Contacts of the strand formed by residues 783 - 792 (chain A) in PDB entry 4QUM
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 783 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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779A CYS* 3.3 3.9 - - - +
780A THR* 2.9 60.9 + - + +
781A ILE 3.8 0.4 - - - -
782A ALA* 1.3 86.4 - - + +
784A VAL* 1.3 75.0 + - - +
785A SER* 4.2 10.3 - - - -
804A LEU* 4.6 1.8 - - + -
805A GLN 3.1 14.1 - - - +
806A TYR* 3.7 9.9 - + + -
807A VAL* 4.3 2.0 - - - +
820A ASP 5.6 1.3 - - - -
823A GLU* 5.8 6.1 - - + -
824A PHE* 3.5 40.8 - + + -
827A TYR* 3.3 41.3 - + - +
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Residues in contact with VAL 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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777A GLU* 5.1 4.5 - - + -
778A ASP 3.4 20.0 - - - +
779A CYS* 4.0 11.9 - - + -
780A THR 5.7 0.2 - - - +
783A TYR* 1.3 79.0 - - - +
785A SER* 1.3 59.3 + - - +
786A ARG* 3.7 43.3 + - + +
803A HIS 3.6 1.9 - - - +
804A LEU* 3.5 3.1 - - - -
805A GLN* 2.8 52.2 + - + +
807A VAL* 4.6 13.5 - - + -
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Residues in contact with SER 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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776A SER* 4.1 1.0 + - - +
777A GLU* 3.8 1.7 - - - -
778A ASP* 2.8 43.4 + - - +
783A TYR* 4.1 13.0 - - - -
784A VAL* 1.3 73.0 - - - +
786A ARG* 1.3 60.9 + - - +
787A GLU* 4.7 5.2 + - - +
802A THR* 4.7 5.2 - - - +
803A HIS 3.5 4.3 - - - -
804A LEU* 3.6 16.6 - - - +
827A TYR* 3.5 19.6 + - - -
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Residues in contact with ARG 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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758A TRP* 3.3 32.4 - - - +
760A ASP* 5.1 4.0 + - - -
774A CYS* 4.0 4.3 - - - -
776A SER 3.3 4.9 - - - +
777A GLU* 3.0 43.5 + - + -
784A VAL* 3.7 28.3 + - + +
785A SER* 1.3 76.7 + - - +
787A GLU* 1.3 65.5 + - - +
788A MET* 3.5 33.2 - - + -
802A THR* 3.6 3.1 - - - +
803A HIS* 2.8 47.7 + - - +
805A GLN* 3.2 32.9 + - - +
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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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774A CYS* 3.7 1.9 - - - -
775A GLN* 2.9 38.5 + - + +
776A SER* 3.2 29.7 + - - +
785A SER* 4.7 4.9 + - - +
786A ARG* 1.3 75.7 - - - +
788A MET* 1.3 63.8 + - - +
800A THR* 4.1 10.3 + - - +
801A VAL 3.7 7.8 - - - +
802A THR* 2.9 38.3 + - - +
827A TYR* 5.6 0.7 + - - -
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Residues in contact with MET 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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729A TRP* 4.2 20.6 - - + -
740A ILE* 5.8 0.2 - - - -
757A TYR* 5.6 0.2 - - - -
758A TRP* 3.5 42.0 - - + -
772A ILE* 4.8 6.3 - - + -
773A GLN 3.5 10.8 - - - +
774A CYS* 4.2 8.1 - - + -
775A GLN* 4.7 3.1 - - - -
786A ARG* 3.5 26.7 - - + -
787A GLU* 1.3 79.7 - - - +
789A LEU* 1.3 62.2 - - - +
790A VAL* 4.1 1.3 - - + -
799A HIS 3.8 0.2 - - - +
800A THR* 3.3 8.4 + - - -
801A VAL* 2.8 49.4 + - + +
803A HIS* 3.7 32.3 - - + -
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Residues in contact with LEU 789 (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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771A HIS 3.3 4.9 - - - +
772A ILE* 3.5 2.6 - - - +
773A GLN* 2.9 65.7 + - + +
775A GLN* 3.4 32.0 - - - +
788A MET* 1.3 73.4 - - - +
790A VAL* 1.3 62.3 + - - +
791A THR* 3.9 9.0 - - - +
798A GLU* 3.8 41.1 - - + +
799A HIS 3.7 15.7 - - - +
800A THR* 4.6 7.2 - - - +
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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
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729A TRP* 3.5 35.9 - - + -
732A VAL* 5.4 0.7 - - + -
733A TRP* 3.8 25.5 - - + -
770A PHE* 4.1 17.3 - - + -
771A HIS 3.4 2.5 - - - -
772A ILE* 3.8 18.8 - - + -
788A MET* 5.0 1.3 - - + +
789A LEU* 1.3 79.1 - - - +
791A THR* 1.3 61.1 + - - +
798A GLU* 3.5 2.9 - - - +
799A HIS* 2.7 49.4 + - + +
801A VAL* 4.3 14.1 - - + -
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Residues in contact with THR 791 (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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770A PHE* 3.5 5.1 - - - -
771A HIS* 2.7 55.0 + - + +
773A GLN* 4.3 6.6 + - - -
789A LEU* 3.9 20.8 - - - +
790A VAL* 1.3 77.0 + - - +
792A ASN* 1.3 74.4 + - - +
793A THR* 3.3 3.7 + - + -
796A GLY* 4.2 13.7 - - - +
797A GLU 3.5 9.0 - - - +
798A GLU* 4.1 10.2 + - + +
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Residues in contact with ASN 792 (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* 3.6 38.8 - - + +
769A GLY 3.9 10.5 - - - +
770A PHE* 4.3 9.7 - - + -
791A THR* 1.3 70.5 - - - +
793A THR* 1.3 63.5 + - - +
794A GLN* 3.0 18.0 + - - +
795A THR* 3.0 35.0 + - - +
796A GLY* 2.8 30.7 + - - -
797A GLU* 3.0 9.3 + - - +
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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