Contacts of the strand formed by residues 462 - 472 (chain A) in PDB entry 3V4P
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 CYS 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A LYS 4.7 1.5 + - - +
452A ASP* 4.0 20.4 - - - +
453A CYS* 1.8 78.0 - - - -
460A SER 3.7 0.8 + - - -
461A VAL* 1.3 76.4 - - - +
463A ILE* 1.3 69.5 + - - +
464A ASP* 4.4 10.8 - - - +
500A PHE* 5.5 0.2 - - - -
528A GLN* 4.3 13.9 - - + +
529A ALA 3.2 14.8 - - - +
530A PHE* 4.1 4.3 - - + -
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Residues in contact with ILE 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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443A PRO* 4.7 16.8 - - + -
445A SER 5.8 0.2 - - - +
446A VAL* 3.7 28.0 - - + -
461A VAL* 5.4 3.1 - - + -
462A CYS* 1.3 79.7 - - - +
464A ASP* 1.3 66.0 + - - +
465A LEU* 3.8 17.9 + - + +
488A LEU* 5.4 2.7 - - + -
500A PHE* 3.5 32.1 - - + -
528A GLN* 3.3 5.4 - - - +
529A ALA* 2.9 46.6 + - + +
542A ILE* 5.2 8.1 - - + -
544A ILE* 6.1 1.3 - - + -
583A ILE* 5.1 7.4 - - + -
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Residues in contact with ASP 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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441A SER* 4.0 4.0 - - - +
443A PRO* 3.5 26.8 - - + +
462A CYS* 4.4 10.6 - - - +
463A ILE* 1.3 79.2 - - - +
465A LEU* 1.3 62.1 + - - +
466A THR* 4.0 3.5 + - - +
526A THR* 4.3 16.4 - - + +
527A HIS 4.0 2.9 - - - -
528A GLN* 4.2 14.2 - - - +
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU* 4.8 2.5 - - + -
441A SER 3.9 13.2 - - - +
442A HIS* 5.1 0.9 - - - +
443A PRO* 4.0 13.5 - - + -
463A ILE* 3.8 17.0 + - + +
464A ASP* 1.3 78.8 - - - +
466A THR* 1.3 62.1 + - - +
467A LEU 4.2 0.3 + - - -
486A MET* 3.6 32.5 - - + +
488A LEU* 3.6 30.7 - - + -
502A PHE* 5.1 3.6 - - + -
525A ARG 4.2 0.2 - - - +
526A THR* 3.3 0.9 - - - +
527A HIS* 2.9 44.1 + - + +
529A ALA* 4.7 9.0 - - + -
544A ILE* 3.6 24.0 - - + -
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Residues in contact with THR 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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439A SER 3.7 0.3 - - - +
440A LEU* 3.3 9.2 - - - +
441A SER* 2.9 52.0 + - - +
464A ASP* 4.0 4.3 + - - +
465A LEU* 1.3 72.0 + - - +
467A LEU* 1.3 64.6 + - - +
468A CYS* 3.9 22.2 + - - -
524A CYS* 4.1 5.8 - - + -
525A ARG* 3.6 9.0 - - - +
526A THR* 2.7 32.2 + - - +
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Residues in contact with LEU 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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439A SER 3.8 5.2 - - - +
440A LEU* 3.6 24.0 - - + -
465A LEU 4.2 0.6 + - - -
466A THR* 1.3 72.7 - - - +
468A CYS* 1.3 60.1 + - - +
469A PHE* 4.0 21.6 - - + -
484A TYR* 3.6 44.0 - - + -
486A MET* 3.9 22.2 - - + -
523A ASN 4.2 0.5 - - - +
524A CYS* 3.1 4.3 - - - +
525A ARG* 2.9 39.5 + - + +
546A ALA* 3.8 7.2 - - + -
579A MET* 3.8 27.8 - - + -
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Residues in contact with CYS 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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437A ASP 3.8 1.2 - - - +
438A ALA* 3.2 5.9 - - - +
439A SER* 2.9 55.3 + - - +
441A SER* 4.5 9.4 - - - -
466A THR* 3.9 11.9 - - - -
467A LEU* 1.3 75.1 - - - +
469A PHE* 1.3 62.7 + - - +
522A ALA* 6.1 0.7 - - + -
524A CYS* 2.0 44.9 - - - -
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Residues in contact with PHE 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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436A VAL* 4.3 6.7 - - + -
437A ASP 3.7 1.6 - - - -
438A ALA* 3.5 27.4 - - + -
467A LEU* 4.0 34.3 - - + -
468A CYS* 1.3 75.7 - - - +
470A SER* 1.3 64.2 + - - +
482A LEU* 3.5 25.6 - - + -
484A TYR* 4.3 13.9 - + + -
515A ILE* 3.9 28.0 - - + -
517A VAL* 3.6 23.0 - - + +
522A ALA* 3.4 3.0 - - - +
523A ASN 3.0 37.3 + - - +
548A TYR* 3.9 30.7 - + + -
579A MET* 5.1 0.2 - - + -
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Residues in contact with SER 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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435A ILE 4.3 0.5 - - - +
436A VAL* 4.7 1.6 - - - +
437A ASP* 2.9 46.2 + - - +
468A CYS 5.7 0.2 - - - -
469A PHE* 1.3 77.0 - - - +
471A TYR* 1.3 62.0 + - - +
472A LYS* 5.9 0.2 - - - +
517A VAL* 4.4 5.3 - - - +
521A GLU 5.1 2.5 - - - -
522A ALA* 3.6 21.8 - - - +
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Residues in contact with TYR 471 (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 VAL* 4.5 16.2 - - + -
435A ILE 3.4 13.2 - - - +
436A VAL* 3.7 18.6 - - + +
470A SER* 1.3 75.2 - - - +
472A LYS* 1.3 74.4 + - - +
476A VAL* 4.2 25.1 - - + -
477A PRO* 5.3 0.8 - - + +
478A GLY* 2.8 37.3 + - - -
479A TYR* 3.2 7.4 + - - -
480A ILE* 3.5 25.1 - - + -
482A LEU* 6.4 0.7 - - + -
517A VAL* 3.4 30.7 - - + +
518A SER 3.7 12.0 + - - +
519A SER* 4.0 18.9 + - - -
520A ARG 5.1 1.9 + - - -
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Residues in contact with LYS 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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434A VAL* 3.7 4.3 - - - -
435A ILE* 2.9 60.1 + - + +
437A ASP* 6.3 2.7 - - - -
470A SER 5.9 0.2 - - - +
471A TYR* 1.3 85.4 - - - +
473A GLY* 1.3 61.8 + - - +
476A VAL* 4.7 3.1 - - - -
519A SER* 5.7 1.3 - - - -
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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