Contacts of the strand formed by residues 449 - 457 (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 ARG 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437A PRO* 5.9 0.2 - - - +
438A GLU* 3.4 27.9 + - - +
447A THR 4.0 1.0 + - - -
448A MET* 1.3 69.8 - - - +
450A LEU* 1.3 58.1 + - - +
453A ARG* 3.3 39.2 - - + +
454A ARG 3.1 21.4 + - - -
478A HIS* 3.4 28.0 + - + -
479A ARG* 3.4 2.1 + - - -
480A HIS* 3.0 48.7 + - + +
481A ARG* 5.0 0.4 - - - +
503A ASP* 3.6 19.4 + - - +
504A VAL 5.5 0.6 - - - +
508A ARG* 3.8 24.3 - - - +
510A GLU* 2.8 40.7 + - - -
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Residues in contact with LEU 450 (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 THR* 6.3 0.7 - - - -
448A MET* 3.2 32.7 + - + +
449A ARG* 1.3 75.8 - - - +
451A GLY* 1.3 65.6 + - - +
453A ARG* 2.8 32.7 + - - +
478A HIS* 3.4 15.0 - - - +
479A ARG* 4.1 19.7 - - + +
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Residues in contact with GLY 451 (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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450A LEU* 1.3 80.1 - - - +
452A ILE* 1.3 69.6 + - - -
453A ARG* 3.6 3.6 + - - +
477A ARG* 4.3 8.1 - - - +
478A HIS 3.1 29.0 + - - -
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Residues in contact with ILE 452 (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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451A GLY* 1.3 73.3 - - - -
453A ARG* 1.3 73.6 + - - +
475A GLU* 4.1 33.4 - - + +
476A GLU* 3.4 13.9 - - - +
477A ARG* 4.2 29.6 - - + +
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Residues in contact with ARG 453 (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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438A GLU* 2.6 45.5 + - - -
448A MET 4.9 0.6 + - - -
449A ARG* 3.3 34.4 - - + +
450A LEU* 2.8 34.9 + - - +
451A GLY 3.8 3.8 - - - +
452A ILE* 1.3 82.8 + - - +
454A ARG* 1.3 62.7 + - - +
455A THR* 3.9 0.5 + - - -
474A ILE 3.6 0.3 - - - +
475A GLU* 3.3 26.1 - - - -
476A GLU 3.0 12.5 + - - +
478A HIS* 3.6 16.1 + - + -
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Residues in contact with ARG 454 (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* 3.1 22.2 + - - +
453A ARG* 1.3 72.6 - - - +
455A THR* 1.3 59.6 + - - +
456A VAL* 4.5 3.3 - - + +
473A PHE* 3.4 56.0 - - + -
474A ILE 3.4 4.7 - - - +
475A GLU* 3.9 20.9 + - - +
503A ASP* 4.1 6.8 - - - -
504A VAL* 3.7 29.8 + - + +
510A GLU* 4.1 0.3 - - - +
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Residues in contact with THR 455 (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 3.9 0.4 + - - -
454A ARG* 1.3 72.9 + - - +
456A VAL* 1.3 65.3 + - - +
457A PHE* 4.0 1.9 + - + +
473A PHE* 3.3 2.8 - - - -
474A ILE* 2.9 47.8 + - + +
478A HIS* 4.0 4.3 + - - -
501A GLY* 4.3 2.2 - - - -
502A GLN 3.3 23.8 - - - +
510A GLU* 2.9 22.0 + - + +
511A ILE* 3.9 30.1 - - + -
525A PHE* 3.9 15.6 - - + -
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Residues in contact with VAL 456 (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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454A ARG* 4.5 3.6 - - + +
455A THR* 1.3 76.5 - - - +
457A PHE* 1.3 71.9 + - - +
458A LYS* 3.6 1.6 + - - +
472A PRO* 3.4 19.3 - - + +
473A PHE* 4.3 10.5 - - + -
501A GLY* 4.5 1.6 - - - -
502A GLN* 2.8 40.1 + - + +
503A ASP 5.0 2.0 - - - +
504A VAL* 3.8 35.7 - - + -
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Residues in contact with PHE 457 (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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455A THR* 4.9 1.3 - - + +
456A VAL* 1.3 83.3 - - - +
458A LYS* 1.3 60.4 + - - +
459A THR 3.4 3.6 - - - +
462A SER* 4.1 6.1 - - - -
464A LEU* 4.2 3.4 - - + -
465A ARG* 3.6 61.6 + - + +
468A TYR* 4.1 19.5 - + + -
471A VAL 3.5 24.7 - - - -
472A PRO 3.3 15.9 + - - +
473A PHE* 4.0 3.4 - - - -
474A ILE* 4.1 24.2 - - + -
500A VAL* 3.5 21.5 - - + -
501A GLY* 4.5 0.2 - - - -
511A ILE* 4.0 24.7 - - + -
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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