Contacts of the strand formed by residues 734 - 743 (chain A) in PDB entry 2VJ0
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 LEU 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730A PHE* 3.3 8.7 - - - +
731A ARG* 2.9 43.6 + - - +
732A GLN* 3.3 1.7 - - + -
733A ASN* 1.3 101.2 - - - +
735A GLY* 1.3 59.5 + - - +
789A ILE 3.3 11.9 - - - +
790A GLU* 3.9 22.4 - - + +
825A PHE* 3.8 6.5 - - - -
1940A DTD 3.8 20.0 - - + -
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Residues in contact with GLY 735 (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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729A GLU 3.2 11.2 - - - -
730A PHE* 3.6 13.4 - - - -
734A LEU* 1.3 75.7 - - - +
736A ARG* 1.3 61.4 + - - +
788A ASN* 3.7 3.5 - - - +
789A ILE* 2.9 40.5 + - - +
1940A DTD 3.7 11.2 - - - -
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Residues in contact with ARG 736 (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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727A LYS 4.1 0.3 - - - +
728A SER* 3.2 3.8 - - - -
729A GLU* 2.8 34.4 + - + +
730A PHE* 5.1 0.2 - - - -
735A GLY* 1.3 75.4 - - - +
737A MET* 1.3 62.3 + - - +
738A PHE* 4.0 27.7 - - + -
786A VAL* 3.8 21.4 - - + +
787A ILE 3.5 3.8 - - - -
788A ASN* 3.1 23.9 + - - +
789A ILE* 4.4 1.1 - - - +
1940A DTD 3.8 47.4 + - + +
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Residues in contact with MET 737 (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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726A LEU* 4.1 22.0 - - + -
728A SER* 3.2 29.8 - - - +
730A PHE* 5.1 2.5 - - + -
736A ARG* 1.3 74.5 - - - +
738A PHE* 1.3 72.4 + - - +
739A ILE* 3.9 12.2 + - + -
785A GLN 3.8 0.5 - - - +
786A VAL* 3.5 2.4 - - - -
787A ILE* 2.7 46.8 + - + +
789A ILE* 4.0 11.4 - - + -
818A LEU* 3.9 34.3 - - + -
819A PRO* 4.2 12.6 - - + +
820A ILE* 3.8 26.5 - - + -
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Residues in contact with PHE 738 (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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725A GLY 3.8 0.3 - - - +
726A LEU* 3.3 6.8 - - - -
727A LYS* 2.8 42.8 + - + +
728A SER* 5.5 0.2 - - - -
736A ARG* 4.0 29.4 - - + -
737A MET* 1.3 77.8 - - - +
739A ILE* 1.3 61.6 + - - +
740A PHE* 3.4 27.2 - + + -
784A GLN* 4.2 20.4 - - - -
785A GLN 3.5 4.3 - - - +
786A VAL* 3.4 29.2 - - + -
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Residues in contact with ILE 739 (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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724A ILE* 3.7 22.4 - - + -
725A GLY 3.5 2.2 - - - -
726A LEU* 3.8 15.9 - - + -
737A MET* 4.1 6.3 - - + -
738A PHE* 1.3 75.2 - - - +
740A PHE* 1.3 62.5 + - - +
741A TYR* 3.4 35.6 - - + +
756A LEU* 4.5 0.2 - - + -
784A GLN* 3.1 5.8 - - - +
785A GLN* 3.0 38.6 + - + +
787A ILE* 3.2 37.5 - - + -
801A LEU* 4.1 11.4 - - + -
818A LEU* 4.3 17.5 - - + -
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Residues in contact with PHE 740 (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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723A GLN 3.4 1.0 - - - +
724A ILE* 3.2 8.3 - - - +
725A GLY 2.9 34.6 + - - -
727A LYS* 4.1 14.4 - - + -
738A PHE* 3.4 39.5 - + + -
739A ILE* 1.3 74.8 - - - +
741A TYR* 1.3 61.7 + - - +
742A GLY 4.1 0.4 - - - -
782A GLN* 3.8 23.8 - - - +
783A VAL 3.4 5.8 - - - +
784A GLN* 3.3 37.9 - - + -
6P VAL* 3.8 31.2 - - + -
8P PHE* 3.5 34.3 - + + -
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Residues in contact with TYR 741 (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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722A LEU* 4.1 4.3 - - + -
723A GLN 3.5 3.6 - - - -
724A ILE* 4.1 21.5 - - + -
739A ILE* 3.4 35.0 - - + +
740A PHE* 1.3 73.9 - - - +
742A GLY* 1.3 60.1 + - - +
743A ASN 4.0 0.5 + - - -
752A PHE* 3.7 32.5 - + + -
754A PRO* 3.2 24.9 - - + +
773A VAL* 5.1 2.9 - - + -
777A VAL* 4.8 2.5 - - + +
781A ALA 3.9 1.4 - - - +
782A GLN* 3.2 4.2 - - - -
783A VAL* 2.8 54.3 + - + +
784A GLN* 4.5 1.3 - - - -
785A GLN* 2.7 37.5 + - + -
801A LEU* 3.7 10.0 - - + +
803A ILE* 4.2 13.2 - - + -
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Residues in contact with GLY 742 (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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722A LEU* 3.3 12.1 - - - +
723A GLN 2.8 36.7 + - - -
740A PHE 4.1 0.6 - - - -
741A TYR* 1.3 71.0 - - - +
743A ASN* 1.3 62.9 + - - -
744A LYS 3.4 1.0 + - - -
781A ALA 3.6 3.8 - - - -
782A GLN* 4.1 8.1 - - - +
5P TRP* 3.3 28.0 - - - -
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Residues in contact with ASN 743 (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 3.7 3.6 - - - -
741A TYR 4.0 1.2 + - - -
742A GLY* 1.3 67.9 - - - -
744A LYS* 1.3 57.1 + - - +
745A THR* 2.8 25.6 + - - -
747A THR 2.8 24.2 + - - -
749A PHE* 3.3 28.9 - - + -
777A VAL* 3.2 26.6 + - + +
778A ASP 3.2 18.7 + - - +
779A GLY* 3.5 3.8 - - - -
780A GLY* 3.1 26.2 + - - -
781A ALA 2.9 12.2 + - - +
2P PRO* 4.9 0.2 - - - +
5P TRP* 3.3 6.0 - - - -
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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