Contacts of the strand formed by residues 492 - 498 (chain A) in PDB entry 4H1S
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 VAL 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A GLN* 3.6 40.4 - - + +
426A LEU 3.4 4.9 - - - +
427A LYS* 4.4 11.0 - - + -
490A ASP 5.4 1.3 - - - +
491A GLU* 1.3 82.7 + - - +
493A TYR* 1.3 71.0 + - - +
494A LYS* 5.8 1.6 - - + -
516A LEU* 3.8 20.2 - - + -
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Residues in contact with TYR 493 (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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386A MET* 4.0 33.0 - - + -
424A VAL 4.0 0.2 - - - +
425A GLN* 3.4 3.1 - - - +
426A LEU* 2.6 44.4 + - - +
428A GLY* 3.7 20.6 - - - -
431A LEU* 4.2 7.4 - - + -
474A VAL* 3.6 19.1 - - + -
475A LEU 5.5 2.0 - - - -
476A CYS* 6.5 0.7 - - - -
477A THR* 6.0 2.5 - - - -
486A PRO 4.2 2.4 + - - -
487A LEU* 3.4 19.1 - - + -
488A LYS* 2.7 45.9 + - - +
491A GLU* 3.7 20.0 - - + +
492A VAL* 1.3 79.5 - - - +
494A LYS* 1.3 63.9 + - - +
495A VAL* 4.1 1.5 + - + -
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Residues in contact with LYS 494 (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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379A MET 5.4 0.4 + - - -
380A PHE* 3.0 60.0 + - + +
381A TRP* 3.9 17.0 - - + -
384A VAL* 3.9 29.2 - - + +
385A SER 4.8 1.0 + - - -
386A MET* 3.7 16.9 + - - +
424A VAL 3.5 3.8 - - - -
425A GLN* 4.7 12.8 - - + +
477A THR* 6.0 11.2 - - + +
492A VAL* 5.8 1.6 - - + +
493A TYR* 1.3 75.2 - - - +
495A VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A TRP* 5.1 0.6 - - - -
384A VAL* 4.4 3.4 - - - -
386A MET* 3.5 35.7 - - + +
387A CYS 4.4 0.9 - - - -
388A ILE* 4.0 26.7 - - + +
422A ASP 3.7 0.2 - - - +
423A LEU* 3.6 3.1 - - - -
424A VAL* 2.9 45.7 + - + +
426A LEU* 4.7 5.8 - - + -
431A LEU* 3.9 18.8 - - + -
455A ILE* 5.9 0.2 - - + -
493A TYR 4.5 3.4 - - - +
494A LYS* 1.3 84.1 - - - +
496A ILE* 1.3 76.6 + - - +
497A LEU* 4.4 6.7 - - + -
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Residues in contact with ILE 496 (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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368A MET* 3.3 43.5 - - + +
369A ILE* 4.0 16.2 - - + -
371A ASN* 6.3 0.2 - - - +
372A ASN* 4.0 10.8 - - + +
384A VAL* 4.0 6.8 - - + +
386A MET 2.9 19.2 + - - +
387A CYS* 3.2 19.3 - - + -
388A ILE 3.1 24.8 + - - +
421A PHE* 4.3 17.0 - - + +
422A ASP 3.2 15.5 - - - +
423A LEU* 3.8 22.9 - - + -
495A VAL* 1.3 73.1 - - - +
497A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 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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368A MET* 3.5 7.9 - - - -
388A ILE* 3.5 35.4 - - + +
421A PHE* 4.4 0.2 - - - -
422A ASP* 2.7 42.2 + - + +
424A VAL* 3.9 33.2 - - + -
426A LEU* 5.0 1.8 - - + -
495A VAL* 4.4 3.8 - - + +
496A ILE* 1.3 78.4 - - - +
498A PRO* 1.3 83.5 - - + +
501A LEU* 4.4 4.5 - - + -
502A ALA* 3.8 21.5 - - + +
511A ILE* 4.0 21.3 - - + -
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Residues in contact with PRO 498 (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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368A MET* 4.4 3.1 - - + -
388A ILE 3.4 13.0 - - - +
389A LEU* 3.7 27.6 - - + -
390A ASN* 4.0 11.4 - - - +
420A THR 3.4 9.9 - - - +
421A PHE* 4.3 12.3 - - + -
497A LEU* 1.3 94.8 - - + +
499A ASN* 1.3 67.0 + - - +
500A PHE* 4.1 12.8 - - + +
501A LEU* 2.9 26.6 + - + +
502A ALA 3.2 8.0 + - - -
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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