Contacts of the helix formed by residues 682 - 686 (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 PRO 682 (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* 3.6 21.8 - - + +
680A LEU 3.8 2.7 - - - +
681A PHE* 1.4 113.4 - - + +
683A PRO* 1.3 72.3 - - + +
684A TYR* 2.9 9.4 + - + +
685A LEU* 3.0 36.1 + - + +
716A GLN* 3.6 38.9 - - + +
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Residues in contact with PRO 683 (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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644A ILE* 4.0 16.4 - - + -
679A PHE* 4.0 26.7 - - + -
681A PHE* 3.3 9.6 - - + +
682A PRO* 1.3 83.3 - - + +
684A TYR* 1.3 58.2 + - + +
685A LEU 3.2 1.2 + - - -
686A SER* 3.2 11.1 + - - -
692A LYS* 2.6 30.2 + - + +
695A ALA* 3.6 23.8 - - + -
696A PHE* 3.7 32.8 - - + -
1873A IOD 4.4 9.4 - - + -
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Residues in contact with TYR 684 (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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640A GLU 4.1 0.7 - - - +
641A VAL* 3.6 6.0 - - + -
642A SER* 2.9 50.0 + - - +
643A SER* 4.5 2.0 - - - -
644A ILE* 3.7 40.2 - - + +
682A PRO* 2.9 11.6 + - + -
683A PRO* 1.3 78.1 - - + +
685A LEU* 1.3 63.8 + - + +
686A SER 3.5 0.6 - - - +
692A LYS* 4.2 0.4 - - - +
713A ALA* 4.3 19.6 - - + +
716A GLN* 4.2 4.7 - - + +
717A ARG* 3.7 58.1 + - + -
1864A SCN 5.0 3.1 + - - -
1873A IOD 4.4 20.2 - - + -
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Residues in contact with LEU 685 (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 ASP* 4.4 1.4 - - - +
635A ILE* 3.8 26.4 - - + +
639A ALA* 5.5 3.4 - - + -
640A GLU 4.1 10.8 - - - +
641A VAL* 3.8 26.2 - - + -
681A PHE* 3.7 17.3 - - + -
682A PRO* 3.0 29.2 + - + +
684A TYR* 1.3 84.8 - - + +
686A SER* 1.3 66.7 + - - +
687A SER* 3.6 1.7 + - - -
716A GLN 3.9 13.7 - - - +
717A ARG 5.2 0.2 - - - +
720A VAL* 3.4 33.9 - - + -
721A LYS* 4.8 6.3 - - + +
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Residues in contact with SER 686 (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 ASP* 3.3 12.6 - - - -
640A GLU* 4.7 7.1 - - - +
642A SER* 4.1 6.2 + - - -
681A PHE* 4.3 7.0 - - - -
682A PRO 3.9 1.8 + - - -
683A PRO 3.3 7.1 + - - -
684A TYR 3.5 0.8 - - - -
685A LEU* 1.3 81.1 - - - +
687A SER* 1.3 63.0 + - - +
688A SER* 3.6 5.9 + - - -
691A ALA 4.5 0.2 - - - -
692A LYS* 3.2 58.6 + - - +
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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