Contacts of the strand formed by residues 496 - 501 (chain A) in PDB entry 4Z1F
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 ASN 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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486A TYR* 4.0 2.3 + - - -
490A MET* 3.4 16.0 - - - +
493A GLY 4.0 2.4 + - - +
495A ARG* 1.3 97.0 - - + +
497A ILE* 1.3 64.0 + - - +
498A TYR* 3.5 38.6 + - + +
545A LYS* 4.4 1.6 - - - -
546A LYS* 3.3 26.5 - - - +
548A ILE* 4.2 22.3 - - + +
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Residues in contact with ILE 497 (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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483A LEU* 4.8 9.0 - - + +
486A TYR* 3.5 30.1 - - + -
487A ALA* 5.8 1.3 - - + -
490A MET* 4.8 3.4 - - + -
496A ASN* 1.3 72.5 - - - +
498A TYR* 1.3 62.7 + - - +
499A TYR* 4.4 1.2 - - + -
525A LEU* 4.2 17.5 - - + -
542A PHE* 4.0 25.4 - - + +
545A LYS* 3.6 32.8 - - + +
546A LYS 2.9 12.7 + - - +
547A LEU* 3.4 31.7 - - + +
548A ILE* 2.9 31.2 + - - +
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Residues in contact with TYR 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A TYR* 3.4 17.6 + - - -
496A ASN* 3.5 31.9 + - + +
497A ILE* 1.3 74.8 - - - +
499A TYR* 1.3 61.7 + - - +
517A MET* 3.3 33.4 - - + -
520A LYS* 4.5 10.4 + - - -
522A THR* 3.6 24.9 - - + +
523A GLU 3.9 9.6 - - - +
524A VAL* 3.7 13.7 - - + -
525A LEU* 2.9 29.1 + - - +
548A ILE* 3.3 30.8 - - + +
550A VAL* 4.3 10.1 - - + -
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Residues in contact with TYR 499 (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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497A ILE* 4.4 1.1 - - + -
498A TYR* 1.3 75.0 - - - +
500A LEU* 1.3 72.8 + - - +
524A VAL* 4.1 2.7 - - - -
525A LEU* 3.2 18.8 - - + +
527A CYS* 4.6 4.9 - - + -
533A GLU* 3.4 34.9 + - + +
536A LEU* 3.7 39.5 - - + -
537A LEU* 3.2 34.7 - - - +
547A LEU* 3.7 22.3 + - + -
548A ILE 3.1 38.5 + - - -
549A SER* 3.6 20.1 + - - -
550A VAL* 3.1 25.3 + - - +
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Residues in contact with LEU 500 (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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499A TYR* 1.3 86.0 - - - +
501A CYS* 1.3 69.6 + - - +
502A ALA* 3.7 3.2 + - + +
508A ALA* 4.1 23.7 - - + +
511A SER* 4.1 30.7 - - - +
513A TYR* 5.0 2.5 - - + -
514A TYR* 4.4 12.8 - - + +
524A VAL* 4.4 6.7 - - + -
525A LEU 2.9 10.5 + - - +
526A PHE* 3.5 9.9 - - + -
527A CYS* 2.9 27.8 + - - +
549A SER* 4.7 5.4 - - - +
550A VAL* 4.6 9.0 - - + -
551A GLU* 3.7 35.0 - - + +
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Residues in contact with CYS 501 (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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500A LEU* 1.3 78.6 - - - +
502A ALA* 1.3 60.3 + - - +
503A PRO* 4.8 0.7 - - - +
527A CYS* 2.0 48.6 - - - +
528A PHE 5.0 0.7 - - - +
529A GLU 3.7 13.7 - - - +
530A GLN* 5.0 1.6 - - - +
533A GLU* 2.6 55.9 + - - +
551A GLU* 4.8 4.5 - - - +
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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