Contacts of the helix formed by residues 460 - 469 (chain A) in PDB entry 2WSC
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 LEU 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455A PHE 4.1 6.9 + - - +
456A HIS* 3.5 29.4 - - - +
457A SER* 5.0 3.8 - - - -
458A PHE* 2.7 7.5 + - - +
459A GLY* 1.3 72.6 - - - +
461A TYR* 1.3 66.5 + - + +
463A HIS* 3.1 21.5 - - - +
464A ASN* 3.3 8.7 + - - -
477A PHE* 4.0 38.7 - - + +
540A LEU* 3.4 44.9 - - + +
543A HIS* 5.8 1.6 - - + -
1789A CLA 4.9 17.5 - - + -
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Residues in contact with TYR 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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457A SER 5.0 1.6 - - - -
458A PHE* 2.8 22.8 + + + +
460A LEU* 1.3 77.1 - - + +
462A ILE* 1.3 54.1 + - - +
464A ASN* 2.7 37.1 + - - +
465A ASP* 3.3 6.5 - - - +
540A LEU* 3.5 33.2 - - + +
541A VAL* 3.0 34.7 + - - +
544A ILE* 4.8 11.0 - - + -
646A SER* 3.3 20.5 - - - -
647A ILE* 3.5 25.3 - - - +
648A THR 4.2 0.2 - - - -
649A ILE* 3.5 33.7 - - + -
652A TRP* 4.3 1.5 + + - -
1811A CLA 3.3 33.2 - - + +
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Residues in contact with ILE 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 PHE* 3.4 17.6 + - + +
459A GLY* 2.8 24.1 + - - +
461A TYR* 1.3 74.0 - - - +
463A HIS* 1.3 61.1 + - - +
465A ASP* 3.6 8.6 + - - +
466A THR* 2.3 35.9 + - - +
649A ILE* 5.1 1.5 - - - +
1789A CLA 3.0 35.0 - - + -
648B TRP* 5.2 0.4 - - - +
655B LEU* 4.6 0.2 - - + -
1786B CLA 3.1 75.2 - - + -
1787B CLA 3.9 9.2 - - + -
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Residues in contact with HIS 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 GLY 2.8 14.2 + - - +
460A LEU* 3.1 15.9 - - - +
462A ILE* 1.3 72.7 - - - +
464A ASN* 1.3 59.8 + - - +
466A THR* 2.6 31.4 + - - -
467A MET* 2.9 43.3 + - + +
475A ASP 3.3 18.6 - - - -
476A MET 3.1 16.8 + - - -
477A PHE* 4.5 6.3 - + + -
1789A CLA 3.0 78.5 + + + +
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Residues in contact with ASN 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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460A LEU 3.3 15.8 + - - -
461A TYR* 2.7 15.3 + - - +
463A HIS* 1.3 79.9 + - - +
465A ASP* 1.3 52.5 + - - +
467A MET* 2.8 3.5 + - - -
468A SER* 2.4 40.6 + - - -
476A MET* 3.6 26.6 + - - +
477A PHE* 3.9 19.5 - - - +
647A ILE* 2.5 44.1 - - - +
648A THR* 4.3 7.0 - - - +
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Residues in contact with ASP 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 TYR 3.3 12.6 - - - +
462A ILE* 3.8 8.6 - - - +
463A HIS 3.3 0.4 - - - -
464A ASN* 1.3 71.3 - - - +
466A THR* 1.3 60.4 + - - +
467A MET 2.7 0.3 + - - -
468A SER* 4.6 1.3 - - - -
469A ALA* 2.6 38.7 + - - +
648A THR* 2.8 34.9 + - - +
649A ILE* 3.5 13.6 - - - +
650A ASN* 4.1 4.5 - - - +
635B ILE* 4.0 21.0 - - + +
648B TRP* 3.6 21.9 - - + +
651B LEU* 5.0 3.3 - - - +
1786B CLA 4.5 11.3 - - + +
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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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462A ILE* 2.3 29.7 + - - +
463A HIS 2.6 11.4 + - - -
465A ASP* 1.3 74.7 - - - +
467A MET* 1.3 49.0 + - - -
470A LEU* 2.6 40.2 - - + +
1789A CLA 3.8 19.8 - - + +
648B TRP* 3.5 26.4 + - + +
1740B CLA 2.9 55.3 - - + +
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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 HIS* 2.9 44.6 - - + +
464A ASN 2.8 1.3 + - - +
466A THR* 1.3 79.8 - - - +
468A SER* 1.3 56.2 + - - +
470A LEU* 3.5 10.9 - - + +
471A GLY 2.7 23.1 + - - -
472A ARG* 3.0 20.4 + - + +
473A PRO* 4.5 1.8 - - - +
475A ASP* 3.0 39.7 - - + +
476A MET* 3.6 10.8 - - + +
1789A CLA 3.8 38.4 - - + +
95B HIS 5.8 0.2 - - - +
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Residues in contact with SER 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 ASN 2.4 29.1 + - - -
465A ASP* 4.6 0.2 - - - -
467A MET* 1.3 71.7 - - - +
469A ALA* 1.3 54.3 + - - -
471A GLY* 3.2 22.2 - - - +
472A ARG 4.6 1.1 - - - +
473A PRO* 4.9 5.1 - - - +
476A MET* 3.4 33.0 - - - +
648A THR* 4.9 4.1 + - - -
635B ILE* 3.7 23.8 + - - +
636B THR 4.9 1.2 + - - -
639B VAL* 5.7 0.2 - - - -
640B CYS* 3.8 15.2 + - - +
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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 ASP 2.6 24.8 + - - +
468A SER* 1.3 70.7 - - - +
470A LEU* 1.3 61.3 + - - +
635B ILE* 3.7 20.1 - - + +
640B CYS* 4.0 7.4 - - - +
644B SER* 3.1 31.9 + - - +
648B TRP* 4.5 9.6 - - + -
1740B CLA 3.1 31.6 - - + +
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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