Contacts of the strand formed by residues 653 - 658 (chain A) in PDB entry 2O8C
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 653 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A SER* 2.7 44.2 + - - -
651A ILE 3.9 5.4 + - - -
652A PRO* 1.3 81.2 - - - +
654A ASP* 1.3 65.7 + - - +
674A GLY 5.6 1.0 + - - -
678A TYR* 3.8 25.8 - - + +
681A GLN* 4.1 7.5 - - - +
815A TYR 3.2 18.8 + - - +
816A GLN* 3.2 25.4 - - - +
817A VAL* 3.4 29.5 + - + +
936A ADP 4.3 5.3 + - - -
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Residues in contact with ASP 654 (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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634A LEU 3.4 5.8 - - - +
635A LYS* 4.3 17.7 + - - +
636A ALA* 3.0 26.0 + - - +
652A PRO 5.3 0.2 - - - -
653A ASN* 1.3 77.0 - - - +
655A VAL* 1.3 57.7 + - - +
656A TYR 4.4 0.2 + - - -
678A TYR* 2.6 24.6 + - - -
800A LEU* 5.4 0.7 - - - +
817A VAL* 4.5 5.6 + - - +
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Residues in contact with VAL 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A ILE 4.2 0.9 - - - +
633A ILE* 3.6 6.8 - - - +
634A LEU* 2.9 53.3 + - + +
637A SER* 3.8 14.4 - - - +
654A ASP* 1.3 78.2 - - - +
656A TYR* 1.3 65.0 + - - +
657A PHE* 3.5 32.1 - - + -
665A HIS* 5.9 0.7 - - + +
678A TYR* 3.6 26.7 - - + +
681A GLN* 5.3 0.9 - - + +
682A THR* 3.7 26.0 - - + +
779A MET* 4.9 3.1 - - + -
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Residues in contact with TYR 656 (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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632A ILE 3.5 2.0 - - - -
633A ILE* 4.3 29.6 - - + -
654A ASP 4.4 0.4 + - - -
655A VAL* 1.3 76.6 - - - +
657A PHE* 1.3 67.3 + - - +
658A GLU* 3.3 42.2 + - + -
661A LYS* 4.6 8.7 - - + +
662A GLN* 3.6 31.6 - - + +
665A HIS* 2.8 38.1 + - + -
678A TYR* 4.9 0.6 + - - -
819A LYS* 6.0 8.5 - - - +
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Residues in contact with PHE 657 (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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630A GLY 4.2 1.6 - - - -
631A ARG* 3.2 7.1 - - - -
632A ILE* 2.8 51.5 + - + +
633A ILE* 4.6 0.5 - - - +
655A VAL* 3.5 23.6 - - + -
656A TYR* 1.3 84.8 - - - +
658A GLU* 1.3 65.2 + - - +
662A GLN 3.3 6.7 - - - -
663A MET* 3.4 26.7 - - - -
665A HIS* 3.5 17.9 - + - -
682A THR* 4.2 13.0 - - + -
744A LEU* 4.8 4.5 - - + -
777A PHE* 3.6 38.4 - + + -
778A CYS 4.0 10.3 - - - -
779A MET* 3.6 26.5 - - + -
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Residues in contact with GLU 658 (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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630A GLY 3.4 7.2 - - - +
631A ARG* 3.8 31.3 + - + -
633A ILE* 3.8 10.7 - - + +
656A TYR* 3.3 37.0 + - + +
657A PHE* 1.3 80.5 - - - +
659A LYS* 1.3 69.6 + - - +
661A LYS* 4.1 20.9 + - + +
662A GLN 2.8 30.2 + - - +
663A MET* 3.3 11.0 - - - +
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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