Contacts of the strand formed by residues 764 - 771 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760E THR* 3.6 27.1 + - + +
761E PRO* 3.4 33.7 + - + +
762E PRO 4.8 0.9 - - - +
763E GLY* 1.3 78.9 + - - +
765E VAL* 1.3 66.7 + - - +
779E PHE* 3.5 32.5 - - + -
780E VAL 3.3 6.1 - - - +
781E GLU* 3.3 32.8 - - + +
782E THR 5.5 0.7 - - - +
866E SER* 4.2 0.4 + - - -
873E VAL* 4.2 8.8 + - - +
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Residues in contact with VAL 765 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760E THR* 5.3 0.4 - - - -
764E VAL* 1.3 80.3 - - - +
766E MET* 1.3 73.3 + - - +
779E PHE* 3.5 5.0 - - - -
780E VAL* 2.7 40.0 + - - +
859E THR* 3.8 15.9 - - + +
862E THR* 3.8 9.6 - - + -
863E ALA* 3.5 36.3 - - + +
873E VAL* 3.8 24.5 - - + -
877E LEU* 4.9 4.5 - - + +
879E MET* 4.1 25.1 - - + -
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Residues in contact with MET 766 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760E THR* 5.3 2.6 - - - +
765E VAL* 1.3 81.7 - - - +
767E GLY* 1.3 62.2 + - - +
777E THR* 3.1 42.8 - - + -
778E LEU 3.7 4.0 - - - +
779E PHE* 4.5 25.4 - - + +
859E THR* 3.9 3.2 - - - +
876E ASN* 5.4 1.8 - - - -
877E LEU 3.7 25.6 + - - +
878E ALA* 3.5 14.7 - - + -
879E MET 3.4 21.1 + - - -
905E ALA* 4.4 6.5 - - + +
907E VAL* 3.7 26.9 - - + -
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Residues in contact with GLY 767 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E VAL 3.7 1.2 + - - -
766E MET* 1.3 75.4 - - - +
768E LEU* 1.3 66.8 + - - -
777E THR* 3.5 3.5 - - - -
778E LEU* 2.7 46.5 + - - +
780E VAL* 4.9 2.0 - - - -
856E ALA* 6.6 0.2 - - - -
859E THR* 3.7 17.0 - - - +
879E MET 3.6 6.7 - - - -
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Residues in contact with LEU 768 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766E MET* 4.9 0.2 - - - -
767E GLY* 1.3 75.7 - - - +
769E ALA* 1.3 61.3 + - - +
776E SER 3.5 1.1 - - - +
777E THR* 3.3 24.7 - - - +
852E ASP* 4.7 0.3 - - - +
855E SER* 4.5 3.5 + - - -
856E ALA* 5.9 2.6 - - - +
878E ALA* 3.6 38.8 - - + +
879E MET* 3.1 23.8 + - - +
880E THR* 3.8 16.7 + - - +
898E LYS* 3.6 39.8 + - + +
899E THR* 6.0 0.4 - - - -
901E ALA* 4.2 2.5 - - + -
902E ALA* 3.8 26.7 - - + +
910E ILE* 4.6 10.8 - - + -
912E LEU* 5.1 4.9 - - + -
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Residues in contact with ALA 769 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767E GLY 3.9 0.2 + - - -
768E LEU* 1.3 75.4 - - - +
770E TRP* 1.3 57.5 + - - +
771E THR* 4.4 3.6 - - + -
775E GLY* 3.5 3.5 - - - -
776E SER* 2.6 44.6 + - - +
778E LEU* 3.5 32.8 - - + -
848E ALA* 4.3 15.9 - - + -
852E ASP* 3.9 3.8 - - - -
898E LYS* 4.1 8.5 - - - +
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Residues in contact with TRP 770 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769E ALA* 1.3 70.1 - - - +
771E THR* 1.3 64.6 + - - +
772E ALA* 5.9 1.0 - - - +
774E GLY 3.6 14.4 - - - -
775E GLY* 4.7 0.7 - - - -
848E ALA* 3.5 4.2 - - - -
849E THR* 3.4 30.5 + - + -
851E LYS* 3.1 45.1 - - + -
852E ASP* 3.0 34.3 + - + +
893E GLY* 3.7 20.6 - - - -
894E GLY* 3.6 28.3 - - - -
897E GLU* 3.9 23.7 + - + +
898E LYS* 3.8 12.9 - - + +
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Residues in contact with THR 771 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769E ALA* 3.9 4.9 - - + +
770E TRP* 1.3 85.9 + - - +
772E ALA* 1.3 66.3 + - - +
773E MET* 3.8 5.7 + - - +
774E GLY* 2.6 38.9 + - - +
775E GLY 3.8 1.0 + - - -
776E SER* 3.4 38.1 - - - +
778E LEU* 5.6 0.2 - - + -
847E GLY* 3.8 26.7 - - - +
849E THR* 4.2 2.0 - - - -
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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