Contacts of the helix formed by residues 359 - 380 (chain A) in PDB entry 3VRY
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 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A LYS 3.2 10.5 - - - +
358A GLN* 1.3 91.3 - - + +
360A LEU* 1.3 65.4 + - - +
361A PRO* 3.9 12.8 - - + -
362A LYS* 3.0 25.7 + - + +
363A LEU* 3.2 10.4 + - - +
458A TYR* 4.5 0.9 - - - +
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Residues in contact with LEU 360 (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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358A GLN 3.9 0.4 + - - -
359A PRO* 1.3 69.6 - - - +
361A PRO* 1.4 64.6 - - + +
363A LEU* 3.2 17.4 + - + +
364A ILE* 2.8 37.3 + - + +
456A VAL* 3.7 30.3 - - + -
458A TYR* 4.6 2.0 + - - -
486A ASN* 3.7 21.8 - - + +
488A PRO* 3.5 35.4 - - + -
491A LEU* 4.6 0.2 - - + -
520A TYR* 3.9 13.9 - - - +
524B GLU* 5.8 1.1 - - - +
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Residues in contact with PRO 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PRO* 3.4 16.6 - - + -
360A LEU* 1.4 95.0 - - + +
362A LYS* 1.3 55.4 + - - +
364A ILE* 3.7 3.5 + - + +
365A ASP* 3.0 24.6 + - - +
520A TYR* 3.8 35.8 - - + +
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Residues in contact with LYS 362 (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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164A LEU 5.8 1.8 + - - -
358A GLN* 3.4 26.1 + - + +
359A PRO* 3.0 21.4 + - + +
361A PRO* 1.3 76.3 - - - +
363A LEU* 1.3 57.1 + - - +
365A ASP* 3.1 21.2 + - + +
366A PHE* 2.8 63.1 + - + -
398A LEU* 3.6 26.6 - - - +
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Residues in contact with LEU 363 (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 LEU* 3.6 30.5 - - + -
358A GLN* 4.0 16.8 - - + +
359A PRO 3.2 9.8 + - - +
360A LEU* 3.2 23.8 + - + +
362A LYS* 1.3 78.2 - - - +
364A ILE* 1.3 62.2 + - + +
366A PHE* 3.1 14.7 + - + +
367A SER* 3.1 19.5 + - - -
455A ILE* 3.7 32.7 - - + +
456A VAL* 4.2 11.2 - - + +
458A TYR* 3.5 34.1 - - + +
486A ASN* 4.8 1.3 - - - +
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Residues in contact with ILE 364 (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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360A LEU* 2.8 30.6 + - + +
361A PRO* 3.8 5.8 - - + +
363A LEU* 1.3 70.3 - - + +
365A ASP* 1.3 66.1 + - - +
367A SER* 2.7 23.2 + - - +
368A ALA* 2.8 10.6 + - - +
488A PRO* 5.1 0.2 - - + -
491A LEU* 3.7 28.9 - - + -
516A LEU* 4.0 28.0 - - + +
519A PHE* 3.4 45.3 - - + -
520A TYR* 3.4 20.2 - - + +
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Residues in contact with ASP 365 (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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157A LYS* 4.0 13.3 + - - +
161A ARG* 2.7 37.8 + - - +
361A PRO 3.0 17.2 + - - +
362A LYS* 3.2 27.8 - - + +
364A ILE* 1.3 74.4 - - - +
366A PHE* 1.3 63.3 + - - +
368A ALA* 3.1 8.2 + - - +
369A GLN* 2.8 52.1 + - - +
516A LEU 6.0 0.2 - - - -
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.3 14.6 - - + -
349A PHE* 4.0 30.5 - + - -
350A LEU* 4.7 2.0 - - + -
358A GLN* 4.4 5.4 - - + -
362A LYS* 2.8 51.5 + - + -
363A LEU* 3.2 29.4 - - + +
364A ILE 3.1 0.2 - - - -
365A ASP* 1.3 72.6 - - - +
367A SER* 1.3 58.5 + - - +
369A GLN* 2.9 30.1 + - - +
370A ILE* 3.0 17.7 + - - +
394A VAL* 5.6 2.2 - - + -
398A LEU* 3.8 30.3 - - + -
400A CYS* 3.8 24.4 - - - -
455A ILE* 4.5 10.5 - - + -
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Residues in contact with SER 367 (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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363A LEU 3.1 7.4 + - - -
364A ILE* 2.7 25.6 + - - +
366A PHE* 1.3 79.5 - - - +
368A ALA* 1.3 54.7 + - - +
370A ILE* 3.4 5.4 + - - +
371A ALA* 3.0 22.9 + - - +
448A PHE* 3.3 12.9 - - - -
452A LEU* 3.3 34.1 - - - +
455A ILE* 3.6 21.4 - - - +
491A LEU* 5.6 1.0 - - - +
516A LEU* 3.8 7.1 - - - +
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Residues in contact with ALA 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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157A LYS* 5.5 1.1 - - - -
161A ARG* 4.1 7.6 - - - +
364A ILE 2.8 11.0 + - - +
365A ASP* 3.5 11.0 - - - +
366A PHE 3.1 0.2 - - - -
367A SER* 1.3 74.1 - - - +
369A GLN* 1.3 61.0 + - - +
371A ALA* 3.4 2.7 + - - +
372A GLU* 2.9 28.6 + - - +
513A GLN* 4.5 1.8 - - - +
516A LEU* 3.6 34.1 - - + +
517A ASP* 3.5 25.1 - - - +
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Residues in contact with GLN 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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161A ARG* 3.6 27.7 - - - +
321A LYS* 3.5 30.3 - - + +
362A LYS* 5.4 0.4 - - - +
365A ASP* 2.8 37.0 + - - +
366A PHE* 3.2 17.8 - - - +
368A ALA* 1.3 78.9 - - - +
370A ILE* 1.3 60.8 + - - +
372A GLU* 3.2 11.3 - - - +
373A GLY 3.1 17.2 + - - -
398A LEU 3.5 17.4 + - - -
399A VAL* 3.4 7.5 - - - +
400A CYS* 2.7 37.8 + - + -
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Residues in contact with ILE 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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321A LYS* 5.6 0.4 - - - -
346A LEU* 4.0 8.3 - - + -
366A PHE 3.0 14.1 + - - +
367A SER* 3.6 6.3 - - - +
369A GLN* 1.3 74.9 - - - +
371A ALA* 1.3 54.0 + - - +
373A GLY* 3.1 3.5 + - - -
374A MET* 2.8 39.7 + - + +
387A LEU* 4.7 1.6 - - + -
392A ILE* 3.8 43.5 - - + -
400A CYS* 4.3 8.1 - - + -
402A ILE* 3.6 10.6 - - + +
448A PHE* 3.6 21.1 - - + -
451A LEU* 4.0 14.4 - - + -
455A ILE* 3.9 25.8 - - + -
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Residues in contact with ALA 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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367A SER 3.0 16.9 + - - +
368A ALA 3.9 3.8 - - - +
370A ILE* 1.3 72.9 - - - +
372A GLU* 1.3 57.0 + - - +
374A MET* 3.5 7.9 - - - +
375A ALA* 2.7 35.2 + - - +
448A PHE* 3.7 18.6 - - + -
509A PHE* 4.0 6.4 - - + +
512A ILE* 3.9 20.4 - - + -
513A GLN* 4.0 16.3 - - - +
516A LEU* 4.2 2.7 - - + -
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Residues in contact with GLU 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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155A SER* 5.2 3.2 + - - -
158A ASP* 4.0 8.5 - - - +
161A ARG* 4.1 13.7 + - - -
319A HIS* 3.6 23.8 + - + +
320A ASP* 5.8 0.2 - - - +
321A LYS* 3.4 33.2 + - - -
368A ALA 2.9 13.0 + - - +
369A GLN* 3.2 11.6 - - - +
371A ALA* 1.3 76.3 - - - +
373A GLY* 1.3 62.7 + - - +
375A ALA* 3.1 12.5 + - - +
376A PHE* 3.1 12.8 + - - +
513A GLN* 3.6 31.5 + - + +
517A ASP* 5.3 3.0 - - - +
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Residues in contact with GLY 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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319A HIS* 4.6 1.6 - - - -
321A LYS* 3.7 17.6 - - - +
322A LEU* 3.8 7.7 - - - +
369A GLN 3.1 7.7 + - - -
370A ILE 3.1 3.8 + - - -
372A GLU* 1.3 79.2 - - - +
374A MET* 1.3 60.7 + - - +
376A PHE* 3.2 8.0 - - - +
377A ILE* 3.2 25.8 + - - +
402A ILE* 3.6 17.3 - - - -
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Residues in contact with MET 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 ILE* 2.8 24.8 + - + +
371A ALA* 3.7 2.0 - - - +
373A GLY* 1.3 74.4 - - - +
375A ALA* 1.3 59.4 + - - +
377A ILE* 3.5 29.4 + - + +
378A GLU* 3.0 27.7 + - - +
384A HIS* 4.1 10.1 - - + -
387A LEU* 4.1 26.7 - - + -
402A ILE* 3.7 18.8 - - + -
441A ILE* 4.1 0.9 - - + -
444A ASP* 3.9 20.9 - - + +
448A PHE* 4.8 0.2 - - + -
509A PHE* 3.3 57.0 - - + -
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Residues in contact with ALA 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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371A ALA 2.7 20.3 + - - +
372A GLU 3.1 2.0 + - - +
374A MET* 1.3 70.9 - - - +
376A PHE* 1.3 60.2 + - - +
378A GLU* 3.6 5.9 - - - +
379A GLN* 2.9 28.9 + - - +
509A PHE* 3.6 8.0 - - - +
510A GLU* 3.6 27.1 - - + +
513A GLN* 3.4 21.5 - - - +
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Residues in contact with PHE 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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317A LEU* 3.8 30.3 - - + -
318A GLN 3.6 26.9 - - - -
319A HIS* 3.4 39.9 - + + +
322A LEU* 4.2 6.1 - - + -
372A GLU 3.1 11.1 + - - +
373A GLY 3.2 13.5 - - - +
375A ALA* 1.3 74.8 - - - +
377A ILE* 1.3 68.2 + - + +
379A GLN* 3.0 11.8 + - + +
380A ARG* 2.9 71.3 + - + +
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Residues in contact with ILE 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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317A LEU* 5.4 2.2 - - + -
322A LEU* 4.0 24.2 - - + -
373A GLY 3.2 13.4 + - - +
374A MET* 3.8 35.7 - - + +
376A PHE* 1.3 82.9 - - + +
378A GLU* 1.3 61.0 + - - +
380A ARG* 3.2 9.7 + - - -
382A TYR* 3.0 63.3 + - + +
383A ILE* 4.1 4.5 - - - +
384A HIS* 4.5 7.4 - - + +
402A ILE* 4.7 1.8 - - + -
405A PHE* 4.0 27.1 - - + -
441A ILE* 4.2 2.9 - - + -
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Residues in contact with GLU 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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374A MET 3.0 18.6 + - - +
375A ALA 3.6 5.4 - - - +
377A ILE* 1.3 77.6 - - - +
379A GLN* 1.3 56.5 + - - +
381A ASN* 3.0 24.7 + - - +
382A TYR 4.8 0.9 - - - -
441A ILE* 3.7 33.7 - - + +
442A LYS* 5.4 0.9 + - - +
445A VAL* 5.2 1.4 - - - +
508A THR* 3.5 16.5 - - - +
509A PHE* 2.9 31.2 + - + -
510A GLU* 3.3 31.2 + - - +
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Residues in contact with GLN 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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375A ALA 2.9 16.1 + - - +
376A PHE* 3.0 16.8 + - + +
378A GLU* 1.3 77.2 + - - +
380A ARG* 1.3 62.9 + - + +
381A ASN* 3.1 11.8 + - - -
510A GLU* 5.5 4.9 - - - +
505B GLU* 5.6 3.6 + - - -
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Residues in contact with ARG 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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316A THR* 3.3 26.3 + - - -
317A LEU* 3.8 26.3 - - + +
318A GLN 4.8 2.0 + - - +
376A PHE* 2.9 46.3 + - + +
377A ILE 3.2 5.3 + - - +
379A GLN* 1.3 79.5 - - + +
381A ASN* 1.3 70.1 + - - +
382A TYR* 3.1 5.1 + - + +
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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
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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