Contacts of the strand formed by residues 492 - 497 (chain A) in PDB entry 3JYT
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 GLU 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A ILE* 2.7 35.3 - - + +
435A VAL 4.1 7.3 - - - +
436A GLY 4.9 6.7 - - - +
437A ALA* 4.1 15.0 - - + +
438A GLU* 4.7 3.5 + - - +
490A GLY* 2.7 8.4 + - - +
491A LEU* 1.3 82.5 - - + +
493A VAL* 1.3 64.4 + - - +
529A GLU* 5.4 1.6 - - + -
530A LYS* 3.5 32.1 + - + +
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Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ILE* 3.2 13.9 - - - +
437A ALA* 4.3 1.3 - - - -
438A GLU 4.5 3.1 - - - -
440A PHE* 3.8 20.0 - - + -
485A ALA 3.5 20.9 - - - +
486A LEU* 5.1 2.0 - - + -
489A SER* 2.9 32.1 - - - +
490A GLY 3.0 21.5 - - - +
492A GLU* 1.3 72.4 - - - +
494A ASN* 1.3 87.3 + - - +
495A ILE* 4.0 10.5 - - + -
528A LYS* 4.7 3.8 - - + -
530A LYS 3.4 5.3 + - - -
531A VAL* 4.0 17.2 - - + -
532A TYR 3.9 6.2 + - - -
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Residues in contact with ASN 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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433A PRO* 3.7 0.4 - - - +
434A ILE* 2.9 45.4 + - - +
437A ALA* 3.1 9.0 + - - +
438A GLU 3.7 9.9 + - - +
439A THR* 3.5 9.9 - - - +
440A PHE 2.9 26.8 + - - +
493A VAL* 1.3 89.4 + - - +
495A ILE* 1.3 62.6 + - - +
532A TYR* 3.2 28.8 - - - +
289B LEU* 3.4 28.2 - - + +
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Residues in contact with ILE 495 (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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440A PHE* 3.8 9.6 - - + +
442A VAL* 3.1 33.2 - - + -
482A ILE* 3.6 20.6 - - + -
485A ALA* 3.2 41.7 - - + +
486A LEU* 3.9 15.0 - - + -
493A VAL* 4.0 9.4 - - + -
494A ASN* 1.3 76.4 - - - +
496A VAL* 1.3 65.5 + - - +
531A VAL* 5.5 5.2 - - + -
532A TYR* 3.3 11.1 + - - +
533A LEU* 3.3 40.9 - - + -
534A ALA 3.6 2.3 + - - -
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Residues in contact with VAL 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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439A THR* 5.5 1.1 - - + -
440A PHE 3.4 17.1 + - - +
441A TYR* 3.8 35.2 - - + -
442A VAL* 3.1 26.5 + - - +
495A ILE* 1.3 77.4 - - - +
497A THR* 1.3 72.7 - - - +
533A LEU* 4.5 1.3 - - - -
534A ALA* 3.3 27.1 - - + +
535A TRP 4.3 0.4 - - - +
536A VAL* 3.9 25.4 - - + -
258B GLN* 5.3 5.4 - - - +
289B LEU* 5.6 10.8 - - + -
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Residues in contact with THR 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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442A VAL* 4.4 6.3 + - - -
478A GLU* 2.7 36.8 + - + -
482A ILE* 5.0 7.6 - - + -
496A VAL* 1.3 82.9 - - - +
498A ASP* 1.3 64.2 + - - +
499A SER* 3.1 22.0 + - - +
502A ALA* 5.7 0.4 - - + -
503A LEU* 4.7 15.3 - - + +
533A LEU* 5.1 10.3 - - + -
534A ALA 3.1 8.3 + - - +
535A TRP* 2.9 32.0 - - + -
536A VAL* 3.0 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