Contacts of the helix formed by residues 587 - 597 (chain B) in PDB entry 2Z66
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 HIS 587 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557B MET* 3.2 28.2 + - + +
558B THR* 4.0 11.2 - - + -
582B ALA* 3.6 38.5 - - + +
584B THR* 2.8 31.1 + - - +
586B GLU* 1.3 88.5 + - + +
588B GLN* 1.3 64.8 + - - +
589B SER 3.2 2.7 - - - -
590B PHE* 3.3 2.4 + - + -
591B LEU* 3.0 28.9 + - + +
2002B SO4 2.8 30.1 + - - +
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Residues in contact with GLN 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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584B THR 3.4 4.3 + - - -
585B CYS 3.2 15.1 + - - +
586B GLU 3.6 0.6 - - - -
587B HIS* 1.3 76.4 - - - +
589B SER* 1.3 59.9 + - - +
591B LEU* 3.5 2.9 + - - +
592B GLN* 3.0 30.3 + - + +
625B ILE* 2.8 42.9 + - + +
626B THR* 3.6 13.9 - - - +
627B CYS* 3.7 19.1 - - - +
2002B SO4 3.9 0.2 + - - -
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Residues in contact with SER 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B GLN* 5.4 10.8 - - - -
587B HIS 3.2 0.6 - - - -
588B GLN* 1.3 78.9 + - - +
590B PHE* 1.3 65.2 + - - +
592B GLN* 3.3 8.1 + - - +
593B TRP* 3.0 22.6 + - - +
2002B SO4 3.4 15.4 + - - -
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Residues in contact with PHE 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B LEU* 4.3 8.7 - - + -
556B ILE* 3.5 28.9 - - + -
557B MET* 3.5 28.0 - - - +
558B THR* 3.4 25.1 - - - -
559B SER* 3.9 3.4 - - - -
564B LEU* 4.0 17.7 - - + -
581B PHE* 4.2 8.5 - + - -
587B HIS 3.3 3.8 + - - +
589B SER* 1.3 74.1 - - - +
591B LEU* 1.3 68.3 + - + +
593B TRP* 3.1 25.3 + + - +
594B ILE* 2.9 54.4 + - + +
2002B SO4 2.9 31.3 + - - +
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Residues in contact with LEU 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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557B MET* 5.7 0.4 - - - +
581B PHE* 4.2 26.0 - - + -
582B ALA 3.6 21.1 - - - +
583B CYS* 3.7 7.2 - - + -
587B HIS* 3.0 23.5 + - + +
588B GLN 4.0 2.9 - - - +
590B PHE* 1.3 82.4 - - + +
592B GLN* 1.3 60.2 + - - +
594B ILE* 3.3 6.8 + - + +
595B LYS* 3.0 35.2 + - - +
620B VAL* 3.8 27.2 - - + +
625B ILE* 3.0 39.5 - - + -
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Residues in contact with GLN 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B GLN* 3.0 21.1 + - + +
589B SER* 3.5 8.1 - - - +
590B PHE 3.3 0.2 - - - -
591B LEU* 1.3 75.3 - - - +
593B TRP* 1.3 63.0 + - - +
595B LYS* 3.3 24.4 + - - +
596B ASP* 3.1 34.7 + - - +
436D GLN* 3.5 28.7 + - - +
440D PHE* 4.8 4.9 - - - -
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Residues in contact with TRP 593 (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 LEU* 4.0 17.5 - - + -
537B THR* 3.6 24.0 - - + -
564B LEU* 3.4 45.3 - - + +
565B GLN 3.1 21.2 + - - -
566B HIS* 5.5 0.6 + + - -
567B PHE* 3.4 31.6 - + - -
574B LEU* 5.0 0.2 - - + -
576B LEU* 5.3 0.9 - - + -
589B SER 3.0 12.7 + - - +
590B PHE* 3.3 14.1 - + - +
592B GLN* 1.3 76.8 - - - +
594B ILE* 1.3 89.9 + - + +
596B ASP* 3.2 14.4 + - + +
597B GLN* 3.0 53.1 + - + +
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Residues in contact with ILE 594 (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 LEU* 4.9 0.2 - - + -
576B LEU* 3.6 26.0 - - + -
581B PHE* 4.2 9.2 - - + -
590B PHE* 2.9 55.0 + - + +
591B LEU* 3.4 12.3 - - + +
592B GLN 3.3 0.2 - - - -
593B TRP* 1.3 90.1 - - + +
595B LYS* 1.3 62.7 + - - +
597B GLN* 3.0 20.1 + - + +
601B LEU* 3.6 9.3 - - + +
607B MET* 3.6 28.0 - - + -
620B VAL* 4.5 10.5 - - + -
621B LEU* 4.3 9.2 - - + -
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Residues in contact with LYS 595 (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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591B LEU* 3.0 21.4 + - - +
592B GLN* 3.3 31.8 + - - +
594B ILE* 1.3 75.0 - - - +
596B ASP* 1.3 58.6 - - - +
598B ARG* 3.1 29.1 + - - +
620B VAL* 4.3 6.3 - - + +
621B LEU* 3.1 49.8 + - + +
622B SER 4.7 0.2 - - - -
623B LEU 2.6 31.7 + - - -
624B ASN* 3.8 15.6 + - - +
625B ILE 5.5 0.7 - - - +
439D GLU* 5.7 0.5 - - - +
1K NAG 5.7 0.4 - - - -
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Residues in contact with ASP 596 (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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592B GLN* 3.1 27.8 + - - +
593B TRP* 3.2 14.8 + - + +
595B LYS* 1.3 76.9 - - - +
597B GLN* 1.3 68.3 + - - +
598B ARG* 3.2 3.1 + - - -
599B GLN* 5.1 2.8 + - - +
436D GLN* 2.7 30.0 + - - +
439D GLU* 3.4 47.3 - - - +
440D PHE* 4.4 4.3 - - - -
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Residues in contact with GLN 597 (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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565B GLN 5.0 1.2 + - - +
566B HIS* 5.0 13.6 + - - -
567B PHE* 4.3 7.3 + - - -
574B LEU* 4.5 10.5 - - + -
576B LEU* 5.9 0.2 - - + -
593B TRP* 3.0 73.1 + - + +
594B ILE* 3.0 12.0 + - + +
596B ASP* 1.3 86.5 + - - +
598B ARG* 1.3 64.5 + - - +
599B GLN 3.2 2.7 - - - -
600B LEU* 2.8 35.7 + - + +
601B LEU* 3.3 22.5 + - + +
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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