Contacts of the strand formed by residues 788 - 796 (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 LEU 788 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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598A TYR* 3.7 40.4 - - + +
772A THR* 4.1 5.4 - - + -
773A SER 3.6 9.0 - - - +
775A LEU* 3.9 9.7 - - - +
784A CYS* 4.0 18.4 - - + +
786A GLY 3.9 13.7 - - - +
787A PRO* 1.3 78.2 - - - +
789A SER* 1.3 62.9 + - - +
838A TYR* 4.0 12.1 - - + -
841A THR* 4.5 11.0 - - + -
843A ARG* 4.9 4.7 - - + -
848A ILE* 4.6 4.7 - - + -
851A LEU* 3.8 40.0 - - + +
1872A IOD 3.6 9.2 - - + +
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Residues in contact with SER 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ARG* 3.0 13.7 + - - -
772A THR* 3.4 4.0 - - - +
773A SER* 2.8 42.3 + - - -
774A CYS 4.1 2.5 - - - -
775A LEU* 3.8 31.2 - - - +
788A LEU* 1.3 76.6 - - - +
790A VAL* 1.3 63.0 + - - +
851A LEU* 4.6 0.9 - - - -
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Residues in contact with VAL 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ARG* 4.3 2.5 - - - -
770A ILE* 3.5 22.0 - - + -
771A ILE 3.4 8.5 - - - +
772A THR* 3.8 1.8 - - + +
789A SER* 1.3 77.8 + - - +
791A SER* 1.3 64.0 + - - +
792A SER* 3.8 9.2 - - - +
826A VAL* 3.9 7.6 - - + -
838A TYR* 3.2 24.9 - - - +
851A LEU* 3.4 40.8 - - + +
854A TYR* 3.2 41.6 - - + +
856A HIS* 4.4 1.8 + - - -
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Residues in contact with SER 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A TYR* 6.0 0.7 - - - -
727A ARG* 3.0 22.8 + - - +
771A ILE* 2.8 39.2 + - - +
790A VAL* 1.3 75.2 - - - +
792A SER* 1.3 63.3 + - - +
793A PHE* 5.7 0.4 - - - -
854A TYR* 5.2 0.7 - - - -
856A HIS* 3.8 31.6 - - - +
858A TYR* 4.0 14.1 + - - -
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Residues in contact with SER 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A SER 3.2 11.4 - - - -
770A ILE* 3.6 8.3 - - - +
790A VAL* 3.8 1.9 - - - +
791A SER* 1.3 80.7 + - - +
793A PHE* 1.3 69.5 + - - +
823A THR* 3.4 10.2 + - - -
824A ALA 3.1 36.0 + - - -
825A ARG 4.6 2.2 - - - -
826A VAL* 3.6 23.4 - - - +
829A ILE* 3.8 17.0 - - - -
856A HIS* 5.3 0.2 - - - +
858A TYR* 5.3 1.7 + - - -
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Residues in contact with PHE 793 (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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712A TRP* 4.5 4.5 - + - -
715A PHE* 3.4 38.8 - + - -
723A TYR* 5.3 0.4 - + - -
767A TYR 4.4 0.7 - - - -
768A TYR* 3.1 28.5 - - - +
769A SER* 2.9 33.1 + - - +
771A ILE* 4.0 11.9 - - + -
791A SER 5.7 0.7 - - - -
792A SER* 1.3 80.9 - - - +
794A ILE* 1.3 65.0 + - - +
795A LEU* 3.3 39.9 - - + -
819A MET* 3.2 36.8 - - + +
822A HIS 3.4 18.4 - - - +
823A THR* 4.2 0.2 - - - -
824A ALA* 4.1 3.1 - - - -
829A ILE* 3.9 1.3 - - - +
858A TYR* 6.0 2.0 - - - -
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Residues in contact with ILE 794 (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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430A LYS* 3.9 23.4 + - + +
737A ILE* 3.9 13.5 - - + -
766A HIS* 3.7 35.2 - - + -
767A TYR 3.6 3.1 - - - +
768A TYR* 4.4 0.2 - - - +
793A PHE* 1.3 79.3 - - - +
795A LEU* 1.3 60.9 + - - +
796A PRO* 3.7 2.3 - - - +
822A HIS* 3.0 31.1 + - - +
824A ALA* 3.5 19.3 - - + -
828A ASP* 3.9 12.1 - - + -
829A ILE* 3.6 26.0 - - + -
832A LEU* 3.9 21.1 - - + -
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Residues in contact with LEU 795 (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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708A PHE* 3.9 21.7 - - + -
711A VAL* 4.1 22.4 - - + -
712A TRP* 4.4 10.1 - - + -
715A PHE* 5.6 1.6 - - + -
766A HIS* 3.0 6.4 - - - -
767A TYR* 2.7 41.3 + - - +
793A PHE* 3.3 35.2 - - + -
794A ILE* 1.3 73.4 - - - +
796A PRO* 1.3 70.0 - - + +
797A HIS* 4.5 0.2 - - - -
818A LEU* 4.7 7.9 - - + +
819A MET* 3.7 40.4 - - + +
822A HIS* 4.2 11.2 - - + -
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Residues in contact with PRO 796 (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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427A HIS* 5.0 13.0 - - + +
708A PHE* 3.4 17.2 - - - -
765A THR 3.8 0.7 - - - +
766A HIS* 3.5 20.4 - - + +
794A ILE 3.7 1.1 - - - +
795A LEU* 1.3 86.0 - - + +
797A HIS* 1.3 61.3 + - - +
798A ARG* 3.3 25.6 + - + +
803A GLU* 3.9 12.1 - - - +
818A LEU* 5.3 5.8 - - + +
822A HIS* 3.7 41.7 - - + +
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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