Contacts of the strand formed by residues 476 - 483 (chain A) in PDB entry 2V1A
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 VAL 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A LYS* 4.4 14.4 - - + +
466A ILE* 4.4 20.0 - - + -
469A ALA* 3.7 21.5 - - + -
474A THR 3.9 0.2 + - - -
475A GLU* 1.3 77.4 - - - +
477A THR* 1.3 68.3 + - - +
478A VAL* 3.9 20.6 - - + -
494A PHE* 3.9 3.8 - - + +
495A HIS* 3.3 6.1 + - - -
496A LEU* 2.9 44.1 + - + +
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Residues in contact with THR 477 (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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476A VAL* 1.3 74.7 - - - +
478A VAL* 1.3 65.7 + - - +
493A LEU* 4.2 8.5 - - + -
494A PHE 3.2 10.8 - - - +
495A HIS* 2.8 24.1 + - - -
529A VAL* 4.2 22.2 - - + -
532A ILE* 4.0 20.6 - - + -
533A LYS* 3.6 13.3 + - - -
1549A GOL 2.5 29.9 + - - -
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Residues in contact with VAL 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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462A THR* 3.7 27.6 - - + +
465A LYS* 4.4 20.0 - - + -
466A ILE* 4.0 25.4 - - + -
476A VAL* 3.9 19.7 - - + -
477A THR* 1.3 81.2 - - - +
479A GLN* 1.3 64.2 + - - +
480A LEU* 4.3 6.3 - - + -
492A ASN 3.7 0.3 - - - +
493A LEU* 3.7 4.8 - - - +
494A PHE* 2.8 43.1 + - + +
1549A GOL 3.8 9.6 - - - +
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Residues in contact with GLN 479 (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 ASP* 6.1 0.2 - - - +
462A THR* 3.7 13.3 + - - +
478A VAL* 1.3 74.6 - - - +
480A LEU* 1.3 64.6 + - - +
491A TRP* 4.0 12.6 - - + +
492A ASN 3.2 6.2 - - - +
493A LEU* 3.4 26.4 + - + +
518A GLU 4.3 1.7 - - - +
519A HIS* 3.4 23.5 + - + +
520A VAL* 2.8 58.2 + - - +
525A GLU* 3.3 4.8 + - - +
1549A GOL 2.9 38.0 + - - +
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Residues in contact with LEU 480 (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 THR* 3.8 23.6 - - + -
459A ASP* 5.3 3.8 - - + +
462A THR* 4.0 14.6 - - + -
463A VAL* 4.1 13.5 - - + -
466A ILE* 4.2 14.8 - - + -
478A VAL* 4.3 7.2 - - + -
479A GLN* 1.3 78.0 - - - +
481A ILE* 1.3 61.6 + - - +
482A ASN* 3.9 7.4 - - - +
491A TRP* 3.8 12.5 - - - -
492A ASN* 2.9 55.0 + - + +
494A PHE* 4.2 16.8 - - + -
1547A FMN 3.6 22.0 - - - +
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Residues in contact with ILE 481 (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 GLU* 3.8 39.5 - - + +
458A THR* 2.7 31.6 + - - +
459A ASP 5.3 1.0 - - - +
480A LEU* 1.3 72.6 - - - +
482A ASN* 1.3 76.2 + - - +
483A TYR* 4.0 18.2 - - + +
489A LYS* 4.1 19.5 - - + +
490A PHE 3.5 7.9 - - - +
491A TRP* 3.7 42.8 - - + +
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Residues in contact with ASN 482 (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 LEU* 3.1 24.9 + - + +
454A GLN* 4.1 2.8 - - - +
480A LEU* 3.7 9.8 + - - +
481A ILE* 1.3 84.0 + - - +
483A TYR* 1.3 66.1 + - - +
489A LYS* 3.4 4.9 - - - -
490A PHE* 2.9 56.0 + - + -
492A ASN* 2.9 22.1 + - + -
1547A FMN 2.8 43.5 + - - +
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Residues in contact with TYR 483 (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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440A TYR* 4.9 1.9 + - - -
452A PHE 4.8 3.1 - - - +
453A LEU* 2.7 37.8 + - - +
454A GLN 5.0 1.8 - - - +
455A GLY* 3.3 36.1 - - - -
456A PRO* 3.7 16.0 - - + +
457A GLU* 2.9 36.5 + - - +
458A THR* 3.9 7.2 - - - -
481A ILE* 4.0 10.1 - - + -
482A ASN* 1.3 79.1 - - - +
484A THR* 1.3 68.8 + - - +
487A GLY* 3.7 25.4 - - - -
488A LYS 3.3 4.0 - - - -
489A LYS* 3.4 25.8 - - + +
490A PHE* 3.9 4.7 - - - -
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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