Contacts of the helix formed by residues 249 - 259 (chain A) in PDB entry 2QJ3
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 ARG 249 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 3.3 46.9 - - + +
224A ASN 2.8 19.7 + - - +
225A ARG 3.9 17.9 - - - +
226A ASP* 5.2 0.2 - - - +
227A GLY 4.8 0.7 + - - -
247A PRO* 4.3 18.6 - - + +
248A VAL* 1.3 70.6 - - - +
250A TRP* 1.3 56.9 + - - +
251A ASP* 2.6 46.3 + - - +
252A LEU* 3.0 49.6 + - + +
253A CYS* 3.4 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.8 26.0 - - + -
88A ALA* 3.8 29.2 - - + -
89A GLY 3.5 26.0 - - - -
90A HIS* 3.8 23.1 - - + +
156A ARG 3.2 0.8 + - - -
157A ASN* 3.6 39.9 - - + +
224A ASN* 3.8 16.2 - - - -
248A VAL* 2.9 10.4 + - + +
249A ARG* 1.3 73.9 - - - +
251A ASP* 1.3 61.3 + - - +
253A CYS* 3.0 17.0 + - + +
254A THR* 2.9 36.8 + - - +
257A LEU* 5.9 2.9 - - + -
274A LEU* 3.8 34.4 + - + +
277A ILE* 4.3 16.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG* 2.8 28.4 + - - +
157A ASN 3.6 16.7 + - - +
158A ALA* 4.5 8.8 - - - +
249A ARG* 2.6 51.8 + - - -
250A TRP* 1.3 72.3 - - - +
252A LEU* 1.3 72.8 + - - +
254A THR* 3.2 8.4 + - - -
255A ALA* 3.0 24.8 + - - +
281A GLU* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 3.3 30.5 - - + +
227A GLY* 3.8 4.1 - - - -
249A ARG* 3.0 45.4 + - - +
251A ASP* 1.3 87.3 + - - +
253A CYS* 1.3 61.9 + - - +
255A ALA* 3.6 14.4 + - + +
256A THR* 2.9 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 4.8 3.6 - - + -
222A LEU* 3.7 20.6 - - + +
223A SER 3.8 13.7 - - - -
224A ASN* 3.9 19.1 - - - -
227A GLY* 3.8 21.5 - - - -
249A ARG 3.4 10.0 + - - -
250A TRP* 3.0 29.3 + - + +
252A LEU* 1.3 75.5 - - - +
254A THR* 1.3 64.2 + - - +
255A ALA 3.2 0.2 - - - -
256A THR* 3.3 4.7 + - - -
257A LEU* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN 4.1 3.3 + - - -
250A TRP* 2.9 31.1 + - - +
251A ASP* 3.2 11.3 + - - -
253A CYS* 1.3 75.8 - - - +
255A ALA* 1.3 61.8 + - - +
257A LEU* 3.3 11.3 + - + +
258A ARG* 3.2 26.0 + - - +
277A ILE* 5.0 5.1 - - + +
278A ALA* 5.4 1.6 - - - -
281A GLU* 4.1 25.1 - - + +
282A LEU* 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ASP 3.0 13.7 + - - +
252A LEU* 3.6 21.8 - - + +
253A CYS 3.2 0.2 - - - -
254A THR* 1.3 77.6 - - - +
256A THR* 1.3 61.5 + - - +
258A ARG* 3.2 30.9 + - - +
259A GLU* 3.2 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 3.9 18.4 - - + -
227A GLY 2.5 29.6 + - - +
228A LYS* 4.7 7.2 + - + +
229A PRO* 4.6 8.7 - - + -
252A LEU 2.9 10.4 + - - -
253A CYS 3.3 7.2 + - - -
255A ALA* 1.3 74.0 - - - +
257A LEU* 1.3 64.8 + - - +
259A GLU* 3.3 26.5 + - - +
260A HIS* 2.8 46.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.9 21.8 - - + -
5A LEU* 4.1 20.6 - - + -
86A ILE* 3.7 43.5 - - + +
88A ALA* 5.5 3.8 - - + -
222A LEU* 4.0 8.5 - - + -
250A TRP* 5.9 2.7 - - + -
253A CYS* 3.1 17.6 + - + +
254A THR* 3.4 12.8 - - + +
255A ALA 3.2 0.2 - - - -
256A THR* 1.3 75.6 - - - +
258A ARG* 1.3 67.7 + - - +
260A HIS* 3.1 17.1 + - - +
261A THR 3.7 0.2 + - - -
262A VAL* 3.4 21.5 - - + +
265A ILE* 4.9 4.0 - - + -
282A LEU* 4.2 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 3.2 9.9 + - - +
255A ALA* 3.2 30.4 + - - +
257A LEU* 1.3 77.7 - - - +
259A GLU* 1.3 59.3 + - - +
260A HIS 2.8 6.8 + - - -
261A THR* 3.0 15.8 + - - -
262A VAL* 5.0 1.3 - - - -
281A GLU* 2.7 38.4 + - - +
282A LEU* 3.8 21.2 - - + +
283A ARG 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS* 4.6 12.2 + - - -
255A ALA* 3.2 9.7 + - - +
256A THR* 3.3 32.1 + - - +
257A LEU 3.3 0.2 - - - -
258A ARG* 1.3 76.3 - - - +
260A HIS* 1.3 64.7 + - + +
261A THR* 3.7 1.1 - - - -
----------------------------------------------------------
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