Contacts of the helix formed by residues 776 - 782 (chain A) in PDB entry 2IVF
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 GLY 776 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ASP* 5.3 6.7 - - - -
486A ASP* 4.0 8.8 + - - -
530A ASN* 4.0 7.4 - - - -
534A MET* 5.5 4.9 - - - -
773A MET 4.4 2.2 + - - -
774A GLY 3.6 1.4 - - - -
775A THR* 1.3 83.7 + - - +
777A VAL* 1.3 66.2 + - - -
778A SER* 3.2 3.4 - - - -
779A ARG* 3.1 15.5 + - - +
780A TYR* 3.7 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 5.5 1.8 - - + -
235A MET 6.2 0.2 - - - +
236A HIS* 3.9 20.4 - - + -
527A GLU* 6.5 0.4 - - + -
530A ASN* 3.3 14.3 + - - +
531A ILE* 5.5 4.7 - - + -
534A MET* 3.4 40.1 - - + +
776A GLY* 1.3 71.6 - - - -
778A SER* 1.3 59.6 + - - +
780A TYR* 2.9 7.1 + - - +
781A ALA* 2.8 36.7 + - + +
955A TYR* 3.5 35.7 - - + +
958A ASN* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 3.6 24.0 + - - +
481A TRP 4.1 0.2 + - - -
482A ALA* 3.5 10.5 - - - -
483A TYR* 2.9 48.2 + - - -
773A MET* 3.9 11.5 - - - +
776A GLY 3.2 1.0 + - - -
777A VAL* 1.3 80.0 - - - +
779A ARG* 1.3 63.4 + - - +
782A HIS* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A VAL 4.9 3.8 + - - -
772A SER* 4.3 19.8 + - - -
773A MET* 3.7 13.9 + - + +
774A GLY 3.2 33.8 + - - +
775A THR* 4.3 7.8 - - - +
776A GLY 3.1 13.4 + - - +
777A VAL 3.1 0.2 + - - -
778A SER* 1.3 80.3 - - - +
780A TYR* 1.3 90.1 + - + +
782A HIS* 4.9 0.2 - - - +
783A ALA 4.4 2.9 + - - -
784A ASN 4.5 4.7 - - - +
797A TRP* 3.6 22.4 - - + -
1983A ACT 4.3 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ASN* 5.8 2.1 + - - -
526A ASP* 3.6 41.8 - - + +
527A GLU* 3.6 35.6 - - + +
530A ASN* 3.5 43.1 - - + +
775A THR* 4.0 6.3 + - - -
776A GLY 3.7 11.9 - - - -
777A VAL* 2.9 3.6 + - + +
779A ARG* 1.3 106.2 + - + +
781A ALA* 1.3 65.8 + - - +
782A HIS 3.3 1.3 - - - -
783A ALA* 3.1 18.4 + - - +
797A TRP* 4.0 11.0 - + + -
803A LYS* 5.0 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 2.7 42.8 + - + +
236A HIS* 3.3 29.8 - - + +
237A MET* 3.2 10.9 - - - +
527A GLU* 3.5 12.5 + - + +
777A VAL* 2.8 22.4 + - + +
780A TYR* 1.3 77.3 - - - +
782A HIS* 1.3 63.8 + - - +
783A ALA* 3.5 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS 3.2 11.2 + - - +
237A MET* 4.0 4.5 - - - +
238A GLY 2.9 41.3 + - - -
482A ALA* 3.6 10.2 - - + +
773A MET* 4.1 15.7 - - + +
778A SER 3.0 20.3 + - - +
779A ARG 4.9 0.4 - - - +
781A ALA* 1.3 78.8 - - - +
783A ALA* 1.3 52.9 + - - +
784A ASN* 3.3 30.7 + - + +
785A GLU 4.8 4.5 + - - -
786A VAL* 5.3 1.0 - - + +
792A ILE* 3.3 23.3 - - + +
793A TYR 3.4 22.8 + - - -
794A PRO* 3.2 12.7 - - + +
795A MET 2.8 28.9 + - - -
----------------------------------------------------------
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