Contacts of the strand formed by residues 775 - 785 (chain A) in PDB entry 4YOC
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 TYR 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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718A MET 4.2 11.3 + - - -
719A HIS* 3.3 51.6 + + + -
720A GLN 4.8 4.0 + - - -
722A LYS 5.4 1.2 + - - -
723A LYS* 3.2 41.4 - - + +
763A VAL 3.9 0.2 - - - +
764A SER* 3.3 0.2 - - - -
765A VAL 2.8 42.2 + - - +
767A PRO* 3.5 27.5 - - + +
773A PRO* 3.9 17.7 - - + +
774A LEU* 1.3 69.4 - - - +
776A LEU* 1.3 65.5 + - - +
796A TRP* 3.6 20.2 - + + -
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Residues in contact with LEU 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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719A HIS* 5.9 0.6 - - - -
763A VAL 3.4 4.0 - - - +
764A SER* 3.8 22.2 - - - -
774A LEU* 3.3 24.0 + - + +
775A TYR* 1.3 83.9 - - - +
777A ALA* 1.3 61.2 + - - +
796A TRP* 3.1 10.2 - - - +
797A PHE* 2.9 43.0 + - + +
814A LEU* 3.7 37.2 - - + -
832A VAL* 4.4 11.7 - - + -
863A TYR* 3.8 30.3 - - + +
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Residues in contact with ALA 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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762A CYS* 3.2 9.0 - - - +
763A VAL* 2.9 42.4 + - + +
765A VAL* 5.6 0.7 - - + -
776A LEU* 1.3 76.7 - - - +
778A ARG* 1.3 60.6 + - - +
794A ALA* 3.7 24.2 - - + -
795A HIS 3.4 9.9 - - - +
796A TRP* 3.5 21.1 - - + -
797A PHE* 3.7 7.6 - - - -
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Residues in contact with ARG 778 (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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760A GLY* 3.6 25.8 + - - +
761A ASP 3.6 9.0 - - - +
762A CYS* 3.8 11.1 - - - +
777A ALA* 1.3 74.2 - - - +
779A VAL* 1.3 73.2 - - - +
780A THR* 3.3 14.2 + - + +
793A HIS 3.3 1.7 - - - +
794A ALA* 3.6 1.5 - - - -
795A HIS* 2.9 46.9 + - + +
797A PHE* 3.1 39.5 - - + -
816A LEU* 5.3 2.0 - - - +
834A VAL 4.9 6.3 + - - -
865A TYR* 4.6 23.1 + - - -
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Residues in contact with VAL 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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757A LEU* 4.0 18.8 - - + -
758A GLU 4.2 7.9 - - - +
759A VAL* 3.7 7.9 - - - +
760A GLY* 2.9 26.2 + - - -
761A ASP 3.0 18.8 + - - +
763A VAL* 4.1 20.9 - - + -
778A ARG* 1.3 71.2 - - - +
780A THR* 1.3 61.6 + - - +
781A ALA 3.9 8.7 - - - +
782A LEU* 3.7 35.4 - - + -
792A PHE* 3.9 20.0 - - + -
793A HIS 3.7 4.0 - - - -
828A ILE* 5.0 0.2 - - + -
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Residues in contact with THR 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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759A VAL* 4.3 4.6 - - - +
778A ARG* 3.6 21.5 - - + +
779A VAL* 1.3 74.8 - - - +
781A ALA* 1.3 61.6 + - - +
793A HIS* 3.0 35.5 + - - +
795A HIS* 3.6 24.9 - - + +
890A PHE 2.9 20.3 - - - +
891A LYS 3.4 8.5 + - - -
892A PHE 3.4 19.6 - - - +
893A CYS* 3.8 16.0 - - + +
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Residues in contact with ALA 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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746A TYR* 4.5 5.2 - - + -
759A VAL* 4.1 4.7 - - - -
779A VAL* 3.5 2.1 - - - +
780A THR* 1.3 88.2 + - - +
782A LEU* 1.3 64.3 + - - +
783A TRP* 4.2 14.8 - - + -
792A PHE* 3.1 10.0 - - - +
793A HIS* 3.0 28.6 + - + -
890A PHE 4.2 2.2 - - - -
891A LYS* 3.6 29.2 - - + +
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Residues in contact with LEU 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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733A TRP* 4.0 11.7 - - + -
746A TYR* 3.3 7.0 - - - +
747A TYR 2.9 33.6 + - - +
748A LYS 3.7 24.0 - - - +
749A LYS* 3.8 9.6 - - - +
750A VAL* 3.8 13.9 - - + +
757A LEU* 3.8 22.2 - - + +
758A GLU 4.4 1.6 - - - -
759A VAL* 3.9 13.3 - - + +
779A VAL* 3.7 16.2 - - + -
781A ALA* 1.3 75.3 - - - +
783A TRP* 1.3 63.9 + - - +
791A MET 3.7 2.0 - - - +
792A PHE* 3.6 22.9 - - + -
825A LEU* 3.9 16.8 - - + -
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Residues in contact with TRP 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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733A TRP* 3.5 10.9 - - - -
744A LYS* 3.4 40.3 - - + +
745A SER 3.3 14.1 - - - +
746A TYR* 3.5 27.4 - + + +
747A TYR 4.5 0.7 - - - +
781A ALA* 4.1 7.9 - - + -
782A LEU* 1.3 81.0 - - - +
784A GLU* 1.3 58.4 + - - +
785A ASP* 3.6 20.5 + - + +
791A MET* 2.7 79.8 + - + +
792A PHE 3.5 24.7 - - - -
793A HIS* 3.5 11.4 - - + -
822A ASP* 3.4 36.3 - - + -
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Residues in contact with GLU 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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733A TRP* 3.0 33.0 + - + +
743A LYS 4.1 1.0 - - - +
744A LYS 3.7 1.0 - - - -
745A SER* 2.9 44.3 + - - +
747A TYR* 4.4 6.7 - - + -
783A TRP* 1.3 72.5 - - - +
785A ASP* 1.3 65.0 + - - +
786A SER* 4.0 10.2 + - - +
789A GLY* 3.6 20.0 - - - +
790A GLN* 3.3 20.1 + - - +
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Residues in contact with ASP 785 (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 LYS* 2.8 35.5 - - - +
744A LYS* 4.5 9.6 + - + +
783A TRP* 3.6 22.8 + - + +
784A GLU* 1.3 73.6 - - - +
786A SER* 1.3 55.0 + - - +
787A SER* 3.0 13.9 + - - -
788A ASN* 2.8 33.9 + - + +
789A GLY* 2.3 48.8 + - - +
791A MET* 4.7 0.6 - - + +
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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