Contacts of the strand formed by residues 722 - 731 (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 722 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717A PHE* 4.0 12.4 - - + +
718A GLU* 3.3 3.5 - - - -
719A ASN* 3.0 33.9 + - - +
720A GLN 3.8 0.6 - - - -
721A LEU* 1.3 85.2 - - + +
723A GLN* 1.3 69.4 + - - +
724A ILE* 4.0 26.9 - - + -
741A TYR* 4.1 14.8 - - + -
742A GLY 3.3 22.7 - - - +
744A LYS* 3.9 4.5 - - - -
749A PHE* 4.3 15.5 - - + -
752A PHE* 4.3 5.4 - - + -
803A ILE* 4.4 13.2 - - + -
805A PHE* 4.1 23.1 - - + -
814A VAL* 5.0 5.4 - - + -
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Residues in contact with GLN 723 (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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715A VAL* 3.8 27.7 - - + +
717A PHE 3.5 2.0 - - - -
718A GLU* 3.1 37.0 + - - +
722A LEU* 1.3 74.1 - - - +
724A ILE* 1.3 66.4 + - - +
725A GLY 4.1 0.5 + - - -
740A PHE 3.4 3.5 - - - +
741A TYR* 3.5 1.6 - - - -
742A GLY 2.8 35.4 + - - -
744A LYS* 4.1 1.9 - - + +
782A GLN* 4.3 3.3 + - - -
5P TRP* 3.8 33.7 - - + -
6P VAL 4.6 1.4 - - - +
8P PHE* 3.7 21.0 - - - -
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Residues in contact with ILE 724 (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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715A VAL* 3.6 2.8 - - - +
716A LEU* 2.8 35.9 + - + -
717A PHE* 2.7 40.1 + - + +
722A LEU* 4.0 20.6 - - + -
723A GLN* 1.3 78.1 - - - +
725A GLY* 1.3 61.3 + - - +
726A LEU* 4.9 0.2 - - + -
739A ILE* 3.7 28.7 - - + -
740A PHE 3.2 4.0 - - - +
741A TYR* 4.1 8.5 - - + -
801A LEU* 4.2 10.5 - - + -
803A ILE* 3.4 37.2 - - + -
816A VAL* 4.9 3.4 - - + -
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Residues in contact with GLY 725 (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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714A GLY 3.4 9.2 - - - -
715A VAL* 4.2 1.3 - - - -
723A GLN 4.0 1.2 + - - -
724A ILE* 1.3 73.5 - - - +
726A LEU* 1.3 64.4 + - - +
739A ILE* 3.5 4.7 - - - +
740A PHE* 2.9 33.8 + - - -
8P PHE* 3.5 31.8 - - - -
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Residues in contact with LEU 726 (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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708A PHE* 4.0 13.7 - - + -
712A ASN 3.8 9.0 - - - +
713A ASN* 3.4 2.3 - - - +
714A GLY 2.8 31.8 + - - +
716A LEU* 4.1 21.1 - - + -
724A ILE* 4.9 0.4 - - + -
725A GLY* 1.3 82.4 - - - +
727A LYS* 1.3 68.2 + - - +
728A SER* 4.9 4.3 - - - +
737A MET* 4.1 15.0 - - + -
738A PHE 3.3 4.5 - - - +
739A ILE* 3.8 32.3 - - + -
818A LEU* 4.3 6.5 - - + -
819A PRO* 3.4 41.1 - - + -
8P PHE* 3.6 2.6 - - - -
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Residues in contact with LYS 727 (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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712A ASN 3.7 3.8 - - - -
713A ASN* 2.7 38.9 + - + +
726A LEU* 1.3 77.6 - - - +
728A SER* 1.3 61.4 + - - +
738A PHE* 2.8 46.6 + - + +
740A PHE* 4.1 15.8 - - + -
6P VAL* 3.4 20.0 - - + -
7P THR 2.9 26.3 + - - -
8P PHE* 3.9 5.6 - - + +
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Residues in contact with SER 728 (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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712A ASN* 3.3 37.7 + - - +
726A LEU* 4.9 0.7 - - - +
727A LYS* 1.3 73.7 + - - +
729A GLU* 1.3 74.9 - - - +
730A PHE* 3.8 22.4 - - - -
736A ARG 3.2 10.8 - - - -
737A MET* 3.2 38.7 - - - +
738A PHE* 5.5 0.4 - - - -
1943A SO4 4.8 1.2 + - - -
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Residues in contact with GLU 729 (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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712A ASN* 4.3 7.3 + - - +
728A SER* 1.3 82.8 - - - +
730A PHE* 1.3 70.9 + - - +
735A GLY* 3.2 2.6 - - - -
736A ARG* 2.8 33.7 + - + +
1940A DTD 3.4 27.0 - - + +
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Residues in contact with PHE 730 (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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712A ASN* 3.6 28.2 - - - +
728A SER* 3.8 20.4 - - - -
729A GLU* 1.3 79.5 + - - +
731A ARG* 1.3 63.6 + - - +
734A LEU 3.3 9.9 - - - +
735A GLY* 3.6 13.9 - - - -
737A MET* 5.1 2.9 - - + -
789A ILE* 3.9 28.7 - - + -
819A PRO 5.1 5.6 - - - -
820A ILE* 4.8 4.7 - - + -
824A LYS* 3.3 56.5 - - + +
825A PHE* 3.8 17.0 - + + -
827A GLN* 4.4 9.3 + - - +
1940A DTD 4.0 4.0 - - - +
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Residues in contact with ARG 731 (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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730A PHE* 1.3 76.7 - - - +
732A GLN* 1.3 111.4 + - + +
733A ASN 3.1 0.5 + - - -
734A LEU* 2.9 36.3 + - - +
827A GLN* 4.8 4.3 - - - +
1940A DTD 4.0 26.3 - - + +
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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