Contacts of the strand formed by residues 838 - 845 (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 838 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788A ALA* 4.4 5.2 - - + -
789A THR 3.3 6.5 - - - +
791A ARG* 4.1 6.2 + - - -
828A HIS* 5.3 2.2 - - + +
831A CYS* 3.8 20.4 - - + -
833A TYR* 3.5 26.5 - - + +
834A ASP 3.4 17.5 - - - +
835A ALA* 3.3 16.6 + - - +
837A ASN* 1.3 77.8 - - - +
839A VAL* 1.3 78.0 + - - +
892A GLU* 4.3 2.4 - - - +
893A TYR* 3.5 38.1 + - + +
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Residues in contact with VAL 839 (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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788A ALA* 3.4 3.5 - - - -
789A THR* 2.9 50.6 + - + +
791A ARG* 3.9 23.1 - - + +
794A VAL* 3.9 24.5 - - + -
837A ASN 3.6 0.2 + - - -
838A VAL* 1.3 84.1 - - - +
840A MET* 1.3 60.6 + - - +
841A PHE* 4.0 3.5 + - + -
890A VAL* 4.0 14.6 - - + -
891A ILE 3.6 9.2 - - - +
892A GLU* 3.5 31.6 - - - +
893A TYR* 4.4 1.6 - - - -
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Residues in contact with MET 840 (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* 4.0 17.5 - - + -
751A MET* 4.7 0.2 - - + -
786A PHE* 3.9 30.3 - - + -
787A TYR 3.9 4.0 - - - -
788A ALA* 3.7 25.4 - - + -
824A ALA* 3.5 28.0 - - + +
827A SER* 4.1 2.5 - - - -
828A HIS* 3.9 12.6 - - + +
839A VAL* 1.3 71.7 - - - +
841A PHE* 1.3 69.8 + - - +
890A VAL* 4.5 0.4 - - - -
891A ILE* 2.8 47.3 + - + +
893A TYR* 3.7 33.8 - - + +
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Residues in contact with PHE 841 (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* 3.6 16.8 - - + -
786A PHE* 3.4 4.7 - - - -
787A TYR* 2.8 39.0 + - + +
789A THR* 3.7 32.5 - - + -
794A VAL* 4.0 27.4 - - + -
797A ILE* 3.6 35.2 - - + -
798A CYS* 3.9 5.8 - - - -
802A PHE* 3.9 26.5 - + + -
839A VAL* 4.3 4.7 - - + -
840A MET* 1.3 80.7 - - - +
842A VAL* 1.3 61.7 + - - +
887A PRO* 4.4 3.4 - - + -
889A TYR 3.3 13.2 - - - -
890A VAL* 3.6 22.7 - - + +
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Residues in contact with VAL 842 (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* 4.5 5.8 - - + -
746A HIS* 5.0 3.4 - - - +
784A LEU* 3.8 35.0 - - + -
785A LEU 3.3 13.0 - - - +
786A PHE* 3.8 18.2 - - + -
841A PHE* 1.3 79.8 - - - +
843A ALA* 1.3 62.2 + - - +
887A PRO* 4.3 0.7 - - - +
888A GLN* 2.9 23.5 + - - -
889A TYR* 2.9 38.6 + - + +
891A ILE* 3.7 29.2 - - + -
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Residues in contact with ALA 843 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783A LYS 3.3 2.6 - - - +
784A LEU* 3.3 6.2 - - - -
785A LEU 2.9 31.2 + - - +
787A TYR* 5.9 0.4 - - + +
802A PHE* 3.9 11.2 - - + -
820A PHE* 3.9 20.0 - - + -
841A PHE* 4.2 0.4 - - + -
842A VAL* 1.3 74.5 - - - +
844A GLN* 1.3 60.1 + - - +
845A VAL* 3.6 4.5 + - + +
885A VAL* 3.8 22.9 - - + -
886A TYR 3.4 12.1 - - - +
887A PRO* 4.2 0.7 - - + -
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Residues in contact with GLN 844 (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* 5.3 4.8 - - - +
771A PHE* 3.4 32.5 - - + -
775A LYS* 4.9 5.0 + - - -
781A GLU* 4.9 1.2 - - - +
782A GLY* 4.1 13.5 + - - -
783A LYS 3.5 5.4 - - - +
784A LEU* 3.8 20.4 - - + +
843A ALA* 1.3 71.9 - - - +
845A VAL* 1.3 59.8 + - - +
885A VAL* 3.3 5.2 - - - +
886A TYR* 2.8 44.4 + - + +
888A GLN* 2.8 30.6 + - + +
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Residues in contact with VAL 845 (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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781A GLU 4.1 1.0 - - - +
782A GLY* 3.6 1.4 - - - -
783A LYS* 2.8 33.8 + - - +
785A LEU* 3.8 26.0 - - + -
820A PHE* 4.1 18.4 - - + -
843A ALA* 3.7 22.4 - - + +
844A GLN* 1.3 79.7 - - - +
846A LEU* 1.3 67.6 + - - +
847A VAL* 3.6 14.3 + - + +
879A ILE* 3.6 36.8 - - + -
884A GLN 3.4 5.8 - - - +
885A VAL* 4.5 2.7 - - + -
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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