Contacts of the helix formed by residues 472 - 491 (chain A) in PDB entry 2VWK
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 ASP 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A THR* 3.4 10.9 - - + +
471A ILE* 1.3 81.4 - - + +
473A PRO* 1.3 62.4 - - - +
474A ILE* 3.1 28.2 + - - +
475A GLU* 3.2 22.6 + - + +
476A LYS* 2.8 33.7 + - - +
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Residues in contact with PRO 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ILE 3.3 10.3 - - - +
472A ASP* 1.3 90.0 - - - +
474A ILE* 1.3 62.0 + - + +
476A LYS* 3.7 17.0 - - + +
477A LYS* 3.2 26.3 + - - +
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Residues in contact with ILE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ASP* 3.1 18.1 + - - +
473A PRO* 1.3 81.3 - - + +
475A GLU* 1.3 69.2 + - - +
477A LYS* 3.2 5.2 + - - +
478A LEU* 3.1 27.4 + - + +
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Residues in contact with GLU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A THR* 3.7 14.4 - - + -
472A ASP* 3.2 22.5 + - + +
474A ILE* 1.3 81.2 - - + +
476A LYS* 1.3 57.2 + - - +
478A LEU* 3.4 8.0 + - - +
479A LEU* 2.9 40.8 + - + +
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Residues in contact with LYS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A MET* 3.2 30.8 + - + +
468A LYS* 4.4 10.3 + - - +
470A THR* 2.8 34.5 + - - +
471A ILE* 4.4 10.2 - - - +
472A ASP 2.8 17.1 + - - +
473A PRO* 3.7 13.7 - - + -
475A GLU* 1.3 77.6 - - - +
477A LYS* 1.3 62.4 + - - +
479A LEU* 3.4 7.2 + - - +
480A ASP* 3.0 21.8 + - + +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A PRO 3.2 18.0 + - - +
474A ILE* 3.7 5.2 - - - +
476A LYS* 1.3 78.3 - - - +
478A LEU* 1.3 63.3 + - - +
480A ASP* 3.1 19.4 + - + +
481A TYR* 3.1 45.7 + - + +
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PRO* 6.0 2.9 - - + -
332A GLN* 4.6 16.8 - - - +
474A ILE* 3.1 18.0 + - + +
475A GLU* 3.6 11.7 - - - +
477A LYS* 1.3 73.6 - - - +
479A LEU* 1.3 65.8 + - + +
481A TYR* 3.0 21.1 + - + +
482A ARG* 2.9 22.0 + - + +
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Residues in contact with LEU 479 (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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463A VAL* 3.2 26.5 - - + +
466A LYS* 3.8 31.6 - - + +
467A MET* 4.0 14.8 - - + -
470A THR* 3.7 24.2 - - + +
475A GLU* 2.9 28.2 + - + +
476A LYS* 3.7 4.3 - - - +
478A LEU* 1.3 77.5 - - + +
480A ASP* 1.3 57.4 + - - +
482A ARG* 3.2 25.0 + - - +
483A GLN* 2.9 25.5 + - - +
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Residues in contact with ASP 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A MET* 3.5 20.2 - - + +
476A LYS* 3.0 13.7 + - + +
477A LYS* 3.1 18.1 + - + +
479A LEU* 1.3 75.2 - - - +
481A TYR* 1.3 66.9 + - - +
483A GLN* 2.8 44.2 + - - +
484A ARG* 3.0 16.5 + - - +
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Residues in contact with TYR 481 (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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324A LYS 5.5 1.0 + - - -
325A GLU* 4.5 18.2 + - - -
328A PRO* 3.6 37.1 - - + +
329A MET* 3.2 37.0 - - + +
332A GLN* 3.5 18.6 - - + -
477A LYS* 3.1 48.5 + - + +
478A LEU* 3.0 20.2 + - + +
480A ASP* 1.3 81.3 - - - +
482A ARG* 1.3 68.0 + - - +
484A ARG* 3.0 1.7 + - + -
485A ALA* 2.9 21.5 + - - +
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Residues in contact with ARG 482 (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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332A GLN* 3.5 21.9 - - - +
335A ARG* 3.8 31.6 - - - +
459A GLU* 2.7 32.9 + - - +
463A VAL* 3.7 23.2 - - + +
478A LEU* 2.9 12.3 + - + +
479A LEU* 3.3 30.4 - - - +
481A TYR* 1.3 78.9 - - - +
483A GLN* 1.3 63.3 + - - +
485A ALA* 3.3 8.4 + - - +
486A ILE* 3.1 26.4 + - + +
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Residues in contact with GLN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ARG* 2.9 54.9 + - + +
463A VAL* 3.7 17.2 - - + +
464A LYS* 3.3 35.5 + - + +
467A MET* 4.3 5.2 - - - +
479A LEU 2.9 14.8 + - - +
480A ASP* 2.8 41.0 + - - +
482A ARG* 1.3 76.3 - - - +
484A ARG* 1.3 66.7 + - - +
486A ILE* 3.3 8.6 + - - +
487A LYS 3.3 9.5 + - - -
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Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 3.9 18.2 - - - -
480A ASP* 3.0 19.3 + - - +
481A TYR* 3.0 5.2 + - + +
483A GLN* 1.3 83.6 - - - +
485A ALA* 1.3 63.4 + - - +
487A LYS* 3.5 19.9 + - + +
488A ILE* 3.3 29.8 + - + +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 3.4 21.3 - - + +
332A GLN* 3.8 17.7 - - + -
333A LEU* 3.5 26.0 - - + +
336A LEU* 3.4 16.9 - - + +
481A TYR 2.9 9.5 + - - +
482A ARG 3.3 5.4 + - - +
484A ARG* 1.3 74.8 - - - +
486A ILE* 1.3 66.3 + - - +
487A LYS 3.2 0.2 - - - -
488A ILE* 3.4 1.5 + - - -
489A LEU 3.1 17.3 + - - -
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Residues in contact with ILE 486 (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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336A LEU* 3.8 31.6 - - + -
456A LEU* 3.3 45.9 - - + +
457A LEU* 5.2 0.4 - - + -
459A GLU* 4.6 17.3 - - + -
460A ARG* 3.8 19.7 - - + -
463A VAL* 5.4 1.6 - - + -
482A ARG* 3.1 27.8 - - + +
483A GLN* 3.5 9.9 - - - +
485A ALA* 1.3 76.4 - - + +
487A LYS* 1.3 53.5 + - - +
489A LEU* 3.4 1.4 + - - +
490A ALA* 2.8 39.5 + - + +
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Residues in contact with LYS 487 (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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460A ARG* 3.7 34.1 - - - +
483A GLN 3.3 3.9 + - - +
484A ARG* 3.5 23.3 - - + +
485A ALA 3.2 0.4 - - - -
486A ILE* 1.3 78.7 - - - +
488A ILE* 1.3 61.7 + - + +
490A ALA* 3.2 4.5 + - - +
491A ASN* 2.9 51.4 + - - +
1774A NA 3.1 19.6 - - - -
1776A SO4 3.4 25.1 + - - +
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Residues in contact with ILE 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 4.7 15.5 - - + -
333A LEU* 4.0 30.3 - - + -
349A THR* 5.0 11.4 - - + -
352A LEU* 5.0 7.0 - - + -
484A ARG* 3.3 22.9 + - + +
485A ALA* 3.8 8.1 - - - +
486A ILE 3.4 0.2 - - - -
487A LYS* 1.3 84.0 - - + +
489A LEU* 1.3 56.3 + - - +
491A ASN* 3.8 3.9 + - - +
492A SER* 2.6 35.0 + - - +
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Residues in contact with LEU 489 (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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333A LEU* 5.0 3.6 - - + -
336A LEU* 3.8 22.0 - - + -
337A VAL* 4.3 9.2 - - + -
352A LEU* 3.8 26.2 - - + +
353A VAL* 3.8 25.1 - - + -
356A PHE* 3.6 35.0 - - + -
456A LEU* 3.8 17.3 - - + -
485A ALA 3.1 16.3 + - - +
486A ILE 3.9 3.1 - - - +
488A ILE* 1.3 77.1 - - - +
490A ALA* 1.3 64.9 + - - +
492A SER* 2.9 18.0 + - - -
493A PHE* 3.2 19.7 - - + -
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Residues in contact with ALA 490 (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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407A SER* 6.0 0.2 - - - +
410A PRO* 3.8 12.5 - - + +
453A LEU* 3.8 17.1 - - + +
456A LEU* 4.6 8.0 - - + +
457A LEU* 3.8 28.7 - - + -
486A ILE* 2.8 23.5 + - + +
487A LYS* 3.7 5.4 - - - +
489A LEU* 1.3 73.3 - - - +
491A ASN* 1.3 64.3 + - - +
492A SER 3.1 4.9 + - - -
493A PHE* 3.3 20.2 + - - +
494A TYR 4.9 0.3 + - - -
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Residues in contact with ASN 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A SER* 4.4 3.1 + - - -
410A PRO* 3.6 24.4 - - - +
487A LYS* 2.9 33.6 + - - +
488A ILE* 4.0 3.8 - - - +
490A ALA* 1.3 76.3 - - - +
492A SER* 1.3 58.9 + - - +
493A PHE 3.5 0.4 - - - -
494A TYR* 4.7 8.6 + - - +
495A GLY 4.9 2.6 + - - -
1776A SO4 3.2 36.9 + - - -
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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
------------------------------------------------------------
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