Contacts of the helix formed by residues 427 - 435 (chain A) in PDB entry 2R8K
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 ILE 427 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A MET* 3.8 10.5 - - + -
423A LEU 3.1 17.9 - - - +
424A THR* 4.5 0.9 - - - -
426A ARG* 1.3 78.8 - - - +
428A GLN* 1.3 61.8 + - + +
430A LEU* 3.3 5.6 + - + +
431A GLU* 3.1 29.5 + - + +
438A VAL* 3.7 28.6 - - + +
440A PRO* 4.5 2.5 - - + -
469A GLN* 3.0 42.0 - - - +
503A ILE* 3.6 14.8 - - + -
506A PHE* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 5.1 3.6 - - - +
424A THR* 3.3 34.0 + - + +
425A SER* 4.2 9.2 - - - +
427A ILE* 1.3 77.6 - - + +
429A ASP* 1.3 62.8 + - - +
430A LEU 2.9 4.3 - - - -
431A GLU* 2.9 25.4 + - - +
432A GLN* 3.0 19.4 + - + +
469A GLN* 5.3 0.9 - - - +
200B ASP* 5.8 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 4.6 28.2 - - + +
133A ARG* 5.4 1.6 + - - -
136A ARG* 2.7 42.0 + - - +
151A ARG* 5.4 2.6 + - - -
425A SER 3.8 17.4 + - - +
426A ARG* 4.2 8.1 - - - +
427A ILE 3.4 0.4 - - - -
428A GLN* 1.3 78.8 - - - +
430A LEU* 1.3 65.3 + - - +
432A GLN* 3.8 7.9 + - - +
433A GLU* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 4.5 8.1 - - - +
392A VAL* 3.2 36.3 - - + -
395A MET* 3.2 17.7 - - + -
426A ARG 3.2 18.7 + - - +
427A ILE* 3.3 8.2 + - + +
428A GLN 2.9 1.0 - - - -
429A ASP* 1.3 84.8 - - - +
431A GLU* 1.3 65.2 + - - +
433A GLU* 3.2 15.5 + - - +
434A TYR* 3.1 59.6 + - + +
438A VAL* 5.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 3.1 20.3 + - - +
428A GLN* 2.9 14.4 + - - +
430A LEU* 1.3 77.4 - - - +
432A GLN* 1.3 53.0 + - + +
435A ASN* 2.5 38.9 + - - -
436A LYS 3.3 17.2 + - - +
437A ILE* 2.9 32.8 - - - +
438A VAL* 2.7 38.0 + - + +
200B ASP* 3.6 16.1 - - - +
201B ILE* 4.0 14.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 4.4 16.2 + - - -
140A LYS* 3.4 18.4 + - - -
428A GLN* 3.0 18.5 + - + +
429A ASP* 4.1 6.8 - - - +
431A GLU* 1.3 79.8 - - - +
433A GLU* 1.3 60.9 + - - +
435A ASN* 3.6 10.3 + - - +
10B ILE* 5.4 4.9 - - - +
197B GLY* 2.8 31.9 + - - -
199B TYR* 3.1 35.9 + - + +
201B ILE* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ARG* 2.8 35.3 + - - +
139A LEU* 4.5 4.9 - - + +
143A LYS* 4.5 18.5 + - - +
151A ARG* 4.0 21.0 + - - +
389A ARG* 2.9 28.7 + - - -
429A ASP* 3.3 10.3 + - - +
430A LEU* 3.2 12.9 + - - +
432A GLN* 1.3 81.0 - - - +
434A TYR* 1.3 79.2 + - + +
435A ASN* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 4.7 13.3 + - - -
390A PRO 4.8 1.0 + - - -
391A VAL* 3.9 23.5 - - + -
392A VAL* 3.5 22.4 + - + +
430A LEU* 3.1 46.2 + - + +
433A GLU* 1.3 99.4 + - + +
435A ASN* 1.3 72.1 + - - +
436A LYS* 2.8 50.8 + - + +
438A VAL* 4.4 9.6 - - + -
508A ILE* 4.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLU 2.5 20.0 + - - -
432A GLN* 3.6 9.1 + - - +
433A GLU 3.3 2.6 - - - +
434A TYR* 1.3 76.2 - - - +
436A LYS* 1.3 56.0 + - - +
7B LYS* 3.2 54.1 + - - +
10B ILE* 3.5 28.8 - - + +
11B GLN* 3.9 20.2 - - - +
201B ILE* 3.9 16.2 - - - +
----------------------------------------------------------
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