Contacts of the helix formed by residues 665 - 672 (chain A) in PDB entry 2XR9
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 665 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564A LEU* 3.4 25.3 - - + +
566A CYS* 4.9 0.7 - - - -
664A GLN* 1.3 78.1 - - - +
666A CYS* 1.3 62.9 + - - +
667A LEU* 3.0 34.1 + - - +
668A ALA* 3.2 30.9 + - - +
669A TYR* 3.4 19.0 - - - -
701A MET* 5.3 0.7 - - - -
759A SER* 5.0 0.4 - - - -
761A ILE* 4.3 1.1 - - - +
1865A SCN 3.3 27.9 - - - -
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Residues in contact with CYS 666 (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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564A LEU 2.8 6.5 + - - -
565A GLY 3.6 17.7 - - - +
566A CYS* 2.1 45.8 - - - -
652A VAL* 3.7 22.0 - - - -
665A ASN* 1.3 73.0 - - - +
667A LEU* 1.3 64.7 + - - +
668A ALA 3.2 0.2 - - - -
669A TYR* 3.1 20.1 + - - +
670A LYS* 3.2 12.6 + - - +
677A TYR* 5.7 4.7 - - - -
701A MET* 4.9 7.2 - - - -
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Residues in contact with LEU 667 (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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564A LEU 3.7 5.4 + - - +
565A GLY* 4.7 8.6 - - - -
665A ASN* 3.0 14.0 + - - +
666A CYS* 1.3 78.3 - - - +
668A ALA* 1.3 56.1 + - - +
670A LYS* 3.0 17.8 + - + +
671A ASN* 2.9 47.8 + - - +
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Residues in contact with ALA 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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665A ASN* 3.2 31.0 + - - +
666A CYS 3.2 0.4 - - - -
667A LEU* 1.3 76.8 - - - +
669A TYR* 1.3 56.3 + - - +
671A ASN* 3.3 8.7 + - - +
672A ASP* 3.1 28.9 + - - +
756A VAL* 3.7 12.3 - - + +
757A GLU 4.1 8.6 - - - +
758A GLY 5.4 1.1 - - - +
759A SER* 3.8 25.1 - - - -
761A ILE* 4.3 3.6 - - + -
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Residues in contact with TYR 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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664A GLN* 2.5 30.0 + - - -
665A ASN 3.4 24.0 - - - -
666A CYS* 3.1 13.5 + - - +
668A ALA* 1.3 79.1 - - - +
670A LYS* 1.3 56.9 + - - +
672A ASP* 3.1 25.1 - - - +
675A MET* 3.7 15.3 - - + +
676A SER* 3.3 32.3 - - - -
677A TYR* 4.0 24.2 - + + -
701A MET* 4.0 14.6 - - + -
702A VAL 3.9 1.2 - - - -
703A PRO* 3.4 34.3 - - + +
756A VAL* 4.0 12.6 - - + -
761A ILE* 4.1 13.3 - - + +
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Residues in contact with LYS 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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666A CYS 3.2 10.9 + - - +
667A LEU* 3.0 21.6 + - + +
669A TYR* 1.3 77.9 - - - +
671A ASN* 1.3 60.3 + - - +
672A ASP 4.6 1.2 - - - -
673A LYS* 4.4 11.4 + - - +
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Residues in contact with ASN 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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667A LEU* 2.9 41.5 + - - +
668A ALA* 3.6 10.0 - - - +
670A LYS* 1.3 78.0 - - - +
672A ASP* 1.3 58.4 + - - +
673A LYS* 3.2 29.5 + - - +
757A GLU* 4.6 23.0 + - + +
758A GLY* 6.2 1.0 - - - -
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Residues in contact with ASP 672 (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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668A ALA 3.1 16.4 + - - +
669A TYR 3.1 14.4 + - - +
670A LYS 3.3 1.7 - - - -
671A ASN* 1.3 74.7 - - - +
673A LYS* 1.3 63.0 + - - +
674A GLN* 3.0 12.8 + - - +
675A MET* 3.0 49.3 + - + +
755A TYR 4.6 1.6 - - - +
756A VAL* 3.9 9.4 - - + -
757A GLU* 3.2 39.2 + - + +
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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