Contacts of the strand formed by residues 462 - 467 (chain A) in PDB entry 4EZJ
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 462 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ILE* 3.5 25.0 - - + +
373A LEU* 4.0 6.9 - - - +
404A PHE* 3.8 19.4 - + - -
432A GLN* 3.5 3.5 - - - -
433A ILE* 3.0 41.7 + - + -
460A LEU* 3.7 7.1 - - - +
461A LEU* 1.3 100.2 - - + +
463A TYR* 1.3 64.4 + - - +
484A MET* 3.8 21.1 - - + -
485A TRP 3.2 9.6 - - - +
486A GLN* 3.7 37.2 + - + -
514A MET* 3.6 38.6 - - + -
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Residues in contact with TYR 463 (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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430A ASN* 4.5 2.5 - - - +
431A LEU 3.4 8.1 - - - +
432A GLN* 3.7 11.2 - - + +
460A LEU* 5.2 0.4 - - + -
462A TYR* 1.3 75.7 - - - +
464A VAL* 1.3 64.6 + - - +
465A ASN* 4.7 4.3 - - - -
484A MET* 3.4 4.5 - - - +
485A TRP* 2.9 66.8 + + + +
486A GLN 4.4 4.4 + - - -
487A ILE* 3.6 31.2 - - + -
500A ASP* 3.2 30.9 + - - +
501A LYS* 3.5 47.2 + - + +
503A THR* 4.7 1.3 - - + -
708A HIS* 3.1 24.9 + - - -
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Residues in contact with VAL 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU 4.0 0.3 - - - +
430A ASN* 4.0 0.3 + - - -
431A LEU* 3.0 40.2 + - + +
463A TYR* 1.3 79.6 - - - +
465A ASN* 1.4 71.7 + - - +
482A LEU* 4.0 15.3 - - + -
483A HIS 3.4 22.7 - - - +
484A MET* 3.6 26.2 - - + -
485A TRP* 4.9 4.7 - - + -
505A ALA 4.7 6.3 - - - +
506A THR* 3.8 20.6 - - + -
516A ILE* 3.8 20.4 - - + -
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Residues in contact with ASN 465 (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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169A HIS* 5.1 0.5 - - - -
388A GLN* 5.2 1.0 - - - +
428A LEU* 3.7 23.1 - - + +
429A LEU 3.3 4.5 - - - +
430A ASN* 2.8 38.1 + - - +
431A LEU* 6.0 0.2 - - - -
463A TYR* 4.7 5.5 - - - -
464A VAL* 1.4 84.0 - - - +
466A LEU* 1.3 63.8 + - - +
482A LEU* 4.8 3.6 - - - +
501A LYS 2.8 26.7 + - - +
502A LEU 3.4 10.5 - - - -
503A THR* 3.0 27.6 + - - +
504A SER* 3.6 20.6 - - - +
506A THR* 5.0 1.9 - - - +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A HIS* 3.3 38.6 - - + +
428A LEU* 3.5 4.1 - - - -
429A LEU* 2.7 53.9 + - + +
431A LEU* 5.5 1.1 - - + -
465A ASN* 1.3 75.0 - - - +
467A LEU* 1.3 61.3 + - - +
468A LEU* 3.4 1.2 + - + -
476A ARG* 3.6 23.8 - - + +
480A TYR* 4.2 11.9 - - + -
482A LEU* 4.2 19.5 - - + -
504A SER* 5.5 1.1 - - - +
518A ILE* 4.3 15.3 - - + -
520A LEU* 3.8 29.2 - - + -
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Residues in contact with LEU 467 (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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172A GLU* 4.1 12.1 - - - +
426A GLY* 4.1 17.0 - - - +
427A ALA 3.6 15.3 - - - +
428A LEU* 3.9 18.4 - - + +
466A LEU* 1.3 73.1 - - - +
468A LEU* 1.3 63.4 + - - +
469A ILE 3.6 11.4 + - - +
476A ARG* 3.2 43.2 + - - +
504A SER* 4.0 18.2 - - - -
671A PRO* 3.5 30.5 - - + +
672A TYR* 3.7 27.6 - - + -
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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