Contacts of the strand formed by residues 584 - 591 (chain B) in PDB entry 4YZ9
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 THR 584 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579B HIS* 3.3 9.0 - - - +
580B GLY* 2.8 35.7 + - - +
581B ALA 2.6 24.2 + - - -
582B GLU* 3.3 5.9 + - - +
583B GLY* 1.3 73.6 - - - +
585B ILE* 1.3 61.1 + - - +
599B LYS* 3.2 36.3 - - + -
600B ARG 3.2 23.1 - - - +
601B ILE* 3.9 12.8 - - + +
605B CYS* 5.7 0.9 - - - +
1001B 4K7 3.7 10.5 - - - +
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Residues in contact with ILE 585 (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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576B VAL* 5.2 5.6 - - + -
578B GLY 4.1 6.3 - - - +
579B HIS* 4.5 14.6 - - + +
583B GLY 4.4 8.3 - - - +
584B THR* 1.3 78.3 - - - +
586B VAL* 1.3 64.2 + - - +
587B TYR* 3.4 38.2 - - + +
598B VAL 3.9 0.2 - - - +
599B LYS* 3.6 0.9 - - - -
600B ARG* 2.7 71.7 + - + +
602B LEU* 6.1 0.4 - - + -
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Residues in contact with VAL 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B VAL* 4.2 4.2 - - - +
577B LEU* 3.1 27.9 + - + -
578B GLY 2.9 24.4 + - - +
580B GLY 4.5 4.7 - - - +
584B THR* 4.8 0.2 - - + -
585B ILE* 1.3 79.0 - - - +
587B TYR* 1.3 70.7 + - - +
597B ALA* 4.0 12.8 - - + -
598B VAL 3.1 13.5 - - - +
599B LYS* 3.9 21.8 - - + -
712B PHE* 3.7 48.7 - - + -
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Residues in contact with TYR 587 (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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571B PHE* 3.6 40.4 - + + -
572B CYS 4.0 1.3 - - - +
573B PRO* 4.1 32.3 - - + -
575B ASP 3.8 12.8 - - - +
576B VAL* 4.8 7.6 - - + -
577B LEU* 3.3 14.4 - - - +
585B ILE* 3.4 42.6 - - + +
586B VAL* 1.3 76.7 - - - +
588B ARG* 1.3 62.0 + - - +
597B ALA* 3.8 0.2 - - - -
598B VAL* 2.8 37.9 + - + +
600B ARG* 3.7 39.4 + - + -
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Residues in contact with ARG 588 (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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571B PHE* 3.4 3.5 - - - +
572B CYS* 3.2 26.9 + - - +
575B ASP* 3.5 27.4 + - + +
577B LEU* 3.6 16.5 - - + +
587B TYR* 1.3 73.4 - - - +
589B GLY* 1.3 66.6 + - - +
590B MET* 5.2 1.2 - - - +
595B ASP* 3.4 36.4 + - - +
596B VAL 4.3 0.2 - - - -
644B LEU* 3.6 41.7 - - - +
698B MET* 5.9 1.6 - - - +
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Residues in contact with GLY 589 (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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570B SER 3.0 13.9 - - - -
571B PHE* 3.7 2.7 - - - -
587B TYR 3.9 1.0 + - - -
588B ARG* 1.3 80.7 + - - +
590B MET* 1.3 69.2 + - - +
595B ASP* 3.9 1.9 - - - -
596B VAL* 2.9 35.4 + - - +
598B VAL* 3.7 10.3 - - - +
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Residues in contact with MET 590 (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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568B LYS 3.6 1.6 - - - +
569B ILE* 3.6 2.1 - - - +
570B SER* 2.7 48.7 + - - +
588B ARG* 5.2 1.1 - - - +
589B GLY* 1.3 80.6 - - - +
591B PHE* 1.3 61.2 + - - +
593B ASN* 5.1 12.8 - - - +
594B ARG 3.1 16.6 - - - +
595B ASP* 3.6 20.0 - - - +
596B VAL* 3.9 4.7 - - - +
598B VAL* 4.4 0.2 - - - +
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Residues in contact with PHE 591 (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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591A PHE* 3.9 17.5 - + - -
629A PHE 4.1 9.6 - - - -
630A CYS* 4.1 12.3 - - + -
568B LYS* 3.8 33.4 - - + +
569B ILE* 4.2 5.4 - - + -
590B MET* 1.3 74.1 - - - +
592B ASP* 1.3 80.2 + - + +
593B ASN 3.1 1.3 - - - -
594B ARG* 2.8 41.7 + - - +
596B VAL* 3.8 14.1 - - + +
629B PHE* 3.8 36.3 - + + -
630B CYS* 3.5 34.3 - - + -
641B ALA* 4.2 8.7 - - + -
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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