Contacts of the strand formed by residues 885 - 895 (chain A) in PDB entry 2X5Y
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 885 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767A LEU 4.8 2.3 - - - +
771A PHE* 3.6 10.7 - - - +
801A ASN* 3.0 28.1 + - - +
802A PHE* 3.7 34.1 - - + -
818A ILE* 5.8 4.0 - - + -
820A PHE* 3.7 24.9 - - + -
843A ALA* 3.8 10.3 - - + -
844A GLN 3.3 4.7 - - - +
845A VAL* 4.5 3.8 - - + -
879A ILE* 3.8 23.3 - - + -
881A GLN 4.3 1.8 - - - +
882A LYS* 2.9 13.6 + - - +
883A ASP* 3.2 2.1 - - - -
884A GLN* 1.3 84.5 - - - +
886A TYR* 1.3 64.6 + - - +
887A PRO* 4.2 0.2 - - - +
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Residues in contact with TYR 886 (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 ILE* 3.4 9.6 + - + -
763A GLU* 3.4 3.8 - - - +
764A ASN* 3.0 45.9 + - + -
767A LEU* 3.8 13.9 - - + -
768A LEU* 3.5 47.1 - - + +
771A PHE* 3.7 23.1 - - + -
843A ALA* 3.4 0.2 - - - -
844A GLN* 2.8 43.8 + - + +
885A VAL* 1.3 76.9 - - - +
887A PRO* 1.3 84.6 - - + +
888A GLN* 3.2 32.9 + - - +
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Residues in contact with PRO 887 (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 ILE* 3.5 34.5 - - + +
767A LEU* 3.9 19.1 - - + -
797A ILE* 3.8 28.0 - - + +
798A CYS* 5.0 1.3 - - - -
801A ASN* 3.5 24.9 - - - +
802A PHE* 3.8 15.7 - - + -
841A PHE* 4.4 2.0 - - + -
842A VAL 4.3 1.1 - - - +
843A ALA* 4.2 9.6 - - + -
885A VAL* 4.2 0.8 - - + +
886A TYR* 1.3 97.4 - - + +
888A GLN* 1.3 59.0 + - - +
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Residues in contact with GLN 888 (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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761A LYS* 3.5 24.8 - - - +
762A ILE* 2.9 43.4 + - - +
784A LEU* 4.4 8.3 - - + -
842A VAL 2.9 16.7 + - - +
844A GLN* 2.8 36.5 + - + +
886A TYR* 3.2 22.1 + - - +
887A PRO* 1.3 74.3 - - - +
889A TYR* 1.3 87.8 + - + +
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Residues in contact with TYR 889 (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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733A ILE* 3.9 16.8 - - + -
739A GLU* 2.5 35.4 + - - +
742A ARG* 5.2 3.5 + - - -
743A VAL* 3.5 29.5 - - + +
759A ILE* 4.2 9.9 - - + -
760A LYS 3.2 15.0 - - - +
761A LYS* 3.9 17.4 - - + -
762A ILE* 4.0 1.8 - - - -
784A LEU* 4.3 18.2 - - + +
840A MET 4.6 0.2 - - - -
841A PHE* 3.3 10.0 - - - -
842A VAL* 2.9 55.5 + - + +
888A GLN* 1.3 98.6 - - + +
890A VAL* 1.3 65.3 + - - +
891A ILE* 4.9 0.4 - - + -
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Residues in contact with VAL 890 (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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730A LEU* 4.2 16.8 - - + -
758A LYS 3.9 0.9 - - - +
759A ILE* 3.5 3.3 - - - +
760A LYS* 2.9 39.4 + - + +
762A ILE* 3.8 9.2 - - + -
794A VAL* 4.5 11.7 - - + -
798A CYS* 4.5 2.9 - - - -
839A VAL* 4.0 33.2 - - + -
840A MET 3.6 4.0 - - - +
841A PHE* 3.6 32.8 - - + +
889A TYR* 1.3 74.5 - - - +
891A ILE* 1.3 66.8 + - - +
892A GLU* 4.2 6.2 + - + +
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Residues in contact with ILE 891 (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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743A VAL* 3.9 17.9 - - + -
747A PHE* 3.7 38.6 - - + -
756A ILE* 4.1 26.9 - - + -
758A LYS 3.5 3.4 - - - +
759A ILE* 4.3 13.5 - - + -
786A PHE* 4.6 0.4 - - + -
839A VAL* 3.6 5.9 - - - +
840A MET* 2.8 44.1 + - + +
842A VAL* 3.7 27.8 - - + -
889A TYR* 4.9 0.7 - - + -
890A VAL* 1.3 76.1 - - - +
892A GLU* 1.3 74.5 + - - +
893A TYR* 3.9 4.9 - - + -
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Residues in contact with GLU 892 (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 ILE* 3.6 4.0 - - - +
757A GLU* 2.7 36.1 + - + -
758A LYS* 2.9 38.7 + - + +
760A LYS* 6.4 1.3 - - + -
791A ARG* 2.9 47.4 + - - +
838A VAL 4.3 2.1 - - - +
839A VAL* 3.5 16.5 - - + +
890A VAL* 4.2 6.8 + - + +
891A ILE* 1.3 72.9 - - - +
893A TYR* 1.3 58.4 + - - +
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Residues in contact with TYR 893 (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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747A PHE* 3.6 28.3 - + + -
751A MET* 3.4 20.0 - - + -
754A PHE* 3.8 19.3 - + - -
755A LYS 3.2 16.4 - - - +
756A ILE* 4.3 1.3 - - - -
757A GLU* 4.1 2.8 - - - +
828A HIS* 2.7 33.8 + + - +
835A ALA 5.2 5.4 - - - +
838A VAL* 3.5 35.2 + - + +
839A VAL 4.4 0.7 - - - -
840A MET* 3.7 33.5 - - + +
891A ILE* 3.9 13.9 - - + -
892A GLU* 1.3 77.5 + - - +
894A THR* 1.3 70.8 + - - +
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Residues in contact with THR 894 (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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754A PHE* 3.2 11.4 - - - +
755A LYS* 2.8 53.8 + - - +
757A GLU* 2.7 33.3 + - + +
893A TYR* 1.3 82.1 - - - +
895A GLU* 1.3 61.5 + - - +
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Residues in contact with GLU 895 (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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753A ASN 3.7 7.9 - - - +
754A PHE* 3.9 17.6 - - + -
755A LYS* 3.0 23.4 + - - -
894A THR* 1.3 75.4 - - - +
896A ASP* 1.3 62.1 + - - +
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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