Contacts of the strand formed by residues 676 - 679 (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 SER 676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A TYR* 3.3 20.5 - - - -
675A MET* 1.3 75.7 - - - +
677A TYR* 1.3 78.0 + - - -
704A MET 2.9 31.7 + - - -
706A PRO* 4.2 7.8 - - - +
709A LYS* 3.7 19.8 - - - +
1864A SCN 4.9 2.4 - - - -
1885A IOD 3.9 18.7 - - - +
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Residues in contact with TYR 677 (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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649A THR 4.3 0.7 + - - -
650A ASN* 3.8 24.9 + - - +
651A CYS 4.2 0.9 + - - -
652A VAL* 3.6 23.4 - - + +
666A CYS* 5.7 4.9 - - - -
669A TYR* 4.0 27.4 - + + -
676A SER* 1.3 89.3 + - - +
678A GLY* 1.3 61.8 + - - +
679A PHE* 3.7 24.0 - + - -
701A MET* 3.5 31.2 - - + -
702A VAL 3.3 12.6 - - - +
704A MET* 3.8 2.9 - - - +
709A LYS* 3.0 25.7 + - - -
1864A SCN 3.6 26.0 - - - -
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Residues in contact with GLY 678 (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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677A TYR* 1.3 74.5 - - - +
679A PHE* 1.3 69.3 + - - -
701A MET* 3.3 9.2 - - - +
702A VAL* 2.9 34.6 + - - -
704A MET* 3.9 18.7 - - - -
709A LYS* 4.2 8.5 - - - -
1864A SCN 5.2 0.2 - - - -
1883A IOD 4.4 4.3 - - - -
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Residues in contact with PHE 679 (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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649A THR 5.7 0.9 - - - -
651A CYS 4.0 7.4 - - - -
652A VAL* 4.3 3.4 - - + -
677A TYR* 3.7 27.1 - + - -
678A GLY* 1.3 78.1 - - - -
680A LEU* 1.3 63.1 + - - +
681A PHE 3.6 9.2 - - - +
683A PRO* 4.0 20.2 - - + -
695A ALA 3.2 21.1 - - - -
696A PHE* 3.7 37.7 - + - -
697A LEU 4.2 4.9 - - - -
700A ASN* 3.3 24.0 - - - +
701A MET* 4.2 16.4 - - + -
702A VAL* 4.7 1.3 - - - -
712A TRP* 2.8 23.6 + - - +
716A GLN* 3.0 10.4 + - - +
1864A SCN 4.3 20.4 - - - -
1873A IOD 3.8 6.6 - - + +
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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