Contacts of the helix formed by residues 705 - 714 (chain A) in PDB entry 2VGE
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 705 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ILE* 5.1 4.3 - - + +
671A ALA* 4.6 9.2 - - - +
673A TYR* 2.6 34.9 + - - -
700A ALA* 2.9 14.5 + - - +
703A CYS* 3.0 12.7 + - + +
704A ASN* 1.3 74.3 - - - +
706A THR* 1.3 60.4 - - - +
707A VAL* 3.4 6.4 + - - +
708A ILE* 3.0 36.5 + - + +
709A CYS* 3.0 26.8 + - - -
744A CYS* 4.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 706 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704A ASN 3.1 7.8 + - - -
705A ASP* 1.3 70.7 + - - +
707A VAL* 1.3 59.5 + - + +
709A CYS* 3.2 3.7 + - - +
710A MET* 2.9 45.9 + - + +
740A GLY 4.6 0.2 + - - -
743A ASP* 2.8 32.1 + - - +
744A CYS* 3.2 28.6 + - - +
747A TYR* 4.0 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A TYR* 4.2 22.4 - - + +
705A ASP* 3.3 8.6 + - - +
706A THR* 1.3 78.7 - - + +
708A ILE* 1.3 64.0 + - + +
710A MET* 3.4 14.7 + - - +
711A ALA* 3.1 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 708 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A ILE* 3.9 25.4 - - + +
671A ALA* 5.8 1.8 - - - -
673A TYR* 3.2 30.7 - - + +
676A VAL* 4.0 31.6 - - + -
700A ALA* 3.9 11.2 - - + -
705A ASP* 3.0 32.9 + - + +
707A VAL* 1.3 73.3 - - + +
709A CYS* 1.3 69.3 + - - +
711A ALA* 3.0 7.1 + - + +
712A LEU* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 709 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A LEU* 4.0 20.6 - - + -
700A ALA* 3.6 19.5 - - - -
701A ALA* 3.8 10.1 - - - -
705A ASP 3.0 17.0 + - - +
706A THR* 3.4 9.9 - - - +
708A ILE* 1.3 76.6 - - - +
710A MET* 1.3 57.1 + - - +
712A LEU* 3.2 3.2 + - - +
713A VAL* 2.8 33.4 + - - +
744A CYS* 3.6 22.7 - - - -
747A TYR* 3.9 18.4 - - + -
748A LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 710 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A THR* 2.9 32.4 + - + +
707A VAL* 3.6 13.9 - - - +
709A CYS* 1.3 76.1 - - - +
711A ALA* 1.3 57.2 + - - +
713A VAL* 3.2 0.5 + - - +
714A GLN* 2.8 58.4 + - - +
747A TYR* 3.3 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 711 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676A VAL* 5.2 3.8 - - + -
677A ASP* 4.6 12.8 - - - +
680A ILE* 4.0 18.9 - - + +
707A VAL* 3.1 10.7 + - + +
708A ILE* 3.0 12.9 + - + +
710A MET* 1.3 78.3 - - - +
712A LEU* 1.3 60.5 + - + +
714A GLN* 4.6 3.6 - - - +
715A HIS* 2.6 39.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 712 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LEU* 4.2 9.9 - - + -
668A ILE* 3.9 4.9 - - + -
676A VAL* 5.2 0.2 - - + -
680A ILE* 4.1 20.0 - - + -
686A VAL* 4.2 20.8 - - + +
696A PRO* 3.5 44.0 - - + +
697A LEU* 3.7 13.0 - - + +
700A ALA* 3.9 4.9 - - + -
708A ILE* 2.9 35.0 + - + +
709A CYS 3.5 5.2 - - - +
711A ALA* 1.3 73.6 - - - +
713A VAL* 1.3 65.7 + - - +
715A HIS* 3.0 13.8 + - - +
716A GLY 3.4 1.0 + - - -
717A ALA* 3.1 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 713 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A LEU* 4.2 12.8 - - + -
709A CYS 2.8 26.1 + - - +
710A MET 3.7 0.4 - - - +
712A LEU* 1.3 73.4 - - - +
714A GLN* 1.3 60.6 + - + +
715A HIS 3.1 5.0 + - - -
716A GLY 3.4 7.6 + - - -
717A ALA* 3.9 9.4 + - + +
719A ILE* 3.8 24.9 - - + -
747A TYR* 3.5 28.3 - - + +
748A LEU* 4.9 2.0 - - + -
751A VAL* 4.3 5.8 - - + -
817A LEU* 4.1 32.7 + - + -
818A PHE* 3.5 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 714 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A MET* 2.8 57.0 + - - +
711A ALA* 4.0 1.5 - - - +
713A VAL* 1.3 76.9 - - + +
715A HIS* 1.3 79.9 + - + +
747A TYR* 4.9 2.5 + - - +
818A PHE* 3.4 47.2 - - + +
819A PRO 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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