Contacts of the strand formed by residues 532 - 536 (chain B) in PDB entry 3ZHT
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 532 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530B LEU 3.8 0.2 - - - -
531B ASP* 1.3 83.0 - - + +
533B VAL* 1.3 66.1 + - - +
534B VAL* 3.8 9.2 - - + -
583B THR* 5.0 1.9 + - - -
595B ILE* 3.7 4.0 - - - +
596B GLU* 3.3 28.6 - - + +
598B SER* 2.6 31.0 + - - -
620B LYS* 2.6 36.9 + - - +
624B LEU* 5.9 1.0 - - + +
636B SER 3.2 3.6 + - - +
637B VAL* 3.3 16.0 - - + +
638B VAL* 2.8 32.8 + - - +
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B VAL* 5.0 3.6 - - + -
522B ILE* 4.1 31.6 - - + -
525B CYS* 3.9 21.3 - - + -
532B GLU* 1.3 76.3 - - - +
534B VAL* 1.3 61.7 + - - +
535B ILE* 4.6 3.8 - - + -
595B ILE* 3.8 21.3 - - + -
596B GLU 3.0 9.6 + - - +
597B VAL* 3.4 7.6 - - + +
598B SER* 3.0 25.6 + - - +
638B VAL* 3.4 17.5 - - + +
640B LEU* 3.7 26.9 - - + -
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Residues in contact with VAL 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLU* 3.6 12.6 - - - +
533B VAL* 1.3 73.5 - - - +
535B ILE* 1.3 62.1 + - - +
598B SER* 3.4 26.0 - - - +
600B THR* 4.8 4.5 - - - +
613B LEU* 3.5 22.3 - - + +
616B LEU* 4.2 21.8 - - + -
617B VAL* 3.8 13.0 - - + -
620B LYS* 4.0 11.2 - - + -
637B VAL* 3.8 24.5 - - + -
638B VAL 2.9 7.8 + - - +
639B PRO* 3.5 0.3 - - - +
640B LEU 2.8 27.9 + - - -
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Residues in contact with ILE 535 (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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518B MET* 3.9 31.0 - - + -
522B ILE* 4.5 1.6 - - + -
533B VAL* 4.6 5.2 - - + -
534B VAL* 1.3 76.1 - - - +
536B ALA* 1.3 68.6 + - - +
537B MET* 4.4 7.2 - - + -
545B VAL* 4.5 6.7 - - + -
549B ILE* 3.9 12.6 - - + -
550B VAL* 4.7 4.3 - - + -
597B VAL* 3.8 25.4 - - + -
598B SER 2.8 15.7 + - - +
599B LEU* 3.4 19.0 - - + +
600B THR* 2.9 32.6 + - - +
613B LEU* 4.0 2.4 - - - +
640B LEU* 3.2 29.2 - - + +
642B LEU* 4.6 3.1 - - + -
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Residues in contact with ALA 536 (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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535B ILE* 1.3 74.9 - - - +
537B MET* 1.3 62.1 + - - +
599B LEU* 4.9 0.9 - - - -
600B THR* 3.9 15.0 - - + -
609B VAL* 3.9 20.4 - - + +
613B LEU* 3.7 32.0 - - + +
640B LEU 3.1 4.9 + - - +
641B MET* 3.5 6.9 - - + -
642B LEU 2.8 27.4 + - - +
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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
------------------------------------------------------------
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