Contacts of the strand formed by residues 775 - 784 (chain A) 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 GLY 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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769A ALA 3.4 11.7 - - - -
771A THR* 4.1 1.8 + - - -
774A GLY* 1.3 75.9 - - - -
776A SER* 1.4 64.5 + - - -
897A GLU* 3.6 24.2 + - - +
900A ILE* 6.3 0.6 - - - +
901A ALA* 3.7 2.7 - - - -
904A ARG* 2.6 30.7 + - - +
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Residues in contact with SER 776 (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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768A LEU* 3.7 1.0 - - - -
769A ALA* 2.9 33.8 + - - +
771A THR* 3.5 21.4 + - - +
775A GLY* 1.4 77.7 + - - -
777A THR* 1.3 63.6 + - - +
778A LEU* 3.4 22.2 + - - -
901A ALA* 3.4 11.0 - - - +
904A ARG* 4.3 4.0 + - - +
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Residues in contact with THR 777 (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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766A MET* 3.4 22.0 - - + +
767A GLY 3.4 4.5 - - - -
768A LEU* 3.3 20.2 - - + -
776A SER* 1.3 73.3 - - - +
778A LEU* 1.3 65.3 + - - +
779A PHE* 4.7 11.4 - - - -
901A ALA* 3.2 36.1 - - - +
902A ALA* 3.5 1.1 - - - +
905A ALA* 3.3 21.6 - - + +
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Residues in contact with LEU 778 (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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765A VAL 3.6 0.3 - - - +
766A MET* 3.4 3.5 - - - -
767A GLY* 2.7 45.0 + - - +
769A ALA* 3.9 20.0 - - + -
776A SER* 3.4 28.0 - - - +
777A THR* 1.3 81.3 - - - +
779A PHE* 1.3 64.9 + - - +
780A VAL* 3.9 2.1 + - + +
845A PRO* 3.6 28.5 - - + +
846A GLU 3.2 29.2 - - - +
847A GLY* 3.9 6.7 - - - +
848A ALA* 4.4 2.2 - - + +
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Residues in contact with PHE 779 (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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756A MET* 4.0 40.4 - - + +
757A TYR* 3.7 59.7 - + + -
760A THR* 3.9 8.7 - - + -
764A VAL* 4.0 16.2 - - + -
765A VAL 3.5 4.7 - - - -
766A MET* 3.6 37.7 - - + -
777A THR* 4.7 13.0 - - - -
778A LEU* 1.3 79.0 - - - +
780A VAL* 1.3 63.0 + - - +
781A GLU* 3.5 11.3 + - + +
843A HIS* 4.4 1.2 + - - +
845A PRO* 3.7 20.2 - - - +
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Residues in contact with VAL 780 (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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763A GLY 3.6 0.7 - - - +
764A VAL* 3.1 8.1 - - - +
765A VAL 2.7 36.3 + - - +
767A GLY* 5.6 1.8 - - - +
778A LEU* 3.9 2.4 + - + +
779A PHE* 1.3 72.3 - - - +
781A GLU* 1.3 62.9 + - - +
842A LEU* 3.7 23.6 - - + -
843A HIS 3.8 4.5 - - - +
844A VAL* 4.8 6.3 - - + -
845A PRO* 4.4 13.9 - - + -
856A ALA* 5.4 4.5 - - + -
859A THR* 3.6 24.0 - - + -
860A ILE* 4.2 17.0 - - + -
863A ALA* 3.7 24.7 - - + -
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Residues in contact with GLU 781 (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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756A MET* 3.9 17.6 - - - +
763A GLY 3.5 2.0 - - - -
764A VAL* 4.0 15.3 - - + +
779A PHE* 3.9 9.5 - - + +
780A VAL* 1.3 81.0 - - - +
782A THR* 1.3 67.8 + - - +
842A LEU* 3.5 1.2 - - - +
843A HIS* 2.8 51.7 + - + +
845A PRO* 6.0 0.3 - - - +
884B SER* 2.9 28.4 + - - -
885B LEU* 3.5 19.2 + - + +
886B THR* 2.5 37.7 + - + +
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Residues in contact with THR 782 (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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762A PRO 4.7 1.0 - - - +
763A GLY* 2.8 41.0 + - - +
764A VAL* 4.8 0.2 - - - +
781A GLU* 1.3 79.8 - - - +
783A SER* 1.3 65.2 + - - +
840A ILE* 4.3 3.1 - - - -
841A HIS 3.2 10.1 - - - +
842A LEU* 4.0 15.0 - - + -
863A ALA* 3.2 35.0 + - + -
864A LEU* 4.0 13.5 - - + -
867A LEU* 3.3 18.8 - - - +
885B LEU* 4.0 2.7 - - - -
886B THR* 4.0 12.6 - - - +
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Residues in contact with SER 783 (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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782A THR* 1.3 76.9 - - - +
784A LEU* 1.4 74.4 + - - +
840A ILE* 3.3 3.1 - - - -
841A HIS* 2.8 33.8 + - - +
867A LEU* 3.8 17.4 - - - +
819B THR* 3.9 11.8 + - - +
823B ALA* 4.3 9.3 - - - +
885B LEU* 3.9 21.3 + - - +
886B THR* 5.0 4.3 - - - -
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Residues in contact with LEU 784 (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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783A SER* 1.4 89.3 + - - +
785A ARG* 1.3 61.0 + - - +
786A ARG 3.7 15.5 - - - +
787A PRO* 5.9 2.7 - - + -
788A GLN 5.7 5.2 - - - +
834A TYR* 3.4 33.4 - - + +
838A SER* 3.9 27.8 - - - +
839A HIS 3.5 9.9 - - - +
840A ILE* 4.5 2.9 - - + -
867A LEU* 4.4 3.3 - - + +
819B THR* 3.7 5.4 - - - +
823B ALA* 3.8 16.9 - - + +
826B MET* 4.7 8.3 - - - -
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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