Contacts of the helix formed by residues 425 - 429 (chain A) in PDB entry 4A7A
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 425 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 2.9 13.8 + - - -
263A ALA* 4.2 11.8 - - - +
264A ILE 5.0 3.6 - - - -
424A ALA* 1.3 78.1 - - - +
426A THR* 1.3 67.5 + - - -
427A GLU* 3.1 8.7 - - - -
428A THR* 2.9 21.9 + - - -
442A ALA* 3.2 7.5 - - - +
600A FAD 3.3 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.8 16.4 - - - +
425A GLY* 1.3 70.2 - - - -
427A GLU* 1.3 75.2 + - - +
428A THR 3.0 1.8 + - - -
429A ALA* 3.1 12.5 + - - +
433A SER* 2.8 16.6 + - - -
434A GLY* 2.9 28.1 + - - +
435A TYR 2.7 26.4 + - - -
438A GLY* 3.5 4.6 - - - -
439A ALA* 3.3 19.0 + - - +
600A FAD 2.8 32.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
42A ARG* 3.0 41.1 + - - -
187A TRP* 4.8 5.0 - - - -
265A PRO* 4.1 5.2 - - - +
266A PRO* 3.5 32.4 - - + +
291A LEU* 4.2 0.5 - - - +
399A THR* 3.4 14.8 + - - +
400A THR* 2.9 39.6 + - + +
402A PHE* 6.0 1.7 - - + -
414A LEU* 3.7 19.7 - - + +
415A ARG* 5.6 0.2 + - - -
424A ALA 5.9 0.2 - - - +
425A GLY* 2.9 4.5 + - - -
426A THR* 1.3 80.7 + - - +
428A THR* 1.3 62.0 + - + +
429A ALA 3.4 2.0 - - - +
433A SER* 3.5 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PRO* 5.7 2.9 - - + -
414A LEU* 3.8 34.1 - - + +
415A ARG* 3.1 40.3 + - + +
423A PHE* 4.2 6.1 - - + +
424A ALA 3.3 18.5 + - - +
425A GLY 2.9 18.6 + - - -
427A GLU* 1.3 80.2 - - + +
429A ALA* 1.3 61.1 + - - +
430A THR* 4.0 1.0 + - - +
441A GLU* 4.6 1.2 - - - +
442A ALA* 3.2 5.4 - - - +
445A ARG* 2.9 28.4 + - - -
463A TRP* 4.9 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TRP* 3.9 11.3 - - - -
415A ARG* 4.3 2.4 + - - -
425A GLY 4.0 0.6 + - - -
426A THR 3.1 12.4 + - - +
427A GLU 4.4 0.7 - - - +
428A THR* 1.3 82.9 + - - +
430A THR* 1.3 61.8 + - - +
431A HIS 3.6 1.3 - - - +
433A SER* 3.5 21.6 + - - -
438A GLY* 3.3 38.4 - - - +
441A GLU* 3.5 17.0 - - - +
442A ALA* 4.2 3.1 - - + +
----------------------------------------------------------
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