Contacts of the helix formed by residues 657 - 664 (chain A) in PDB entry 1ZY7
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 657 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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633A TYR* 3.8 0.2 - - - -
656A ASN* 1.3 88.6 - - + +
658A TYR* 1.3 67.9 + - - +
659A HIS* 3.8 12.1 - - + +
660A GLU* 3.1 21.4 + - + +
661A SER* 3.0 21.7 + - - -
695A ASP 3.8 6.3 - - - +
696A GLN* 3.5 33.2 - - - +
697A PHE 3.4 9.6 - - - +
698A SER* 3.4 13.7 - - - +
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Residues in contact with TYR 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ARG* 5.3 0.2 + - - -
532A LEU* 3.5 26.3 - - + +
629A LYS* 3.7 28.1 - - + +
632A LEU* 5.1 4.7 - - - +
633A TYR* 3.4 46.2 - + + -
656A ASN 3.5 2.4 + - - -
657A VAL* 1.3 69.8 - - - +
659A HIS* 1.3 62.3 + - - +
661A SER* 3.1 4.5 + - - -
662A LYS* 3.0 34.5 + - - +
695A ASP* 3.3 41.1 - - + +
697A PHE* 2.8 36.2 + + + +
901A IHP 2.5 35.4 + - - -
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Residues in contact with HIS 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A VAL* 3.3 3.8 - - + -
658A TYR* 1.3 72.1 - - - +
660A GLU* 1.3 73.7 + - - +
662A LYS* 3.3 11.9 + - + +
663A LEU* 3.1 54.5 + - + +
692A THR* 3.3 32.2 - - + +
695A ASP* 2.9 40.5 + - + +
696A GLN* 3.7 18.6 + - - +
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Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ILE* 4.8 1.5 - - - +
656A ASN 6.2 0.2 - - - +
657A VAL* 3.1 29.9 + - + +
659A HIS* 1.3 87.6 + - - +
661A SER* 1.3 65.6 + - - +
663A LEU* 3.1 20.5 + - - +
664A ALA* 3.1 20.3 + - - +
696A GLN* 5.0 5.4 + - - +
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Residues in contact with SER 661 (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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532A LEU* 3.8 17.0 - - - -
535A ILE* 3.5 13.9 - - - +
633A TYR* 2.8 30.3 + - - -
636A TRP* 4.7 2.9 - - - -
652A ILE* 3.6 24.1 - - - +
655A PRO* 3.7 8.4 - - - +
656A ASN 3.9 3.8 + - - -
657A VAL 3.0 6.3 + - - -
658A TYR 3.1 7.2 + - - -
660A GLU* 1.3 77.0 - - - +
662A LYS* 1.3 62.4 + - - +
664A ALA* 3.2 16.3 + - - +
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Residues in contact with LYS 662 (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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531A SER* 3.2 21.0 - - - +
532A LEU* 4.0 17.5 - - + -
629A LYS* 4.2 0.4 - - - +
658A TYR* 3.0 29.3 + - + +
659A HIS* 3.5 10.8 - - + +
661A SER* 1.3 77.6 - - - +
663A LEU* 1.3 62.4 + - + +
665A ALA* 3.1 17.6 + - - +
669A GLN* 3.0 21.2 + - - +
695A ASP* 2.8 29.4 + - - +
901A IHP 2.8 71.7 + - - +
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Residues in contact with LEU 663 (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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659A HIS* 3.1 48.9 + - + +
660A GLU* 3.1 23.7 + - - +
662A LYS* 1.3 76.1 - - + +
664A ALA* 1.3 62.4 + - - +
665A ALA 3.3 1.9 + - - -
666A LYS* 3.9 17.8 + - - +
669A GLN* 4.1 28.6 - - + +
672A LYS* 5.8 0.9 - - - +
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Residues in contact with ALA 664 (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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535A ILE* 4.4 4.0 - - + -
650A SER* 3.2 17.9 - - - -
651A LYS 3.9 17.1 - - - +
652A ILE* 3.7 25.6 - - + -
660A GLU 3.1 8.5 + - - +
661A SER 3.4 11.2 - - - +
662A LYS 3.2 0.4 - - - -
663A LEU* 1.3 78.0 - - - +
665A ALA* 1.3 55.2 + - - +
666A LYS* 2.8 19.2 + - - +
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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