Contacts of the strand formed by residues 479 - 487 (chain A) in PDB entry 3V4P
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 TYR 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A TYR* 3.3 7.0 + - - -
477A PRO* 3.7 18.6 - - + +
478A GLY* 1.3 75.3 - - - +
480A ILE* 1.3 80.9 + - + +
481A VAL* 4.6 10.8 - - + -
516A GLN* 3.7 35.7 - - + +
517A VAL 3.6 7.0 - - - +
518A SER* 4.1 9.4 - - - +
553A HIS* 5.3 16.0 - + + +
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Residues in contact with ILE 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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434A VAL* 5.7 7.4 - - + -
471A TYR* 3.5 34.1 - - + -
477A PRO* 5.2 5.8 - - + -
479A TYR* 1.3 87.4 - - + +
481A VAL* 1.3 73.4 + - - +
482A LEU* 4.5 14.1 - - + -
516A GLN* 3.3 7.1 - - - +
517A VAL* 2.9 37.9 + - + +
550A LEU* 3.5 30.7 - - + -
551A GLY 4.9 1.1 - - - +
553A HIS* 3.6 35.7 - - + +
568A PRO* 5.7 2.7 - - + -
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Residues in contact with VAL 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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479A TYR* 4.6 12.3 - - + -
480A ILE* 1.3 84.8 - - - +
482A LEU* 1.3 73.5 + - - +
483A PHE* 4.0 26.0 - - + -
514A SER* 4.6 4.7 - - - -
515A ILE 3.5 10.3 - - - +
516A GLN* 4.3 18.6 - - + +
550A LEU* 4.0 2.9 - - - +
551A GLY* 3.1 32.6 + - - +
553A HIS* 6.6 0.4 - - + -
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Residues in contact with LEU 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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436A VAL* 4.4 13.2 - - + -
469A PHE* 3.5 43.3 - - + -
471A TYR* 6.4 0.9 - - + -
480A ILE* 4.5 11.2 - - + -
481A VAL* 1.3 85.2 - - - +
483A PHE* 1.3 66.8 + - - +
484A TYR 3.8 1.1 + - - -
514A SER* 3.2 5.0 - - - -
515A ILE* 2.9 44.6 + - + +
517A VAL* 4.3 8.3 - - + -
548A TYR* 4.6 10.8 - - + -
549A HIS 3.6 12.1 - - - +
550A LEU* 3.8 23.6 - - + -
570A LEU* 4.7 7.4 - - + -
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Residues in contact with PHE 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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481A VAL* 4.0 15.5 + - + -
482A LEU* 1.3 73.2 - - - +
484A TYR* 1.3 59.4 + - - +
513A GLY 3.5 4.3 - - - +
514A SER* 3.5 29.6 - - - -
548A TYR* 3.0 4.1 - - - -
549A HIS* 2.9 76.8 + + + +
551A GLY* 4.3 18.8 - - - -
552A PRO* 4.4 11.2 - - + -
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Residues in contact with TYR 484 (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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467A LEU* 3.6 30.7 - - + -
469A PHE* 4.3 9.2 - + + -
482A LEU 4.2 2.5 - - - -
483A PHE* 1.3 74.8 - - - +
485A ASN* 1.3 70.8 + - - +
486A MET* 4.9 2.9 - - + -
511A ILE* 5.4 1.3 - - + -
512A THR* 3.4 3.8 - - - -
513A GLY* 2.9 72.0 + - - +
514A SER 3.5 3.8 - - - -
515A ILE* 4.0 23.3 - - + -
525A ARG* 3.1 39.3 + - + -
527A HIS* 3.1 33.8 + + - -
547A ALA 3.2 11.7 - - - +
548A TYR* 4.2 8.1 - - + -
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Residues in contact with ASN 485 (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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484A TYR* 1.3 78.9 - - - +
486A MET* 1.3 63.1 + - - +
487A SER* 5.3 2.1 + - - -
510A VAL* 4.8 8.7 - - + +
511A ILE 3.1 14.1 - - - +
512A THR* 3.6 17.1 - - + +
545A GLU 3.6 1.6 - - - +
546A ALA* 3.3 2.9 - - - +
547A ALA* 2.9 48.2 + - - +
549A HIS* 6.1 3.2 - - - -
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Residues in contact with MET 486 (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 LEU* 4.0 23.6 - - + -
465A LEU* 3.6 46.0 - - + +
467A LEU* 3.9 28.5 - - + -
484A TYR* 4.9 2.0 - - + -
485A ASN* 1.3 78.8 - - - +
487A SER* 1.3 63.7 + - - +
488A LEU* 4.3 2.2 - - + -
502A PHE* 4.2 6.7 - - + -
509A ASP 3.8 1.6 - - - +
510A VAL* 3.2 7.6 - - - +
511A ILE* 2.9 44.3 + - + +
527A HIS* 5.0 15.7 - - - -
544A ILE* 4.5 6.1 - - + -
545A GLU 3.3 4.5 - - - +
546A ALA* 3.8 13.2 - - + -
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Residues in contact with SER 487 (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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485A ASN* 5.3 3.3 + - - -
486A MET* 1.3 76.5 + - - +
488A LEU* 1.3 64.3 + - - +
490A VAL* 4.0 26.7 - - - +
509A ASP* 3.8 7.2 - - - -
510A VAL* 4.0 15.2 - - - +
543A GLN 4.1 0.9 - - - +
544A ILE* 3.2 8.7 - - - +
545A GLU* 2.9 38.3 + - - +
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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