Contacts of the helix formed by residues 365 - 385 (chain A) in PDB entry 6VW1
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 THR 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A THR* 3.7 19.5 - - + +
297A MET* 3.6 10.5 - - - +
363A LYS* 3.0 15.2 + - + +
364A VAL* 1.3 81.6 - - - +
366A MET* 1.3 59.9 + - - +
367A ASP* 4.0 8.6 + - - +
368A ASP* 3.2 29.6 + - - +
369A PHE* 2.9 26.5 + - - +
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Residues in contact with MET 366 (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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291A ILE* 3.2 29.6 - - + +
292A ASP* 4.1 8.1 - - - +
293A VAL* 3.7 29.8 - - + +
294A THR* 3.3 14.4 + - - +
297A MET* 3.9 6.0 - - - -
365A THR* 1.3 69.9 - - - +
367A ASP* 1.3 68.6 + - - +
369A PHE* 3.2 11.6 + - + +
370A LEU* 3.0 43.0 + - + +
413A ALA* 4.7 8.3 - - + +
418A LEU* 3.7 28.5 - - + -
438A PHE* 6.1 2.9 - - + -
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A THR* 3.3 8.5 + - - +
366A MET* 1.3 81.5 - - - +
368A ASP* 1.3 60.1 + - - +
370A LEU* 3.3 11.9 + - - +
371A THR* 2.9 36.3 + - + +
441A LYS* 5.4 6.2 + - - -
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Residues in contact with ASP 368 (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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307A ILE* 4.5 2.8 - - + +
360A MET* 3.7 17.3 - - + +
361A CYS 4.2 1.2 - - - +
362A THR* 3.6 7.1 - - + +
363A LYS* 2.6 54.7 + - - +
365A THR* 3.2 14.9 + - - +
367A ASP* 1.3 79.6 - - - +
369A PHE* 1.3 60.5 + - - +
371A THR* 3.0 9.6 + - - +
372A ALA* 2.8 30.8 + - - +
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Residues in contact with PHE 369 (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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293A VAL* 6.0 0.7 - - + -
297A MET* 4.5 9.0 - - + -
302A TRP* 4.2 24.9 - + - -
307A ILE* 4.0 25.0 - - + +
310A GLU* 4.4 17.9 - - + -
365A THR 2.9 13.2 + - - +
366A MET* 3.2 15.5 + - + +
368A ASP* 1.3 76.1 - - - +
370A LEU* 1.3 74.0 + - + +
372A ALA* 3.2 4.2 + - - +
373A HIS* 3.1 57.5 + + - -
412A ALA* 4.1 21.5 - - + -
417A HIS* 4.8 11.2 - + - -
418A LEU* 4.4 14.6 - - + -
421A ILE* 5.0 4.7 - - + -
423A LEU* 4.8 9.9 - - + -
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Residues in contact with LEU 370 (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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366A MET* 3.0 37.1 + - + +
367A ASP* 3.8 11.0 - - - +
369A PHE* 1.3 84.5 - - + +
371A THR* 1.3 59.2 + - + +
373A HIS* 3.2 9.0 + - - +
374A HIS* 3.0 24.4 + - - +
409A SER* 3.7 23.1 - - - +
412A ALA* 3.7 14.1 - - + +
413A ALA* 3.7 44.2 - - + +
418A LEU* 5.6 0.4 - - + -
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Residues in contact with THR 371 (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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346A PRO* 5.7 6.5 - - + -
360A MET* 3.2 14.4 - - - +
367A ASP* 2.9 23.8 + - + +
368A ASP* 3.0 18.0 + - - +
370A LEU* 1.3 74.0 - - + +
372A ALA* 1.3 59.8 + - - +
374A HIS* 3.2 10.0 + - + +
375A GLU* 2.9 37.8 + - - +
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Residues in contact with ALA 372 (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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307A ILE* 3.8 20.9 - - + -
308A PHE* 4.0 31.2 - - + -
311A ALA* 4.6 6.0 - - + +
360A MET* 4.3 7.1 - - + +
368A ASP 2.8 18.3 + - - +
369A PHE 3.2 5.4 + - - +
371A THR* 1.3 73.9 + - - +
373A HIS* 1.3 67.1 + - - +
375A GLU* 3.4 1.8 + - - +
376A MET* 2.9 27.4 + - - +
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Residues in contact with HIS 373 (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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310A GLU* 4.6 1.3 + - + -
311A ALA* 3.7 33.2 + - + +
314A PHE* 3.8 38.1 - + + +
315A PHE* 3.4 11.9 - + - -
369A PHE* 3.1 62.1 + + - +
370A LEU 3.2 9.4 + - - +
372A ALA* 1.3 77.9 - - - +
374A HIS* 1.3 56.3 + - - +
377A GLY 2.9 23.0 + - - -
408A MET* 3.8 16.2 - - + +
412A ALA* 3.6 26.2 - - + +
417A HIS* 4.4 4.6 + - - -
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Residues in contact with HIS 374 (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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370A LEU 3.0 13.2 + - - +
371A THR* 3.2 14.3 + - + +
373A HIS* 1.3 76.6 - - - +
375A GLU* 1.3 76.1 + - - +
377A GLY* 3.1 4.0 + - - -
378A HIS* 3.0 52.2 + + - -
402A GLU* 3.4 41.4 + - + +
405A GLY* 3.1 24.0 + - - +
406A GLU* 3.0 29.9 + - + +
409A SER* 4.6 1.6 - - - -
518A ARG* 5.1 0.7 - - - -
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Residues in contact with GLU 375 (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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346A PRO* 3.6 37.7 - - + +
347A THR* 3.8 2.0 - - - +
348A ALA* 3.5 26.0 + - + +
358A ILE* 4.0 20.6 - - + -
360A MET* 4.8 4.9 - - - -
371A THR* 2.9 26.7 + - - +
372A ALA* 4.1 4.7 - - - +
374A HIS* 1.3 86.8 - - + +
376A MET* 1.3 57.5 + - - +
378A HIS* 3.1 15.0 + - - +
379A ILE* 3.0 28.4 + - - +
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Residues in contact with MET 376 (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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308A PHE* 3.7 44.2 - - + +
311A ALA* 3.8 4.9 - - + -
312A GLU* 3.6 27.6 - - - -
315A PHE* 3.4 27.4 - - + -
323A MET* 3.7 40.8 - - + +
327A PHE* 4.2 7.4 - - + -
328A TRP* 5.3 0.2 - - + -
358A ILE* 3.9 7.9 - - + +
372A ALA 2.9 16.7 + - - +
375A GLU* 1.3 73.2 - - - +
377A GLY* 1.3 60.9 + - - +
379A ILE* 3.2 2.7 + - - +
380A GLN* 2.9 27.5 + - - +
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Residues in contact with GLY 377 (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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315A PHE* 3.3 19.9 - - - -
373A HIS 2.9 12.4 + - - -
374A HIS 3.1 5.1 + - - -
376A MET* 1.3 73.0 - - - +
378A HIS* 1.3 65.1 + - - +
380A GLN* 3.2 3.9 + - - +
381A TYR* 3.0 23.0 + - - +
404A VAL* 4.1 16.9 - - - +
405A GLY* 4.8 0.7 - - - -
408A MET* 4.2 9.4 - - - -
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Residues in contact with HIS 378 (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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348A ALA* 3.6 14.9 - - + +
374A HIS* 3.0 56.9 + + - -
375A GLU* 3.1 19.8 + - - +
377A GLY* 1.3 75.1 - - - +
379A ILE* 1.3 61.5 + - - +
381A TYR* 3.2 6.0 + - - +
382A ASP* 3.0 28.5 + - - +
401A HIS* 3.4 57.6 + + + -
402A GLU* 3.8 11.8 + - + -
404A VAL* 6.1 0.2 - - - -
405A GLY* 4.5 0.4 - - - -
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Residues in contact with ILE 379 (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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323A MET* 3.9 28.9 - - + -
327A PHE* 4.8 2.2 - - + -
348A ALA* 3.7 13.7 - - + -
349A TRP 3.7 15.9 - - - +
356A PHE* 4.2 15.5 - - + -
357A ARG 3.2 26.2 - - - +
358A ILE* 3.6 21.1 - - + -
375A GLU 3.0 16.5 + - - +
376A MET* 3.6 9.2 - - - +
377A GLY 3.2 0.4 - - - -
378A HIS* 1.3 75.3 - - - +
380A GLN* 1.3 58.7 + - - +
382A ASP* 3.3 8.5 + - - +
383A MET* 2.9 36.1 + - - +
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Residues in contact with GLN 380 (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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312A GLU* 6.2 0.6 - - - +
315A PHE* 3.6 32.3 - - + +
320A LEU* 3.6 33.8 - - + +
321A PRO* 3.0 36.7 + - - +
322A ASN 4.6 0.6 + - - -
323A MET* 3.3 22.4 - - + +
376A MET 2.9 20.3 + - - +
377A GLY* 3.6 7.0 - - - +
379A ILE* 1.3 74.7 - - - +
381A TYR* 1.3 66.3 + - - +
383A MET* 3.3 8.1 + - - +
384A ALA* 2.9 24.8 + - - +
404A VAL* 6.2 0.7 - - + -
408A MET* 6.2 1.1 - - + -
558A LEU* 5.4 4.7 - - + -
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Residues in contact with TYR 381 (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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377A GLY 3.0 12.8 + - - +
378A HIS* 3.2 10.1 + - - +
380A GLN* 1.3 75.4 - - - +
382A ASP* 1.3 62.8 + - - +
384A ALA* 3.0 10.9 + - - +
385A TYR* 3.1 31.5 + + - -
395A GLY* 3.7 5.7 - - - -
396A ALA* 3.4 21.8 + - - +
400A PHE* 3.7 22.0 - + + -
401A HIS* 3.5 44.9 - + + +
404A VAL* 4.3 14.8 - - + +
557A MET* 3.6 21.8 + - - -
558A LEU* 3.3 47.9 - - + +
561A GLY 4.6 4.7 + - - -
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Residues in contact with ASP 382 (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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348A ALA* 4.4 6.9 - - - +
350A ASP* 3.5 25.8 + - + +
356A PHE* 3.7 23.6 - - + -
378A HIS* 3.0 17.1 + - - +
379A ILE* 3.3 15.3 + - - +
381A TYR* 1.3 75.9 - - - +
383A MET* 1.3 63.0 + - - +
384A ALA 3.4 0.5 + - - -
385A TYR* 2.4 40.8 + - - -
386A ALA* 3.4 16.8 + - - +
401A HIS* 2.9 16.3 + - - -
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Residues in contact with MET 383 (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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321A PRO* 3.7 24.2 - - + -
322A ASN 3.6 19.3 - - - +
323A MET* 3.8 27.6 - - + +
324A THR* 4.3 21.5 - - + -
356A PHE* 3.7 33.9 - - + -
379A ILE* 2.9 23.9 + - - +
380A GLN* 3.7 9.2 - - - +
382A ASP* 1.3 76.2 - - - +
384A ALA* 1.3 61.8 + - - +
386A ALA* 3.5 14.7 + - - +
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Residues in contact with ALA 384 (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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320A LEU* 6.1 0.2 - - + -
380A GLN 2.9 17.3 + - - +
381A TYR 3.0 5.1 + - - +
383A MET* 1.3 79.9 - - - +
385A TYR* 1.3 58.2 + - - +
386A ALA 3.4 1.1 + - - -
387A ALA* 4.8 3.5 + - - +
555A PHE* 3.7 30.4 - - + -
558A LEU* 3.6 28.9 - - + -
559A ARG* 3.5 19.6 + - - +
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Residues in contact with TYR 385 (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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350A ASP* 3.9 10.5 + - - -
381A TYR* 3.1 48.2 + + - -
382A ASP* 2.4 38.7 + - - -
383A MET 3.4 0.2 - - - -
384A ALA* 1.3 75.5 - - - +
386A ALA* 1.3 62.2 + - - +
387A ALA 3.3 2.7 - - - -
388A GLN* 3.4 15.0 + - + +
393A ARG* 3.5 38.6 + - + +
394A ASN* 3.6 18.2 + - - -
401A HIS* 3.2 21.7 + + - -
558A LEU 3.6 9.9 - - - +
559A ARG 4.0 7.6 - - - +
561A GLY* 3.8 23.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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