Contacts of the strand formed by residues 764 - 770 (chain D) in PDB entry 2X36
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 VAL 764 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760D THR* 4.4 13.7 - - + +
761D PRO* 3.5 49.4 + - + +
762D PRO 3.5 5.3 - - - +
763D GLY* 1.3 83.1 - - - +
765D VAL* 1.3 71.6 + - - +
779D PHE* 3.9 27.8 - - + -
780D VAL 3.3 6.1 - - - +
781D GLU* 4.1 23.8 - - + +
782D THR 5.5 0.9 - - - +
866D SER* 4.3 1.6 + - - -
873D VAL* 3.9 8.7 + - - +
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Residues in contact with VAL 765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760D THR* 6.0 0.9 - - - -
764D VAL* 1.3 76.1 - - - +
766D MET* 1.3 66.7 + - - +
767D GLY 3.6 0.7 + - - -
779D PHE* 3.4 7.5 - - - -
780D VAL* 2.9 32.6 + - - +
859D THR* 3.2 34.7 - - + +
862D THR* 3.7 13.9 - - + -
863D ALA* 3.9 12.6 - - - +
866D SER* 5.0 0.7 - - - -
873D VAL* 3.0 38.4 - - + -
877D LEU* 5.5 2.2 - - + +
879D MET* 3.9 22.9 - - + -
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Residues in contact with MET 766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D VAL* 1.3 79.0 - - - +
767D GLY* 1.3 63.0 + - - +
768D LEU* 4.6 0.7 - - + -
777D THR* 3.5 32.1 - - + +
778D LEU 3.5 8.1 - - - +
779D PHE* 4.2 24.2 - - + -
859D THR* 3.7 6.6 - - - +
876D ASN* 5.8 0.4 - - - -
877D LEU 3.5 15.8 + - - +
878D ALA* 2.7 46.8 - - + -
879D MET 2.9 23.6 + - - -
905D ALA* 5.7 0.7 - - - -
907D VAL* 3.2 38.1 - - + -
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Residues in contact with GLY 767 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D VAL 3.6 3.2 + - - -
766D MET* 1.3 75.8 - - - +
768D LEU* 1.3 64.1 + - - +
777D THR* 3.7 1.9 - - - -
778D LEU* 2.6 54.9 + - - +
780D VAL* 4.9 2.0 - - - +
859D THR* 3.7 12.5 - - - +
879D MET 3.4 10.1 - - - -
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Residues in contact with LEU 768 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766D MET* 4.6 0.9 - - + -
767D GLY* 1.3 77.3 - - - +
769D ALA* 1.3 60.3 + - - +
776D SER 3.6 3.4 - - - +
777D THR* 3.6 23.3 - - - +
778D LEU* 4.9 1.3 - - - +
852D ASP* 4.4 0.3 - - - +
855D SER* 4.4 4.9 + - - -
856D ALA* 6.1 0.5 - - - -
878D ALA* 3.4 35.0 - - + -
879D MET* 3.4 18.6 + - - +
880D THR* 4.0 15.6 + - - +
898D LYS* 3.5 47.2 - - + +
899D THR* 5.3 0.7 - - - -
901D ALA* 5.5 0.2 - - + -
902D ALA* 4.1 15.7 - - + +
910D ILE* 4.1 13.9 - - + -
912D LEU* 5.0 9.6 - - + -
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Residues in contact with ALA 769 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768D LEU* 1.3 75.2 - - - +
770D TRP* 1.3 62.5 + - - +
771D THR* 3.9 1.1 - - + -
775D GLY* 3.4 4.9 - - - -
776D SER* 2.7 40.5 + - - +
778D LEU* 3.5 34.5 - - + -
848D ALA* 4.1 21.5 - - + +
852D ASP* 3.6 4.0 - - - -
898D LYS* 4.1 10.1 - - - +
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Residues in contact with TRP 770 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769D ALA* 1.3 73.4 - - - +
771D THR* 1.3 73.4 + - - +
774D GLY* 3.9 1.8 - - - -
775D GLY* 4.8 0.4 - - - -
848D ALA* 3.2 2.8 - - - -
849D THR* 2.9 38.3 + - + +
851D LYS* 5.8 7.4 - - + -
852D ASP* 3.0 35.8 + - + +
893D GLY* 3.5 25.4 - - - -
894D GLY* 3.4 27.4 - - - -
897D GLU* 3.8 30.9 - - + +
898D LYS* 3.9 8.5 - - + -
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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