -
365A VAL* 3.9 31.2 - - + -
368A SER* 5.7 3.4 - - - +
369A GLN* 5.0 7.0 - - - -
501A 2SR 5.8 0.2 - - - -
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Residues in contact with GLU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ALA* 3.7 11.1 - - + +
334A ASP 2.9 19.8 + - - +
335A ARG* 3.5 8.9 - - - +
337A MET* 1.3 76.8 - - - +
339A GLU* 1.3 61.5 + - - +
341A PHE* 4.2 7.1 - - - +
342A ARG* 2.4 63.9 + - + +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.2 6.9 - - + +
158A ALA* 4.3 6.2 - - + +
159A TYR* 2.9 18.0 + - + +
160A HIS* 2.6 54.6 + - - -
204A HIS* 4.0 1.0 - - - -
206A GLY* 3.4 40.2 - - - +
335A ARG 2.9 13.1 + - - +
336A ILE* 3.5 13.1 - - + +
338A GLU* 1.3 78.3 - - - +
340A PHE* 1.3 66.0 + - + +
342A ARG* 3.4 8.7 + - - +
343A GLN* 3.1 20.6 + - - +
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A HIS* 5.5 2.7 - + - -
336A ILE* 2.7 53.8 + - + +
337A MET* 3.7 15.5 - - - +
339A GLU* 1.3 76.3 - - + +
341A PHE* 1.3 60.6 + - - +
343A GLN* 3.0 11.1 + - + +
344A GLY 2.9 23.6 + - - -
356A PRO 5.3 0.4 - - - -
357A MET* 3.6 53.2 - - + +
358A CYS* 3.3 24.6 - - - +
501A 2SR 3.8 33.4 - + + -
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A MET* 2.9 60.8 + - + +
338A GLU* 4.2 6.1 - - - +
340A PHE* 1.3 72.9 - - - +
342A ARG* 1.3 51.9 + - + +
344A GLY* 3.1 1.4 + - - -
345A ASP* 2.7 42.2 + - - +
357A MET 3.7 8.3 - - - -
358A CYS 3.5 10.6 - - - +
359A ASP 3.9 0.2 - - - -
360A LYS* 3.5 51.5 - - + +
363A ALA* 3.8 20.2 - - + -
365A VAL* 4.6 7.6 - - + -
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ASP* 3.4 26.0 + - - +
158A ALA* 3.6 17.5 - - - +
338A GLU* 2.4 60.8 + - + +
339A GLU* 3.6 7.3 - - - +
340A PHE 3.2 0.4 - - - -
341A PHE* 1.3 80.3 - - + +
343A GLN* 1.3 60.2 + - - +
345A ASP* 3.5 12.0 + - + +
346A ARG* 3.1 32.5 + - - +
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Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY 4.4 2.2 + - - +
207A VAL* 3.3 18.7 - - + -
208A SER* 3.0 46.1 + - - -
211A PHE* 3.8 18.7 - - + +
339A GLU 3.1 11.4 + - - +
340A PHE* 3.0 15.0 + - - +
342A ARG* 1.3 73.8 - - - +
344A GLY* 1.3 61.2 + - - +
346A ARG* 3.2 6.3 + - - +
347A GLU* 2.9 53.9 + - - +
355A SER* 3.3 13.9 + - - -
358A CYS* 4.5 8.5 - - - -
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Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE 2.9 10.7 + - - -
341A PHE 3.1 0.4 + - - -
343A GLN* 1.3 77.5 - - - +
345A ASP* 1.3 57.0 + - - +
347A GLU* 3.3 14.0 + - - -
348A ARG* 2.9 30.7 + - - +
354A ILE* 3.2 14.1 - - - +
358A CYS* 3.2 25.3 - - - +
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Residues in contact with ASP 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PHE* 2.7 26.1 + - - +
342A ARG* 3.6 13.5 - - + +
344A GLY* 1.3 73.8 - - - +
346A ARG* 1.3 59.1 + - + +
348A ARG* 2.7 29.5 + - - +
349A GLU* 2.9 41.7 + - + +
360A LYS* 3.1 31.0 + - - +
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Residues in contact with ARG 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PRO* 4.3 11.7 + - - +
206A GLY 5.4 0.2 - - - -
207A VAL* 3.6 29.7 - - - +
211A PHE* 4.3 22.4 - - + -
342A ARG* 3.1 22.2 + - - +
343A GLN* 3.2 4.7 + - - +
345A ASP* 1.3 76.3 - - + +
347A GLU* 1.3 61.6 + - - +
349A GLU* 3.5 19.8 - - - +
350A ARG* 3.2 34.8 + - - +
116C ARG* 4.6 4.0 - - - +
151C ASP* 3.0 41.7 + - - +
152C HIS* 5.4 1.2 + - - -
501C EDO 4.3 18.0 + - - -
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 3.6 22.6 - - + +
214A ASN* 5.9 0.7 + - - -
343A GLN* 2.9 35.0 + - - +
344A GLY* 3.5 16.3 + - - +
346A ARG* 1.3 77.2 - - - +
348A ARG* 1.3 60.8 + - - +
350A ARG* 3.2 6.4 + - - -
352A MET* 2.9 48.7 + - + +
353A GLU 3.8 7.7 - - - +
354A ILE* 3.5 8.7 - - + -
355A SER* 2.3 50.6 + - - -
358A CYS* 4.2 0.2 - - - +
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Residues in contact with ARG 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A GLY 2.9 16.8 + - - +
345A ASP* 2.7 33.7 + - - +
347A GLU* 1.3 68.3 - - - +
349A GLU* 1.3 64.6 + - - +
350A ARG 2.8 7.6 + - - -
351A GLY* 3.0 13.1 + - - +
352A MET 4.5 2.2 - - - -
354A ILE* 3.4 23.8 - - + +
359A ASP* 3.4 30.5 + - - +
360A LYS* 4.0 19.6 - - - +
361A HIS* 4.0 20.8 + - - -
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ASP* 2.9 26.7 + - + +
346A ARG* 3.5 22.0 - - - +
348A ARG* 1.3 75.2 - - - +
350A ARG* 1.3 59.3 + - + +
351A GLY 3.6 0.4 + - - -
116C ARG* 3.1 38.9 + - - +
143C ILE* 4.9 4.7 - - - +
144C THR* 5.5 0.5 + - - -
147C MET* 3.4 40.5 - - + +
151C ASP* 5.1 0.2 - - - +
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Residues in contact with ARG 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 4.3 7.5 - - - -
215A THR* 3.9 23.6 - - - +
346A ARG* 3.2 33.3 + - - +
347A GLU 3.2 3.7 + - - +
348A ARG 2.9 1.2 - - - -
349A GLU* 1.3 83.6 + - + +
351A GLY* 1.3 62.4 + - - +
352A MET* 3.0 27.0 + - + +
144C THR* 4.3 31.8 + - + +
147C MET* 4.3 12.2 - - - +
148C THR* 3.2 36.4 + - - +
151C ASP* 3.0 26.3 + - - -
243C GLU* 4.7 4.6 + - - -
246C CYS* 5.5 1.0 - - - -
501C EDO 4.7 2.8 + - - -
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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