Contacts of the helix formed by residues 32 - 41 (chain B) in PDB entry 2RGZ
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 32 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 1.3 78.5 - - - +
33B LEU* 1.3 64.1 + - - +
34B SER* 3.7 8.0 + - - +
35B GLU* 3.2 18.8 + - + +
36B LEU* 3.2 12.2 + - - +
207B ASN* 3.3 32.4 + - - +
216B LYS* 4.5 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA 3.6 2.8 + - - -
32B ASP* 1.3 71.2 - - - +
34B SER* 1.3 63.3 + - - +
35B GLU 3.0 1.6 + - - -
36B LEU* 3.1 20.4 + - + -
37B LEU* 3.2 26.1 + - + +
150B VAL* 4.8 10.3 - - + -
206B MET* 3.9 30.5 - - + +
207B ASN* 2.8 10.4 + - - +
209B LEU* 5.1 3.1 - - + +
211B LEU* 4.9 7.6 - - + -
216B LYS* 3.8 43.0 - - + +
219B ILE* 4.0 39.7 - - + -
220B VAL* 4.8 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 3.7 6.4 - - - +
33B LEU* 1.3 73.6 - - - +
35B GLU* 1.3 59.8 + - - +
37B LEU* 4.4 5.9 - - - +
38B LYS* 4.2 14.4 + - - +
154B TYR* 5.0 1.7 + - - -
203B ARG* 3.7 32.3 + - - +
206B MET* 3.9 18.5 - - - +
207B ASN* 2.6 40.5 + - - -
265B HEM 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 5.9 3.4 - - + -
32B ASP* 3.2 12.8 + - + +
33B LEU 3.0 0.8 - - - -
34B SER* 1.3 80.9 + - - +
36B LEU* 1.3 60.9 + - - +
37B LEU 3.1 2.2 - - - -
38B LYS* 3.3 25.3 + - - +
39B GLU* 2.9 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B MET* 4.5 17.5 - - - -
31B ALA* 4.2 13.7 - - + +
32B ASP 3.2 14.0 + - - +
33B LEU* 3.1 9.1 + - + +
35B GLU* 1.3 75.8 - - - +
37B LEU* 1.3 54.1 + - - +
39B GLU* 4.7 11.2 + - + +
40B GLY* 2.6 33.1 + - - +
213B MET* 4.1 10.3 - - + -
216B LYS* 3.5 44.2 - - + -
217B GLU* 5.4 3.8 - - + +
220B VAL* 3.3 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.2 27.9 + - + +
34B SER* 4.4 2.7 - - - +
35B GLU 3.1 0.6 - - - -
36B LEU* 1.3 76.9 - - - +
38B LYS* 1.3 51.7 + - - +
41B THR* 2.5 45.4 + - - +
150B VAL* 5.3 2.0 - - + -
151B ALA* 4.9 2.0 - - - -
154B TYR* 3.6 49.1 - - + -
206B MET* 4.4 14.4 - - + -
219B ILE* 4.2 15.7 - - + -
220B VAL* 3.6 18.2 - - + -
223B ALA* 3.4 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER 4.2 8.0 + - - +
35B GLU* 3.3 24.9 + - - +
37B LEU* 1.3 79.5 - - - +
39B GLU* 1.3 63.5 + - + +
41B THR* 3.5 6.0 + - - -
42B LYS* 3.2 20.4 + - - -
154B TYR* 4.1 15.6 + - - +
203B ARG* 5.8 0.9 - - - +
265B HEM 4.4 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 2.9 47.0 + - + +
36B LEU* 4.3 12.0 - - + +
38B LYS* 1.3 74.0 - - + +
40B GLY* 1.3 64.3 + - - +
42B LYS* 3.2 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU 2.6 25.4 + - - -
39B GLU* 1.3 76.3 - - - +
41B THR* 1.3 56.7 + - - +
42B LYS* 3.2 2.8 + - - +
43B GLU* 5.1 1.0 + - - +
220B VAL* 3.7 12.9 - - - +
224B ASN* 3.0 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 2.5 33.2 + - + +
38B LYS* 3.5 6.6 + - - -
40B GLY* 1.3 72.9 - - - +
42B LYS* 1.3 54.5 + - - +
43B GLU 3.2 2.5 - - - -
44B ALA* 2.4 37.8 + - - +
45B HIS* 3.2 8.1 + - - +
154B TYR* 4.9 5.2 + - + -
220B VAL* 3.9 4.7 - - + +
223B ALA* 3.4 35.2 - - + +
224B ASN* 3.3 27.8 - - - +
227B PHE* 4.6 11.0 - - + -
----------------------------------------------------------
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