Contacts of the helix formed by residues 447 - 470 (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 GLY 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ASN* 2.9 21.3 + - - +
421A ASP* 3.5 20.2 - - - -
422A THR* 4.0 6.3 - - - -
446A PRO* 1.3 72.8 - - - +
448A PHE* 1.3 66.1 + - - -
449A ILE 3.3 2.9 - - - -
450A PRO* 3.6 8.9 - - - +
451A SER* 3.0 25.0 + - - -
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Residues in contact with PHE 448 (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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357A LEU* 3.9 11.2 - - + -
361A ALA* 3.7 29.2 - - + -
364A ARG* 3.9 39.3 - - + +
366A GLU* 4.2 28.0 - - + +
419A SER* 5.2 0.7 - - - +
421A ASP* 3.3 19.3 + - - +
446A PRO 3.8 1.6 + - - -
447A GLY* 1.3 70.1 - - - -
449A ILE* 1.3 67.7 + - + +
451A SER* 3.1 18.9 + - - -
452A LEU* 3.3 41.5 - - + +
504A TRP* 3.6 43.5 - + + +
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Residues in contact with ILE 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.7 33.4 - - + -
413A ILE* 4.7 5.2 - - + -
419A SER* 4.3 3.4 + - - +
420A PRO* 4.8 3.8 - - + -
448A PHE* 1.3 82.9 - - + +
450A PRO* 1.4 72.1 - - + +
452A LEU* 3.1 8.1 + - - +
453A LEU* 2.9 21.0 + - + +
493A PHE* 3.6 25.2 - - + -
496A TYR* 4.6 2.2 - - + -
497A TYR* 3.1 39.0 - - + +
504A TRP* 3.7 42.0 - - + -
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Residues in contact with PRO 450 (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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413A ILE* 3.8 28.7 - - + +
414A ILE* 3.8 13.8 - - + +
417A ASN* 3.3 32.1 - - - +
418A VAL 3.6 17.0 - - - +
419A SER* 3.5 17.0 - - - -
446A PRO* 6.0 0.4 - - + -
447A GLY* 3.5 6.3 - - - +
449A ILE* 1.4 95.5 - - + +
451A SER* 1.3 57.0 + - - +
453A LEU* 3.3 4.9 + - + +
454A GLY* 2.9 26.0 + - - -
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 2.4 34.8 + - - -
446A PRO* 4.4 16.4 - - - -
447A GLY 3.0 15.4 + - - +
448A PHE* 3.1 7.4 + - - -
450A PRO* 1.3 74.2 - - - +
452A LEU* 1.3 62.8 - - - +
454A GLY* 3.3 2.9 + - - +
455A ASP* 3.1 30.1 + - - +
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A PHE* 4.3 12.1 - - + -
357A LEU* 3.6 29.2 - - + -
360A LYS* 3.8 40.6 - - + +
364A ARG* 4.0 21.5 - - - +
448A PHE* 3.3 36.6 - - + +
449A ILE* 3.1 5.5 + - - +
451A SER* 1.3 73.6 + - - +
453A LEU* 1.3 66.1 + - - +
455A ASP* 3.3 13.2 + - + +
456A LEU* 3.0 26.5 + - - +
493A PHE* 5.1 3.1 - - + -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PRO* 3.7 33.7 - - + +
413A ILE* 3.9 33.0 - - + -
414A ILE* 3.9 9.0 - - + -
449A ILE 2.9 10.6 + - - +
450A PRO 3.5 8.5 - - - +
452A LEU* 1.3 72.7 - - - +
454A GLY* 1.3 66.3 + - - +
456A LEU* 2.9 8.8 + - + +
457A LEU* 2.9 27.4 + - + +
490A ALA* 3.8 27.1 - - + +
493A PHE* 3.8 42.7 - - + -
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Residues in contact with GLY 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ILE* 3.7 23.8 - - - +
450A PRO 2.9 13.8 + - - -
451A SER* 3.7 4.9 - - - -
452A LEU 3.2 0.4 - - - -
453A LEU* 1.3 75.9 - - - +
455A ASP* 1.3 57.5 - - - +
457A LEU* 3.3 3.1 + - - +
458A GLU* 3.0 39.5 + - - +
574A LEU* 5.5 1.6 - - - -
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 5.7 1.7 + - - -
451A SER* 3.1 15.5 + - - +
452A LEU* 3.5 14.7 - - + +
454A GLY* 1.3 73.7 - - - +
456A LEU* 1.3 60.2 + - - +
458A GLU* 3.5 12.9 + - - +
459A GLU* 2.9 29.6 + - - +
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Residues in contact with LEU 456 (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* 4.1 23.3 - - + -
356A PHE* 4.1 15.5 - - + -
452A LEU 3.0 15.5 + - - +
453A LEU* 2.9 17.3 + - + +
455A ASP* 1.3 72.7 - - - +
457A LEU* 1.3 60.3 + - - +
459A GLU* 3.1 5.3 + - + +
460A ARG 2.9 25.8 + - - -
486A ILE* 3.3 33.4 - - + +
489A LEU* 3.8 19.3 - - + -
490A ALA* 4.6 7.6 - - + +
493A PHE* 3.8 34.3 - - + -
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Residues in contact with LEU 457 (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 19.7 - - - +
410A PRO* 3.9 20.9 - - + -
411A SER* 4.5 6.5 - - - +
414A ILE* 3.6 25.6 - - + -
453A LEU* 2.9 19.0 + - + +
454A GLY 3.7 6.7 - - - +
456A LEU* 1.3 72.1 - - - +
458A GLU* 1.3 63.2 + - + +
460A ARG* 3.4 12.0 + - + +
461A GLN* 3.1 22.5 + - - +
486A ILE* 5.8 0.4 - - + -
490A ALA* 3.8 28.3 - - + -
574A LEU* 4.6 10.3 - - + -
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Residues in contact with GLU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLY* 3.0 25.5 + - - +
455A ASP* 3.8 12.0 - - - +
457A LEU* 1.3 76.1 - - + +
459A GLU* 1.3 64.5 + - - +
461A GLN* 3.5 7.7 + - - +
462A LYS* 3.2 22.7 + - - +
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Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP 2.9 18.7 + - - +
456A LEU* 3.6 7.2 - - + +
458A GLU* 1.3 72.7 - - - +
460A ARG* 1.3 66.5 + - - +
462A LYS* 3.2 22.9 + - - +
463A VAL* 2.9 35.3 + - + +
482A ARG* 2.7 32.8 + - - +
486A ILE* 4.6 14.6 - - + -
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Residues in contact with ARG 460 (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* 4.9 3.8 + - - -
456A LEU 2.9 11.9 + - - +
457A LEU* 3.5 16.5 - - + +
459A GLU* 1.3 76.9 - - - +
461A GLN* 1.3 58.0 + - - +
463A VAL* 3.1 5.2 + - - +
464A LYS* 2.8 48.2 + - + +
483A GLN* 2.9 55.1 + - + +
486A ILE* 3.8 16.9 - - + +
487A LYS* 3.7 34.0 - - - +
490A ALA* 6.3 0.4 - - - -
1774A NA 3.3 26.3 - - - -
1776A SO4 4.0 16.0 + - - -
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Residues in contact with GLN 461 (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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406A ARG* 5.6 8.1 - - - +
457A LEU 3.1 10.3 + - - +
458A GLU* 3.6 11.9 - - - +
459A GLU 3.3 0.2 - - - -
460A ARG* 1.3 80.4 - - - +
462A LYS* 1.3 57.1 + - - +
464A LYS* 3.5 8.9 + - + +
465A LYS* 2.9 47.3 + - + +
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Residues in contact with LYS 462 (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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458A GLU 3.2 14.3 + - - +
459A GLU* 3.6 25.8 - - - +
461A GLN* 1.3 77.9 - - - +
463A VAL* 1.3 59.0 + - + +
465A LYS* 3.3 13.4 + - + +
466A LYS* 3.1 31.3 + - + +
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Residues in contact with VAL 463 (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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459A GLU* 2.9 28.8 + - + +
460A ARG* 3.5 5.8 - - - +
462A LYS* 1.3 73.9 - - + +
464A LYS* 1.3 54.9 + - - +
466A LYS* 3.1 8.5 + - - +
467A MET* 2.8 33.5 + - + +
479A LEU* 3.2 38.8 - - + +
482A ARG* 3.7 42.8 - - + +
483A GLN* 3.7 17.3 - - + +
486A ILE* 5.4 1.8 - - + -
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Residues in contact with LYS 464 (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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406A ARG* 5.3 10.1 - - - +
460A ARG* 2.8 46.4 + - + +
461A GLN* 3.6 8.3 - - - +
463A VAL* 1.3 72.9 - - - +
465A LYS* 1.3 60.9 + - - +
467A MET* 3.2 18.6 + - + +
468A LYS* 3.1 49.7 + - - +
483A GLN* 3.3 36.8 + - + +
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Residues in contact with LYS 465 (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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461A GLN* 2.9 31.9 + - + +
462A LYS* 3.4 15.0 - - + +
463A VAL 3.3 0.2 - - - -
464A LYS* 1.3 73.4 - - - +
466A LYS* 1.3 60.8 + - - +
468A LYS* 3.7 11.1 + - - +
469A ALA* 3.3 22.5 + - - +
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Residues in contact with LYS 466 (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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462A LYS* 3.1 16.3 + - + +
463A VAL* 3.1 10.1 + - - +
465A LYS* 1.3 75.7 - - - +
467A MET* 1.3 61.8 + - - +
469A ALA* 3.3 8.8 + - - +
470A THR* 2.6 39.8 + - - +
479A LEU* 4.0 21.5 - - + -
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Residues in contact with MET 467 (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 2.8 13.1 + - - +
464A LYS* 3.4 25.6 - - + +
466A LYS* 1.3 77.7 - - - +
468A LYS* 1.3 87.3 + - + +
470A THR* 3.3 7.3 + - - +
476A LYS* 3.2 50.6 + - + +
479A LEU* 4.0 15.4 - - + +
480A ASP* 3.5 38.4 - - + +
483A GLN* 4.3 6.3 - - - +
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Residues in contact with LYS 468 (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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464A LYS* 3.1 39.2 + - - +
465A LYS* 4.2 10.4 - - - +
466A LYS 3.3 0.2 - - - -
467A MET* 1.3 93.0 - - + +
469A ALA* 1.3 58.9 + - - +
470A THR 3.4 0.6 + - - -
476A LYS* 4.4 9.1 + - - +
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Residues in contact with ALA 469 (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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465A LYS 3.3 16.7 + - - +
466A LYS* 3.3 12.9 + - + +
467A MET 3.2 1.0 - - - -
468A LYS* 1.3 77.6 - - - +
470A THR* 1.3 60.5 + - - +
471A ILE* 3.6 3.6 + - - +
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Residues in contact with THR 470 (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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466A LYS* 2.6 29.0 + - - +
467A MET* 3.3 5.9 + - - -
468A LYS 3.4 0.6 - - - -
469A ALA* 1.3 76.1 - - - +
471A ILE* 1.3 61.2 + - - +
472A ASP* 3.4 26.0 - - + +
475A GLU* 3.7 20.9 - - + -
476A LYS* 2.8 35.9 + - - +
479A LEU* 3.7 11.7 - - + +
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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