Contacts of the helix formed by residues 667 - 676 (chain A) in PDB entry 5J3V
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 ASN 667 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A VAL* 3.7 12.6 - - - +
617A GLN* 3.2 32.5 + - - +
666A SER* 1.3 72.7 - - - +
668A ILE* 1.3 57.8 + - - +
669A LEU* 3.1 4.0 - - - -
670A THR* 3.2 16.0 + - - +
671A LEU* 3.0 46.4 + - - +
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Residues in contact with ILE 668 (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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609A TYR* 3.3 36.6 - - + +
613A VAL* 4.8 8.5 - - + +
645A LEU* 5.9 0.7 - - + -
648A LEU* 3.9 20.4 - - + -
659A ILE* 6.4 0.2 - - + -
663A VAL* 3.7 23.3 - - + +
666A SER* 3.3 7.5 + - - +
667A ASN* 1.3 77.8 + - - +
669A LEU* 1.3 62.5 + - + +
671A LEU* 3.8 12.6 - - + +
672A MET* 2.9 36.8 + - + +
690A LEU* 3.8 28.0 - - + -
694A LEU* 4.1 12.8 - - + -
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Residues in contact with LEU 669 (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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663A VAL* 4.6 15.3 - - + +
664A ALA* 6.3 0.7 - - - -
666A SER 5.5 3.8 - - - +
667A ASN* 3.1 1.5 - - - +
668A ILE* 1.3 82.5 - - + +
670A THR* 1.3 65.9 + - - +
672A MET* 3.5 24.0 + - + +
673A TYR* 3.2 20.6 + - - +
694A LEU* 5.1 0.4 - - + -
701A HIS* 3.2 37.2 - - + +
702A VAL* 4.4 21.5 - - + -
705A CYS* 4.5 19.1 - - - -
709A PHE* 3.9 17.0 - - + -
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Residues in contact with THR 670 (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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667A ASN* 3.2 19.4 + - - +
669A LEU* 1.3 76.0 - - - +
671A LEU* 1.3 66.0 + - + +
673A TYR* 3.2 14.0 + - + +
674A GLN* 3.2 40.4 + - + +
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Residues in contact with LEU 671 (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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613A VAL* 3.8 40.6 - - + +
616A VAL* 4.2 13.9 - - + -
617A GLN* 3.9 21.5 - - + +
620A LEU* 3.7 20.5 - - + +
645A LEU* 6.4 0.7 - - + -
667A ASN* 3.0 39.5 + - - +
668A ILE* 3.8 8.3 - - + +
669A LEU 3.3 0.2 - - - -
670A THR* 1.3 75.9 - - + +
672A MET* 1.3 60.3 + - + +
674A GLN* 3.1 15.3 + - - +
675A CYS* 2.9 32.6 + - - -
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Residues in contact with MET 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LEU* 5.0 5.6 - - + -
668A ILE* 2.9 28.3 + - + +
669A LEU* 3.6 33.4 - - + +
671A LEU* 1.3 75.8 - - + +
673A TYR* 1.3 57.7 + - - +
675A CYS* 3.0 8.5 + - - +
676A MET* 2.9 48.0 + - + +
687A SER* 4.3 11.4 - - - +
690A LEU* 3.6 40.6 - - + -
691A LEU* 4.3 14.4 - - + -
694A LEU* 3.7 19.5 - - + -
702A VAL* 6.2 0.2 - - + -
709A PHE* 4.7 6.1 - - + -
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Residues in contact with TYR 673 (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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669A LEU 3.2 11.9 + - - +
670A THR* 3.2 19.0 + - + +
672A MET* 1.3 79.2 - - - +
674A GLN* 1.3 63.1 + - + +
676A MET* 3.9 5.5 + - - +
677A GLN* 3.0 53.2 + - - +
708A ASP* 3.8 39.4 + - + -
709A PHE* 4.0 19.0 - + + -
712A ILE* 3.6 21.8 - - + -
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Residues in contact with GLN 674 (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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620A LEU* 3.6 35.8 - - + +
624A MET* 4.7 13.8 - - - +
670A THR* 3.3 33.4 + - + +
671A LEU* 3.1 14.6 + - - +
672A MET 3.1 0.6 - - - -
673A TYR* 1.3 81.8 - - + +
675A CYS* 1.3 64.6 + - - +
676A MET 3.3 0.7 - - - -
677A GLN* 3.5 17.6 + - - +
678A ASP* 3.6 10.0 + - - +
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Residues in contact with CYS 675 (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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616A VAL* 3.8 18.8 - - - -
620A LEU* 3.9 5.4 - - - -
641A MET* 3.7 28.5 - - - -
645A LEU* 4.0 11.4 - - + -
671A LEU 2.9 21.6 + - - -
672A MET* 3.0 10.0 + - - +
674A GLN* 1.3 76.0 - - - +
676A MET* 1.3 63.5 + - - +
677A GLN 3.2 0.4 - - - -
678A ASP* 3.3 19.2 - - - +
683A VAL* 3.5 17.1 - - + +
684A ARG* 3.8 5.7 - - - +
687A SER* 3.8 19.4 + - - -
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Residues in contact with MET 676 (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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672A MET* 2.9 25.0 + - + +
673A TYR* 4.2 2.7 - - - +
674A GLN 3.3 0.4 - - - -
675A CYS* 1.3 76.7 - - - +
677A GLN* 1.3 57.3 + - - +
678A ASP 3.3 0.9 - - - -
684A ARG* 3.2 24.0 - - - +
687A SER* 3.6 20.0 - - - +
688A PHE* 3.5 26.0 - - + -
691A LEU* 3.7 36.1 - - + -
709A PHE* 3.6 43.5 - - + +
712A ILE* 3.7 36.5 - - + +
713A LEU* 5.5 0.2 - - - -
716A ASN* 4.4 2.3 + - - -
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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