Contacts of the strand formed by residues 778 - 788 (chain A) in PDB entry 3PT6
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 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A LYS 5.2 0.4 - - - -
721A LEU* 4.0 26.5 - - + -
723A GLN* 2.5 37.2 + - - +
724A GLY 4.3 5.5 + - - -
725A LYS 4.5 1.3 + - - -
726A LYS* 4.0 22.0 - - + -
767A SER* 3.2 5.9 - - - -
768A VAL* 2.9 46.5 + - + +
770A PRO* 3.8 38.3 - - + +
775A LYS* 4.1 4.5 - - + +
776A PRO 3.3 4.6 + - - -
777A LEU* 1.3 76.5 - - - +
779A LEU* 1.3 62.7 + - - +
799A TRP* 3.4 31.9 - + + -
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Residues in contact with LEU 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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721A LEU* 5.0 1.8 - - - +
765A CYS* 6.3 0.9 - - + -
766A VAL 3.5 5.6 - - - +
767A SER* 4.6 6.7 - - - -
777A LEU* 3.0 31.6 - - + +
778A TYR* 1.3 78.6 - - - +
780A ALA* 1.3 62.1 + - - +
799A TRP* 3.8 4.8 - - - -
800A PHE* 2.8 42.0 + - + +
817A LEU* 4.3 20.0 - - + -
835A VAL* 3.5 30.3 - - + -
837A VAL* 5.2 0.4 - - + -
867A TYR* 3.6 39.9 - - + +
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Residues in contact with ALA 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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765A CYS* 3.1 7.2 - - - +
766A VAL* 2.9 35.4 + - + +
768A VAL* 6.0 2.7 - - + +
779A LEU* 1.3 77.7 - - - +
781A ARG* 1.3 62.1 + - - +
795A PHE* 5.8 1.1 - - + -
797A ALA* 3.8 17.5 - - + -
798A HIS 3.1 21.3 - - - +
799A TRP* 3.7 18.2 - - + -
800A PHE* 3.8 9.8 - - - -
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Residues in contact with ARG 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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763A GLY* 3.7 20.4 + - - +
764A ASP 3.5 10.3 - - - +
765A CYS* 3.9 16.1 - - - -
780A ALA* 1.3 74.5 - - - +
782A VAL* 1.3 73.2 + - - +
783A THR* 3.3 10.6 + - + +
795A PHE* 5.6 0.2 - - - -
796A HIS 3.6 1.0 - - - +
797A ALA* 3.7 1.9 - - - -
798A HIS* 2.8 46.2 + - + +
800A PHE* 4.2 10.4 - - + -
819A LEU* 5.2 9.4 - - + +
837A VAL* 5.2 5.9 + - - +
839A TYR* 5.5 2.0 - - - +
869A PHE* 4.1 30.8 - - - -
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Residues in contact with VAL 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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760A LEU* 5.8 6.1 - - + -
761A GLU 4.0 11.4 - - - +
762A VAL* 3.6 9.9 - - - -
763A GLY* 2.8 30.1 + - - -
764A ASP* 2.9 23.0 + - + +
766A VAL* 4.6 17.9 - - + -
780A ALA 5.3 0.4 - - - +
781A ARG* 1.3 72.0 - - - +
783A THR* 1.3 60.3 + - - +
784A ALA 3.6 20.9 - - - +
785A LEU* 3.9 17.7 - - + -
795A PHE* 4.0 21.1 - - + -
796A HIS 3.6 4.7 - - - -
831A ILE* 5.2 5.8 - - + -
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Residues in contact with THR 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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762A VAL* 4.6 8.1 - - - +
781A ARG* 3.4 23.1 - - + +
782A VAL* 1.3 74.2 - - - +
784A ALA* 1.3 66.1 + - - +
796A HIS* 3.0 34.3 + - + +
798A HIS* 3.6 23.3 - - + +
894A HIS 4.1 1.9 - - - +
895A LYS* 3.4 19.4 + - - -
896A PHE 3.4 21.9 + - - +
897A CYS* 3.6 14.4 - - + +
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Residues in contact with ALA 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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749A TYR* 4.3 14.1 - - + -
762A VAL* 4.2 8.1 - - - -
782A VAL* 3.6 3.8 - - - +
783A THR* 1.3 88.7 + - - +
785A LEU* 1.3 64.5 - - - +
786A TRP* 4.1 9.2 - - + -
795A PHE* 3.3 23.2 - - - +
796A HIS* 3.3 8.8 + - + -
894A HIS 4.0 5.4 - - - +
895A LYS* 3.8 24.9 - - + -
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Residues in contact with LEU 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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736A TRP* 3.6 11.9 - - + -
749A TYR* 3.0 9.9 - - - +
750A TYR 2.9 32.3 + - - +
751A GLN 3.4 31.6 - - - +
752A LYS 3.9 6.3 - - - +
753A VAL* 3.8 27.6 - - + +
760A LEU* 4.7 2.7 - - + +
761A GLU* 4.7 1.6 - - - -
762A VAL* 4.2 11.4 - - + +
782A VAL* 3.9 10.5 - - + -
784A ALA* 1.3 82.8 - - - +
786A TRP* 1.3 67.2 + - - +
794A MET 3.8 2.9 - - - +
795A PHE* 3.6 17.7 - - + -
828A LEU* 3.9 15.7 - - + -
894A HIS 5.2 0.4 + - - -
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Residues in contact with TRP 786 (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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736A TRP* 3.4 11.4 - - - -
747A ARG* 3.6 43.4 - - + +
748A THR 3.0 20.4 - - - +
749A TYR* 3.2 28.3 - + + +
750A TYR 4.3 0.4 - - - +
784A ALA* 4.0 5.2 - - + -
785A LEU* 1.3 84.7 - - - +
787A GLU* 1.3 61.8 + - - +
788A ASP* 3.9 14.4 + - - -
794A MET* 2.7 64.7 + - + +
795A PHE* 3.3 35.9 - - - -
796A HIS* 3.4 10.3 - - + -
825A ASN* 3.6 28.3 - - + -
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Residues in contact with GLU 787 (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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736A TRP* 3.1 35.5 + - + +
747A ARG* 3.7 0.9 - - - +
748A THR* 3.0 45.6 + - + +
750A TYR* 4.4 2.5 + - + -
786A TRP* 1.3 77.3 - - - +
788A ASP* 1.3 65.0 + - - +
791A GLY* 3.3 29.3 - - - +
792A GLN 3.3 17.0 - - - +
793A MET* 4.0 8.4 - - + +
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Residues in contact with ASP 788 (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 ASN* 3.0 15.6 - - - +
747A ARG* 4.2 18.8 + - - +
748A THR* 5.8 0.2 - - - +
786A TRP* 3.9 20.0 + - - +
787A GLU* 1.3 79.1 - - - +
789A LYS* 1.3 86.9 + - - +
790A ASN* 3.0 24.7 + - - +
791A GLY* 3.0 13.6 + - - -
792A GLN* 2.8 15.0 + - + +
794A MET* 5.0 6.6 - - + +
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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