Contacts of the helix formed by residues 424 - 432 (chain D) in PDB entry 4QG0
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 424 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D TYR* 3.0 17.8 + - + +
147D ILE* 3.6 5.0 - - - -
148D LYS* 2.8 51.5 + - - +
212D PRO* 3.4 1.7 - - - +
213D PHE* 2.8 45.5 + - + -
423D THR* 1.3 78.4 - - - +
425D ASN* 1.3 61.5 + - - +
426D ILE 2.9 2.1 + - - -
427D PHE* 2.9 23.5 + - - +
428D LEU* 4.0 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ASN* 2.2 43.5 + - - +
428A LEU* 3.5 35.7 - - + +
429A GLU* 4.7 2.9 + - - -
432A TYR* 3.9 20.8 - - + -
146D TYR* 4.7 0.4 + - - +
423D THR* 3.1 8.7 + - - +
424D ASP* 1.3 77.8 - - - +
426D ILE* 1.3 51.7 + - + +
427D PHE 3.2 0.2 - - - -
428D LEU* 2.9 11.6 + - - +
429D GLU* 2.8 41.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TYR* 6.5 0.4 - - + -
212D PRO* 3.7 9.4 - - + -
390D PHE* 3.5 37.7 - - + -
397D ILE* 5.2 10.1 - - + -
399D ILE* 5.3 3.1 - - + -
409D ILE* 4.1 16.8 - - + -
421D LYS 5.0 4.3 - - - +
422D LEU* 3.6 35.9 - - + -
423D THR 3.5 14.8 - - - +
424D ASP 2.9 2.3 + - - +
425D ASN* 1.3 75.2 - - + +
427D PHE* 1.3 60.7 + - - +
429D GLU* 3.8 20.4 - - + +
430D ILE* 2.7 44.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 3.5 21.8 - + - -
155D TYR* 3.8 20.2 - + - -
213D PHE* 3.7 28.3 - + + -
386D ILE* 4.0 24.5 - - + -
390D PHE* 4.6 6.3 - - + -
424D ASP 2.9 14.4 + - - +
426D ILE* 1.3 82.6 - - - +
428D LEU* 1.3 77.7 + - + +
430D ILE* 4.8 0.2 - - - -
431D LEU* 3.0 33.0 + - + +
445D LEU* 3.2 51.4 - - + +
448D ILE* 4.5 12.1 - - + -
449D GLU* 5.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 4.0 39.9 - - + -
423A THR* 4.1 1.8 - - - +
425A ASN* 3.5 33.9 - - + +
424D ASP 5.2 1.3 - - - +
425D ASN* 2.9 14.2 + - - +
427D PHE* 1.3 100.6 - - + +
429D GLU* 1.3 61.1 + - - +
431D LEU* 4.1 8.7 - - + +
432D TYR* 2.8 66.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ASN* 5.4 2.5 - - - +
432A TYR* 5.9 2.1 - - - -
397D ILE* 3.9 32.9 - - + +
398D GLU 5.2 3.6 + - - +
425D ASN* 2.8 23.8 + - - +
426D ILE* 3.0 22.9 + - + +
428D LEU* 1.3 77.1 - - - +
430D ILE* 1.3 63.2 - - - +
432D TYR* 4.0 3.3 - - - +
433D SER* 3.3 22.2 + - - -
438D LEU* 5.4 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D ALA* 4.4 3.8 - - + +
390D PHE* 3.9 31.0 - - + -
393D ALA* 3.6 26.2 - - + -
397D ILE* 4.4 14.1 - - + -
409D ILE* 4.8 6.3 - - + -
426D ILE* 2.7 25.2 + - + +
429D GLU* 1.3 73.1 - - - +
431D LEU* 1.3 59.6 + - - +
433D SER* 2.8 26.1 + - - +
438D LEU* 5.0 4.0 - - + +
441D ALA* 3.8 24.7 - - + -
442D ARG* 3.6 14.8 - - - +
445D LEU* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 5.5 0.7 - - + -
421A LYS* 5.6 0.9 - - - +
427D PHE* 3.0 24.2 + - + +
428D LEU* 2.9 20.1 + - + +
430D ILE* 1.3 77.5 - - - +
432D TYR* 1.3 79.8 + - + +
433D SER 3.3 1.0 + - - -
442D ARG* 3.8 10.8 - - - +
445D LEU* 3.7 28.9 - - + +
446D LYS* 3.6 50.3 + - + +
449D GLU* 3.4 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 5.9 0.5 - - - -
146A TYR* 4.5 4.0 - - - -
420A THR 4.4 3.3 + - - -
421A LYS* 3.7 67.0 + - + +
423A THR* 3.2 30.2 + - - +
425A ASN* 3.5 32.3 - - - -
428D LEU* 2.8 39.6 + - + +
429D GLU* 4.0 3.1 - - - +
431D LEU* 1.3 97.6 - - + +
433D SER* 1.3 66.1 + - - +
434D THR* 3.8 3.3 + - - +
----------------------------------------------------------
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