Contacts of the helix formed by residues 716 - 730 (chain A) in PDB entry 2VUW
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 ASP 716 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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652A TRP* 5.0 5.5 + - - -
714A ASP* 3.5 1.2 - - - -
715A GLY* 1.3 81.1 + - - +
717A TYR* 1.3 69.2 + - - +
718A GLN* 2.8 38.1 + - - +
719A PHE* 3.0 37.3 + - + +
720A ASP* 4.0 6.3 + - - +
723A ARG* 5.5 0.2 + - - -
747A TYR* 3.6 0.7 + - - -
751A LYS* 2.9 32.2 + - - -
755A GLN* 4.9 4.6 + - - +
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Residues in contact with TYR 717 (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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716A ASP* 1.3 73.9 + - - +
718A GLN* 1.3 65.4 + - - +
720A ASP* 2.9 38.3 + - + -
721A ILE* 3.2 30.9 + - + +
724A LEU* 4.4 12.4 - - + +
743A LEU* 5.1 1.2 - - - +
746A HIS* 2.7 41.5 + + - +
747A TYR* 3.6 35.9 - + + -
750A ASP* 4.1 25.1 - - + +
751A LYS* 4.7 3.0 - - - +
782A LEU* 4.6 6.4 - - - +
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Residues in contact with GLN 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A HIS* 3.7 32.5 - - + +
652A TRP* 5.4 2.8 + - - -
716A ASP* 2.8 24.3 + - + +
717A TYR* 1.3 77.6 - - - +
719A PHE* 1.3 79.5 + - + +
721A ILE* 3.1 24.8 + - - +
722A TYR* 2.9 39.9 + - + +
744A TRP* 4.0 11.1 - - + -
747A TYR* 3.6 21.3 + - + -
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Residues in contact with PHE 719 (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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710A LEU 4.9 2.4 - - - +
713A GLY* 3.5 37.2 - - - +
714A ASP* 3.6 24.5 - - - +
716A ASP* 3.0 30.6 + - + +
718A GLN* 1.3 98.0 - - - +
720A ASP* 1.3 64.4 + - - +
722A TYR* 3.6 31.4 + + + +
723A ARG* 3.4 22.1 + - - +
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Residues in contact with ASP 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ASP* 5.7 0.2 - - - +
716A ASP 4.0 3.7 - - - +
717A TYR* 2.9 42.3 + - + +
719A PHE* 1.3 76.5 - - - +
721A ILE* 1.3 60.7 + - - +
723A ARG* 2.9 35.7 + - - +
724A LEU* 2.8 37.5 + - + +
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Residues in contact with ILE 721 (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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717A TYR* 3.2 47.1 + - + +
718A GLN* 3.1 9.7 + - - +
720A ASP* 1.3 77.0 - - - +
722A TYR* 1.3 58.0 + - - +
724A LEU* 3.2 8.0 + - + -
725A MSE 2.8 32.7 + - + +
743A LEU* 3.7 39.5 - - + +
744A TRP* 3.4 42.4 - - + +
747A TYR* 3.9 15.0 - - + -
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Residues in contact with TYR 722 (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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648A ARG 4.0 4.9 - - - -
649A ASP* 2.5 32.2 + - - -
651A HIS* 4.5 0.2 - - - -
690A LEU* 4.4 2.5 - - + -
710A LEU* 3.4 53.8 - - + +
711A PHE* 3.4 22.9 - - + -
718A GLN* 2.9 39.6 + - - +
719A PHE* 3.6 31.8 + + - +
720A ASP 3.2 0.6 - - - -
721A ILE* 1.3 78.6 - - - +
723A ARG* 1.3 60.5 + - - +
725A MSE 3.4 21.8 + - + +
726A LYS 3.1 17.2 + - - -
744A TRP* 3.7 15.7 - + - -
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Residues in contact with ARG 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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711A PHE* 2.8 53.4 + - + +
712A THR* 3.8 2.4 - - - +
713A GLY 2.8 34.7 + - - +
714A ASP* 4.9 6.7 + - - +
716A ASP 5.5 0.2 + - - -
719A PHE* 3.4 20.2 + - - +
720A ASP* 2.9 35.7 + - - +
722A TYR* 1.3 75.6 - - - +
724A LEU* 1.3 59.8 + - + +
726A LYS* 3.2 5.4 + - - +
727A LYS* 3.0 26.9 + - - +
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Residues in contact with LEU 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A TYR* 4.4 15.7 - - + +
720A ASP* 2.8 28.2 + - + +
721A ILE* 3.7 13.5 - - + +
723A ARG* 1.3 76.6 - - + +
725A MSE 1.3 58.1 + - - +
727A LYS* 3.3 20.4 + - + +
728A GLU* 3.0 28.1 + - - +
743A LEU* 3.9 31.3 - - + +
782A LEU* 6.5 0.4 - - + -
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Residues in contact with MSE 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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648A ARG* 3.2 38.1 - - + +
690A LEU* 5.6 1.8 - - + -
710A LEU* 5.7 1.1 - - + -
721A ILE* 2.8 20.2 + - + +
722A TYR* 3.5 34.3 - - + +
724A LEU* 1.3 73.4 - - - +
726A LYS* 1.3 56.9 + - - +
728A GLU* 3.2 6.0 + - - +
729A ASN* 3.0 35.9 + - - +
733A TRP* 3.8 23.6 - - + -
740A SER* 3.8 29.8 - - - -
743A LEU* 4.1 11.0 - - + -
744A TRP* 3.6 20.2 - - + +
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Residues in contact with LYS 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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705A SER 4.6 4.0 + - - -
707A ASP 4.8 2.8 + - - -
711A PHE* 3.8 45.9 - - + +
722A TYR 3.1 11.3 + - - +
723A ARG* 3.2 9.4 + - - +
725A MSE 1.3 76.7 - - - +
727A LYS* 1.3 60.4 + - - +
729A ASN* 3.5 7.0 - - - -
730A ASN* 3.0 24.6 + - - -
731A ASN* 3.2 52.8 + - + +
733A TRP* 3.9 3.8 - - + -
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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
----------------------------------------------------------
723A ARG 3.0 13.8 + - - +
724A LEU* 3.5 24.7 - - + +
726A LYS* 1.3 79.0 - - - +
728A GLU* 1.3 62.8 + - - +
729A ASN 3.4 0.3 + - - -
730A ASN* 3.5 15.2 + - - +
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Residues in contact with GLU 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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724A LEU 3.0 17.6 + - - +
725A MSE 3.2 7.6 + - - +
727A LYS* 1.3 79.1 - - - +
729A ASN* 1.3 59.2 + - - +
730A ASN* 3.7 6.4 + - - -
737A HIS* 2.9 47.4 + - + +
739A TYR* 3.8 40.8 - - + +
740A SER* 5.1 4.0 - - - +
743A LEU* 5.1 1.8 - - + -
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Residues in contact with ASN 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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646A GLU* 5.7 1.6 + - - -
648A ARG* 5.1 5.2 - - - +
725A MSE 3.0 20.8 + - - +
726A LYS* 3.3 6.8 - - - +
728A GLU* 1.3 75.7 - - - +
730A ASN* 1.3 70.9 + - - +
731A ASN* 2.8 31.9 + - - -
732A ARG* 2.8 34.1 + - - +
733A TRP* 3.3 39.8 - - - +
735A GLU* 4.0 4.0 - - - +
737A HIS* 3.5 33.5 - - + +
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Residues in contact with ASN 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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726A LYS 3.0 10.0 + - - -
727A LYS* 3.5 9.2 + - - +
728A GLU 3.4 8.1 + - - -
729A ASN* 1.3 79.8 - - - +
731A ASN* 1.3 67.4 + - - +
732A ARG* 3.2 39.9 + - - +
735A GLU* 5.6 1.0 + - - -
737A HIS* 5.7 2.2 - - - -
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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