Contacts of the strand formed by residues 522 - 531 (chain B) in PDB entry 4A9C
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 ILE 522 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B ILE* 3.8 31.9 - - + -
514B VAL* 4.3 13.5 - - + -
518B HIS 3.3 15.7 + - - +
519B GLU* 3.7 17.1 - - - +
520B ASN 3.3 5.4 - - - +
521B ARG* 1.3 76.6 - - - +
523B SER* 1.3 63.7 + - - +
525B VAL* 3.7 25.9 - - + +
548B PHE* 3.7 28.7 - - + -
549B MET 3.3 5.8 - - - +
550B PHE* 3.6 32.1 - - + -
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Residues in contact with SER 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B ARG 4.8 2.3 + - - -
522B ILE* 1.3 74.5 - - - +
524B HIS* 1.4 78.3 + - - +
525B VAL* 3.4 6.8 + - - -
548B PHE* 3.7 1.9 - - - +
549B MET* 2.8 46.9 + - - +
551B ASN 4.8 4.2 + - - -
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Residues in contact with HIS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B SER* 1.4 90.7 - - - +
525B VAL* 1.3 64.2 + - - +
526B SER* 3.4 4.9 + - - -
547B SER* 3.3 11.1 + - - +
548B PHE* 3.6 4.0 - - - -
549B MET* 4.2 21.2 - - + +
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Residues in contact with VAL 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ILE* 3.4 29.2 - - + +
501B ALA* 3.8 17.9 - - + -
522B ILE* 3.7 30.3 - - + -
523B SER* 4.4 4.3 - - - +
524B HIS* 1.3 71.8 - - - +
526B SER* 1.3 64.5 + - - +
527B THR* 5.3 1.6 - - + -
546B VAL* 5.0 1.1 - - + -
547B SER 3.4 8.1 - - - +
548B PHE* 4.2 7.2 - - + -
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Residues in contact with SER 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B HIS 4.4 3.8 - - - -
525B VAL* 1.3 74.9 - - - +
527B THR* 1.3 70.6 + - - +
546B VAL* 3.4 5.9 - - - +
547B SER* 2.7 50.4 + - - +
584B SER 4.3 10.7 + - - -
585B LEU* 3.8 7.7 - - - +
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Residues in contact with THR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501B ALA* 4.1 15.5 - - + -
502B MET 4.2 11.2 + - - +
503B GLN* 3.4 24.3 + - + +
525B VAL* 5.3 2.0 - - + -
526B SER* 1.3 83.2 + - - +
528B SER* 1.3 62.6 + - - +
545B GLY 3.4 6.1 - - - -
546B VAL* 3.8 20.2 - - + -
584B SER 4.5 1.7 - - - +
585B LEU* 3.9 2.5 - - - -
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Residues in contact with SER 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B GLN* 3.4 15.2 - - - +
527B THR* 1.3 75.8 - - - +
529B SER* 1.3 67.2 + - - +
544B VAL* 3.5 0.2 - - - -
545B GLY 2.8 32.1 + - - -
582B LEU 5.2 0.3 + - - -
583B LEU* 3.7 13.2 - - - +
584B SER* 3.4 42.6 + - - -
585B LEU* 3.8 10.1 - - - -
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Residues in contact with SER 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B GLN* 3.7 18.7 + - - +
504B SER 4.9 0.4 - - - -
505B LEU* 3.8 25.1 - - - +
528B SER* 1.3 80.4 + - - +
530B VAL* 1.3 68.6 + - - +
531B LYS* 6.0 0.2 - - - -
543B ALA 3.3 11.2 - - - -
544B VAL* 4.2 7.9 - - - -
583B LEU* 4.2 1.3 - - - -
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Residues in contact with VAL 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B LEU* 3.3 6.9 - - - +
529B SER* 1.3 79.5 - - - +
531B LYS* 1.3 69.8 + - - +
532B THR* 4.2 3.6 - - + -
542B GLY* 3.2 4.7 - - - -
543B ALA 2.9 32.7 + - - +
578B ASP 4.4 0.2 - - - +
579B ILE* 3.9 32.1 - - + +
582B LEU* 3.6 26.5 - - + +
583B LEU* 3.5 43.5 - - + +
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Residues in contact with LYS 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B LEU* 3.8 26.0 - - + -
506B TRP* 3.6 37.0 - - + +
529B SER 6.0 0.2 - - - -
530B VAL* 1.3 76.0 - - - +
532B THR* 1.3 63.2 + - - +
541B LYS 4.0 5.4 - - - +
578B ASP* 5.9 0.3 - - - +
582B LEU* 5.1 6.1 - - - +
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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