Contacts of the helix formed by residues 471 - 488 (chain A) in PDB entry 3VOQ
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 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A PRO 3.5 10.1 - - - +
449A SER* 3.5 16.2 + - - +
470A SER* 1.3 87.1 + - - +
472A ALA* 1.3 65.0 + - - +
473A ALA* 2.9 32.9 + - - +
474A THR* 3.0 27.1 + - - -
475A VAL* 3.1 19.8 + - - +
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Residues in contact with ALA 472 (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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445A GLU* 3.1 28.0 - - + +
447A SER 3.9 14.1 - - - +
448A PRO* 3.0 23.4 + - + +
451A ALA* 4.0 12.1 - - + +
470A SER 3.7 0.4 + - - -
471A ASP* 1.3 72.6 - - - +
473A ALA* 1.4 53.6 + - - +
475A VAL* 3.8 0.9 - - - +
476A ASN* 2.8 42.5 + - - +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A PRO 4.8 0.8 + - - -
471A ASP* 2.9 10.8 + - - +
472A ALA* 1.4 74.4 - - - +
474A THR* 1.3 59.3 + - - +
476A ASN* 3.4 6.8 + - - +
477A GLU* 3.0 30.7 + - - +
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Residues in contact with THR 474 (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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386A PHE* 4.2 14.1 - - + -
387A LYS 5.1 2.5 - - - +
388A VAL* 4.1 6.7 - - + -
470A SER* 3.6 20.1 + - - +
471A ASP* 3.0 27.9 + - - -
473A ALA* 1.3 71.1 - - - +
475A VAL* 1.3 59.1 + - - +
477A GLU* 3.3 11.4 + - - +
478A ILE* 3.0 47.3 + - + +
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Residues in contact with VAL 475 (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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442A LEU* 3.9 28.3 - - + -
451A ALA* 3.4 30.7 - - + +
452A ILE 4.6 0.9 - - - -
453A PHE* 3.8 36.6 - - + -
470A SER* 3.8 14.4 - - - +
471A ASP 3.1 18.8 + - - +
472A ALA 3.8 3.4 - - - +
474A THR* 1.3 77.7 - - - +
476A ASN* 1.3 61.3 + - - +
478A ILE* 3.2 4.1 + - - +
479A VAL* 2.9 30.5 + - + +
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Residues in contact with ASN 476 (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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442A LEU* 4.6 19.9 - - - +
445A GLU* 3.6 20.4 + - - +
472A ALA* 2.8 26.4 + - - +
473A ALA* 4.0 5.4 - - - +
475A VAL* 1.3 79.5 - - - +
477A GLU* 1.3 61.3 + - - +
479A VAL* 4.1 4.8 - - - +
480A LEU* 3.0 26.2 + - - +
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Residues in contact with GLU 477 (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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376A ASP* 5.4 7.9 - - - +
384A LYS* 2.5 39.0 + - - +
386A PHE* 3.6 19.6 - - + -
473A ALA 3.0 18.5 + - - +
474A THR* 3.5 8.4 - - - +
475A VAL 3.2 0.2 - - - -
476A ASN* 1.3 74.6 - - - +
478A ILE* 1.3 60.3 + - - +
480A LEU* 3.6 8.5 - - + +
481A LYS* 2.9 32.4 + - + +
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Residues in contact with ILE 478 (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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386A PHE* 3.7 44.6 - - + -
388A VAL* 3.9 12.6 - - + -
402A LEU* 4.2 3.6 - - + -
404A ILE* 3.6 21.3 - - + -
453A PHE* 3.6 39.7 - - + -
474A THR* 3.0 34.4 + - + +
475A VAL* 3.2 4.0 + - - +
477A GLU* 1.3 71.7 - - - +
479A VAL* 1.4 69.9 + - - +
481A LYS* 3.2 5.6 + - - +
482A VAL* 2.8 29.7 + - + +
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Residues in contact with VAL 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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440A CYS* 3.9 20.4 - - - +
441A ASP* 4.7 0.7 - - - -
442A LEU* 4.2 20.9 - - + +
453A PHE* 3.6 32.8 - - + -
475A VAL* 2.9 26.3 + - + +
476A ASN* 4.1 6.3 - - - +
478A ILE* 1.4 78.0 - - - +
480A LEU* 1.3 64.4 + - - +
482A VAL* 3.6 0.3 + - - -
483A ASN* 2.8 44.9 + - - +
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Residues in contact with LEU 480 (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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373A THR* 6.5 0.2 - - + -
376A ASP* 4.4 14.8 - - + +
476A ASN 3.0 19.6 + - - +
477A GLU* 3.6 8.1 - - + +
479A VAL* 1.3 79.1 - - - +
481A LYS* 1.3 59.6 + - - +
483A ASN* 3.3 3.9 + - + +
484A TYR* 2.8 74.3 + - + +
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Residues in contact with LYS 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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379A SER 3.6 6.3 + - - -
380A SER* 2.8 34.9 + - - +
382A HIS* 2.7 29.5 + - - +
384A LYS* 4.2 14.6 - - + +
386A PHE* 4.2 19.1 - - + -
404A ILE* 3.4 40.6 - - + -
405A SER* 4.7 0.4 - - - +
477A GLU* 2.9 18.2 + - + +
478A ILE* 3.2 5.4 + - - +
480A LEU* 1.3 80.4 - - - +
482A VAL* 1.3 64.4 + - - +
484A TYR* 3.1 13.1 + - - +
485A ILE* 3.0 26.1 + - + +
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Residues in contact with VAL 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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404A ILE* 3.9 31.4 - - + -
409A VAL* 5.1 4.0 - - + -
437A LEU* 4.3 17.5 - - + -
440A CYS* 3.6 35.4 - - + -
453A PHE* 6.1 0.2 - - + -
455A LEU* 4.2 17.0 - - + -
478A ILE* 2.8 25.1 + - + +
479A VAL 4.3 0.2 - - - +
481A LYS* 1.3 72.1 - - - +
483A ASN* 1.3 59.5 + - - +
485A ILE* 3.2 10.8 + - + +
486A LEU* 2.9 33.0 + - + +
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Residues in contact with ASN 483 (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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440A CYS* 2.8 32.6 + - - +
479A VAL* 2.8 36.3 + - - +
480A LEU* 3.9 5.1 - - + +
482A VAL* 1.3 73.4 - - - +
484A TYR* 1.3 62.7 + - + +
486A LEU* 3.8 21.9 - - - +
487A GLU* 2.8 32.6 + - - +
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Residues in contact with TYR 484 (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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373A THR* 4.5 8.0 + - - +
376A ASP* 4.2 9.0 - - + +
377A MET* 3.6 48.0 - - + +
380A SER* 3.7 31.4 - - - +
381A HIS* 3.8 3.7 - - - -
480A LEU* 2.8 60.4 + - + +
481A LYS* 3.1 8.9 + - - +
483A ASN* 1.3 78.4 - - + +
485A ILE* 1.3 61.9 + - - +
487A GLU* 3.9 19.3 - - - +
488A SER* 3.2 24.8 + - - -
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Residues in contact with ILE 485 (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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380A SER 3.7 22.9 - - - +
381A HIS* 3.8 20.9 - - + +
404A ILE* 3.8 21.5 - - + -
405A SER* 3.5 26.0 - - - +
406A GLY* 4.1 15.3 - - - +
434A SER* 4.3 19.1 - - - +
437A LEU* 5.0 9.0 - - + -
481A LYS* 3.0 17.0 + - + +
482A VAL* 3.5 9.0 - - + +
484A TYR* 1.3 76.6 - - - +
486A LEU* 1.4 63.6 + - + +
488A SER* 2.9 19.1 + - - -
489A ARG* 4.0 8.3 + - - +
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Residues in contact with LEU 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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434A SER 4.9 0.2 - - - +
437A LEU* 3.6 41.3 - - + +
438A CYS 3.8 19.3 - - - +
439A ALA* 3.9 14.4 - - - -
440A CYS 4.3 3.1 - - - +
482A VAL* 2.9 26.8 + - + +
483A ASN* 3.8 26.2 - - - +
485A ILE* 1.4 73.2 - - + +
487A GLU* 1.3 64.2 + - - +
488A SER 3.3 0.7 + - - -
489A ARG* 3.3 46.2 + - - +
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Residues in contact with GLU 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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483A ASN 2.8 20.8 + - - +
484A TYR* 3.9 26.6 - - - +
486A LEU* 1.3 75.3 - - - +
488A SER* 1.3 61.1 + - - +
489A ARG 3.1 9.9 + - - +
490A ALA* 5.2 0.5 - - - +
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Residues in contact with SER 488 (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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381A HIS* 2.7 35.7 + - - -
484A TYR 3.2 11.3 + - - -
485A ILE 2.9 12.5 + - - -
486A LEU 3.3 0.4 - - - -
487A GLU* 1.3 73.6 - - - +
489A ARG* 1.3 64.7 + - - +
490A ALA* 3.5 10.0 + - - +
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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