Contacts of the strand formed by residues 533 - 539 (chain A) in PDB entry 2VK8
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 ILE 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ILE* 4.7 0.7 - - + -
457A MET* 3.8 33.0 - - + -
458A ILE* 4.5 13.0 - - + +
462A LEU 3.6 15.7 + - - +
463A LYS* 3.8 8.5 - - - +
464A PRO* 3.7 25.1 - - + +
466A LEU* 4.2 8.5 - - + -
499A LEU* 3.8 28.3 - - + -
504A ALA* 5.0 1.8 - - + -
506A ASP 3.6 8.4 + - - +
507A TYR* 3.2 24.0 - - + +
508A GLU 3.1 20.3 + - - -
532A LYS* 1.3 72.8 - - - +
534A ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 534 (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 PRO 3.2 9.4 + - - +
465A TYR* 3.2 27.1 + - + -
466A LEU* 2.8 32.1 + - - +
499A LEU* 4.4 3.8 - - - -
508A GLU* 2.9 48.9 + - + +
510A HIS* 4.7 1.3 - - + -
526A SER* 3.0 19.2 + - - -
527A PHE* 3.4 32.8 - - - +
529A ASP 2.8 29.7 + - - -
530A ASN* 4.2 1.8 - - - +
531A SER* 3.2 16.8 + - - +
532A LYS* 3.6 15.4 + - - +
533A ILE* 1.3 81.6 - - - +
535A MET* 1.3 61.0 + - - +
536A ILE* 4.2 12.1 - - + -
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Residues in contact with MET 535 (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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447A LEU* 4.8 1.6 - - + -
454A ILE* 3.8 28.3 - - + -
466A LEU* 3.3 22.2 - - + +
468A VAL* 4.1 20.0 - - + -
495A HIS* 3.2 43.1 - - - +
496A LEU* 3.9 12.5 - - + +
498A LEU* 4.1 13.7 - - + -
499A LEU* 3.9 19.9 - - + +
508A GLU 3.0 7.5 + - - +
509A THR* 3.2 6.7 - - + -
510A HIS* 3.0 25.1 + - - +
534A ARG* 1.3 74.9 - - - +
536A ILE* 1.3 66.2 + - - +
537A GLU 4.1 0.4 - - - +
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Residues in contact with ILE 536 (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 TYR* 4.5 2.5 - - + -
466A LEU 2.8 18.4 + - - +
467A PHE* 3.4 38.5 - - + -
468A VAL 2.8 26.8 + - - -
510A HIS* 3.3 14.4 - - + +
512A VAL* 4.1 21.1 - - + -
521A LEU* 3.9 21.5 - - + -
527A PHE* 3.9 34.5 - - + -
534A ARG* 4.2 15.0 - - + +
535A MET* 1.3 82.8 - - - +
537A GLU* 1.3 61.1 + - - +
538A VAL* 3.5 2.9 + - + +
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Residues in contact with GLU 537 (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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468A VAL* 3.6 8.7 - - + +
470A ASN* 2.9 27.6 + - + -
493A TRP 4.8 2.3 - - - +
495A HIS* 2.8 37.2 + - + +
496A LEU* 4.0 18.8 + - + +
510A HIS 2.8 12.1 + - - +
511A ARG* 2.9 44.0 + - - +
512A VAL* 3.0 27.0 + - - +
536A ILE* 1.3 69.7 - - - +
538A VAL* 1.3 60.3 + - - +
539A MET* 3.8 13.7 - - - +
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Residues in contact with VAL 538 (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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365A LEU* 3.9 23.8 - - + -
370A MET* 3.9 21.3 - - - -
441A PHE* 5.2 0.2 - - + -
467A PHE* 4.1 20.6 - - + -
468A VAL 2.8 9.4 + - - +
469A LEU* 3.7 23.0 - - + -
470A ASN 2.8 29.2 + - - +
512A VAL* 3.6 14.4 - - + -
518A TRP* 4.3 4.5 - - + -
536A ILE* 3.9 11.4 - - + +
537A GLU* 1.3 74.1 - - - +
539A MET* 1.3 64.1 + - - +
540A LEU* 3.6 15.2 + - + +
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Residues in contact with MET 539 (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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365A LEU* 4.0 15.8 - - - +
470A ASN* 3.7 28.3 - - - +
511A ARG* 4.0 22.2 - - + +
512A VAL 2.9 21.7 + - - +
513A ALA* 4.0 20.4 - - + +
537A GLU* 3.8 32.5 - - - +
538A VAL* 1.3 69.1 - - - +
540A LEU* 1.3 66.8 + - - +
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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