Contacts of the strand formed by residues 479 - 485 (chain A) in PDB entry 3BK0
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 ASP 479 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A LEU* 3.7 9.8 - - + +
475A VAL* 2.9 17.7 + - - +
476A HIS* 2.9 46.9 + - - +
477A SER 3.3 1.2 - - - +
478A GLY* 1.3 78.0 - - - +
480A PHE* 1.3 58.3 + - - +
495A VAL* 3.3 3.1 - - - -
496A LEU 2.9 25.1 + - - -
546A HIS* 5.7 0.7 - - - -
547A ARG* 3.0 53.0 + - - +
549A VAL* 3.8 8.5 - - + -
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Residues in contact with PHE 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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460A TRP* 4.7 11.1 - + - +
474A LEU* 4.3 4.5 - - - -
478A GLY 3.7 8.5 - - - +
479A ASP* 1.3 75.1 - - - +
481A LEU* 1.3 68.6 + - - +
493A LEU* 3.6 15.0 - - + -
494A SER 3.0 13.2 - - - +
495A VAL* 3.8 16.2 - - + -
527A ILE* 3.7 35.0 - - + -
531A LEU* 3.8 18.8 - - + -
545A LEU* 3.9 22.2 - - + -
547A ARG 3.0 27.5 + - - -
548A ALA* 3.3 38.3 - - + -
549A VAL* 2.9 28.0 + - - +
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Residues in contact with LEU 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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460A TRP 3.6 13.9 - - - +
462A HIS* 3.7 22.2 - - + +
465A ILE* 4.1 5.4 - - + -
470A VAL* 4.4 9.9 - - + -
473A LEU* 3.8 31.0 - - + -
474A LEU* 3.8 20.2 - - + -
480A PHE* 1.3 82.5 - - - +
482A VAL* 1.3 78.5 + - - +
483A ARG* 3.9 24.9 - - + -
493A LEU* 3.6 4.2 - - - +
494A SER* 2.9 39.1 + - - +
549A VAL* 4.4 2.9 - - + +
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Residues in contact with VAL 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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455A LEU* 4.4 2.9 - - + -
460A TRP* 3.1 34.8 + - + -
461A TYR* 3.4 18.7 - - + -
462A HIS 2.8 26.5 + - - -
480A PHE* 4.9 1.1 - - + -
481A LEU* 1.3 80.8 - - - +
483A ARG* 1.3 70.9 + - - +
491A TYR* 4.5 5.4 - - + -
492A VAL 3.3 11.0 - - - +
493A LEU* 4.0 7.6 - - + -
506A ILE* 4.1 17.3 - - + -
523A ILE* 4.3 11.7 - - + -
527A ILE* 3.8 23.6 - - + -
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Residues in contact with ARG 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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2A SO4 2.8 44.6 + - - -
461A TYR* 3.9 11.7 - - - -
462A HIS 4.5 2.5 - - - -
463A GLY 3.2 17.0 - - - +
465A ILE* 4.4 14.3 + - + -
467A ARG* 4.0 11.0 - - - +
470A VAL* 3.7 25.9 - - - +
481A LEU* 3.9 9.4 - - + -
482A VAL* 1.3 76.4 - - - +
484A GLU* 1.3 68.8 + - - +
485A SER* 4.4 2.0 - - - +
491A TYR* 3.4 7.8 - - - +
492A VAL* 2.9 48.9 + - + +
494A SER* 2.9 18.2 + - - -
503A HIS* 3.2 28.2 + - - -
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Residues in contact with GLU 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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461A TYR* 3.6 18.9 + - - +
463A GLY* 2.9 18.0 + - - +
464A ALA* 4.6 19.4 - - - +
465A ILE 5.4 1.0 - - - +
483A ARG* 1.3 84.4 + - - +
485A SER* 1.3 73.3 + - - +
486A GLN* 3.3 9.9 + - - +
489A GLN* 5.5 3.5 - - - -
490A GLU 3.7 9.6 - - - +
491A TYR* 4.2 12.7 + - + -
628A GLN 4.7 5.7 - - - +
629A LYS* 4.8 5.2 - - - +
630A GLN* 5.0 3.3 + - - +
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Residues in contact with SER 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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2A SO4 3.0 34.9 + - - -
8A EDO 3.7 1.1 + - - -
483A ARG* 4.1 1.9 + - - +
484A GLU* 1.3 73.8 - - - +
486A GLN* 1.3 56.5 + - - +
487A GLY 3.9 0.3 + - - -
488A LYS* 3.0 28.4 + - - +
489A GLN* 2.9 31.7 + - - -
490A GLU 2.8 20.2 + - - -
492A VAL* 3.8 18.0 - - - +
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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