Contacts of the strand formed by residues 473 - 480 (chain A) in PDB entry 2VKT
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 PHE 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ARG* 3.4 52.5 - - + -
455A THR 3.3 14.6 - - - +
456A VAL* 4.1 16.4 - - + -
457A PHE* 4.2 4.3 - - - -
471A VAL* 3.2 26.8 + - + +
472A PRO* 1.3 98.7 - - + +
474A ILE* 1.3 71.4 + - - +
475A GLU* 3.9 16.2 - - + -
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Residues in contact with ILE 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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453A ARG 3.6 0.2 - - - +
454A ARG* 3.4 5.7 - - - +
455A THR* 2.9 47.1 + - + +
457A PHE* 4.1 12.3 - - + -
468A TYR* 3.5 56.1 - - + +
471A VAL* 5.1 4.9 - - + -
473A PHE* 1.3 78.7 - - - +
475A GLU* 1.3 65.7 + - - +
476A GLU* 4.3 6.1 - - + -
511A ILE* 4.3 10.3 - - + -
525A PHE* 3.6 33.9 - - + -
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Residues in contact with GLU 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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452A ILE* 4.1 24.5 - - + +
453A ARG 3.3 11.4 - - - +
454A ARG* 3.9 27.0 + - - -
473A PHE* 3.9 15.7 - - + -
474A ILE* 1.3 80.5 - - - +
476A GLU* 1.3 71.4 + - - +
530A SER* 5.1 2.6 + - - -
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Residues in contact with GLU 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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452A ILE* 3.4 8.1 - - - -
453A ARG 3.0 28.5 + - - -
468A TYR* 2.7 33.3 + - - +
474A ILE* 4.3 10.7 - - + -
475A GLU* 1.3 81.0 - - - +
477A ARG* 1.3 60.8 + - - +
478A HIS* 3.1 8.6 + - - +
525A PHE* 3.6 37.9 - - + -
526A HIS 4.7 1.5 - - - +
527A PRO* 4.0 18.7 - - - +
529A PHE* 6.1 0.3 - - - +
530A SER* 2.8 31.5 + - - -
537A SER* 4.8 1.9 + - - -
538A PRO* 5.1 1.4 - - - +
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A GLY* 3.6 18.6 - - - +
452A ILE* 4.2 19.4 - - + +
476A GLU* 1.3 77.0 + - - +
478A HIS* 1.3 68.5 - - - +
525A PHE* 3.3 2.8 - - - +
526A HIS* 2.9 32.4 + - + +
529A PHE* 3.5 72.6 + - + +
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Residues in contact with HIS 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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449A ARG* 3.4 34.1 + - + +
450A LEU* 3.4 16.8 - - - +
451A GLY 3.1 13.6 + - - +
453A ARG* 3.6 27.3 + - + +
455A THR* 4.0 7.7 + - - -
476A GLU* 3.1 29.2 + - - +
477A ARG* 1.3 81.3 - - - +
479A ARG* 1.3 64.2 + - - +
480A HIS* 3.0 23.2 + - + +
510A GLU* 3.4 30.7 - - - -
525A PHE* 3.7 22.3 - + + +
526A HIS* 5.0 0.9 - - - +
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Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A PHE* 3.3 53.9 - - - -
399A CYS* 3.9 13.3 - - - -
448A MET* 3.0 42.3 - - + +
449A ARG 3.4 4.0 - - - -
450A LEU* 4.1 10.6 - - + +
478A HIS* 1.3 76.5 - - - +
480A HIS* 1.3 67.5 + - - +
526A HIS* 4.3 16.5 + - + +
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Residues in contact with HIS 480 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399A CYS* 4.0 15.3 - - - -
403A GLN* 4.8 3.1 - - - +
448A MET* 3.4 10.1 - - - +
449A ARG* 3.0 43.8 + - - +
478A HIS* 3.0 31.6 + - + -
479A ARG* 1.3 84.9 - - - +
481A ARG* 1.3 61.6 + - - +
482A PHE 4.7 2.0 - - - +
483A GLU* 2.5 37.9 + - - +
508A ARG* 4.9 0.2 + - - -
510A GLU* 3.3 18.9 + - - -
524A GLN* 3.2 34.6 + - - +
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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