Contacts of the helix formed by residues 425 - 433 (chain A) in PDB entry 1GVJ
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 THR 425 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A TRP* 4.1 1.8 - - - -
419A GLN* 4.3 10.3 - - + -
424A TYR* 1.3 76.5 - - - +
426A PRO* 1.3 74.2 - - - +
427A GLU* 3.6 13.6 + - - +
428A GLU* 2.9 53.5 + - - +
429A LEU* 3.2 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLY* 3.3 39.7 - - - +
361A TRP* 3.6 38.3 - - + +
419A GLN* 4.1 10.3 - - + +
425A THR* 1.3 86.5 - - - +
427A GLU* 1.3 77.8 + - - +
429A LEU* 3.2 4.0 + - + +
430A HIS* 2.8 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A GLY 5.5 0.7 - - - +
360A GLY* 4.7 8.1 + - - -
425A THR* 3.2 11.9 - - - +
426A PRO* 1.3 103.8 - - - +
428A GLU* 1.3 57.6 + - + +
430A HIS* 3.4 14.3 + - + +
431A ALA* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLY 4.1 4.7 - - - +
424A TYR* 3.4 21.6 - - + +
425A THR* 2.9 50.3 + - - +
427A GLU* 1.3 77.6 - - + +
429A LEU* 1.3 61.6 - - - +
431A ALA* 3.3 7.5 + - - +
432A MET* 3.0 30.5 + - + +
305B LYS* 5.5 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 4.0 26.9 - - + -
321A ILE* 5.1 1.8 - - + -
342A LEU* 5.9 0.4 - - + -
346A THR* 4.3 19.1 - - + -
356A TRP* 4.7 7.2 - - + +
361A TRP* 3.6 34.3 - - + -
422A LEU* 4.7 8.7 - - + -
424A TYR* 3.8 37.9 - - + -
425A THR 3.2 1.9 + - - +
426A PRO* 3.2 7.2 + - + +
428A GLU* 1.3 76.3 - - - +
430A HIS* 1.3 70.7 + - + +
432A MET* 3.2 8.2 + - - +
433A LEU* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TRP* 3.6 42.7 + + + +
358A GLY* 4.0 27.1 - - - -
360A GLY 3.1 27.9 + - - -
361A TRP* 5.9 0.4 - + - -
426A PRO* 2.8 35.0 + - + +
427A GLU* 3.6 15.0 - - + +
429A LEU* 1.3 76.0 - - + +
431A ALA* 1.3 57.8 + - - +
433A LEU* 3.2 1.3 + - - -
434A ASP 2.8 10.0 + - - -
435A VAL* 2.7 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLU 3.0 14.3 + - - +
428A GLU* 3.5 12.1 - - - +
430A HIS* 1.3 76.5 - - - +
432A MET* 1.3 63.1 + - + +
434A ASP* 3.2 16.1 + - - +
435A VAL 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.9 31.0 - - + -
348A LYS* 5.1 4.0 + - - +
424A TYR* 3.7 30.5 - - + +
428A GLU* 3.0 21.4 + - - +
429A LEU* 3.2 17.0 + - - +
431A ALA* 1.3 76.5 - - + +
433A LEU* 1.3 65.7 + - + +
434A ASP* 3.4 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 4.5 9.6 - - + -
345A LEU 3.1 26.0 - - - +
346A THR* 3.7 35.0 - - + +
347A ASP 4.7 0.2 - - - -
348A LYS* 4.2 20.5 - - + +
351A GLN* 2.8 35.0 + - - +
356A TRP* 3.5 18.4 - - + +
429A LEU* 2.9 24.1 + - + +
430A HIS 4.0 2.2 - - - +
432A MET* 1.3 82.1 - - + +
434A ASP* 1.3 75.7 + - - +
435A VAL* 3.4 8.3 + - + +
----------------------------------------------------------
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