Contacts of the helix formed by residues 294 - 300 (chain A) in PDB entry 2RJC
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 294 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 2.8 10.2 + - - -
293A ALA* 1.3 71.0 - - - +
295A TRP* 1.3 63.5 + - - +
296A PHE* 3.3 3.8 + - - -
297A GLU* 3.4 12.7 + - - +
298A LYS* 3.2 40.4 + - - +
316A TRP* 3.3 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.5 10.5 + - + +
255A TYR* 3.3 44.9 - + - -
291A HIS* 3.4 38.6 + + + -
292A PRO* 3.0 25.0 + - + +
293A ALA 3.4 0.6 + - - -
294A GLY* 1.3 78.2 - - - +
296A PHE* 1.3 73.5 + - + +
298A LYS* 3.3 7.9 + - - -
299A THR* 2.6 45.0 + - + +
301A HIS* 3.2 40.6 - + + -
336A GLN* 3.6 30.6 - - + -
337A SER* 2.8 29.6 + - - -
371A VAL* 3.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.0 40.2 + - - +
255A TYR* 5.3 4.0 - - + -
294A GLY 3.3 0.9 - - - -
295A TRP* 1.3 85.4 - - + +
297A GLU* 1.3 99.5 + - + +
299A THR* 3.8 1.6 - - - -
300A GLY 3.1 10.7 + - - -
301A HIS* 2.9 59.1 + - + +
302A LYS 4.8 3.4 - - - +
303A LEU* 3.9 46.7 - - + -
314A PHE* 4.7 10.3 - + + -
316A TRP* 4.0 17.0 - + - -
239C LYS* 3.7 8.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLY* 3.6 11.4 - - - +
295A TRP 3.2 0.2 - - - -
296A PHE* 1.3 116.7 - - + +
298A LYS* 1.3 62.6 + - + +
299A THR 3.4 0.3 + - - -
300A GLY* 4.1 3.8 + - - -
314A PHE 4.7 1.6 - - - +
315A SER* 5.4 2.3 - - - -
316A TRP* 5.7 4.5 + - - -
235C LYS* 3.3 49.7 + - + +
236C ASN* 4.0 25.7 + - - +
239C LYS* 4.3 6.3 + - - +
263C VAL* 4.3 6.1 - - - +
265C GLY 4.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ALA 5.1 0.8 + - - -
294A GLY* 3.2 30.6 + - - +
295A TRP* 3.8 6.7 - - - +
297A GLU* 1.3 78.0 - - + +
299A THR* 1.3 63.3 + - + +
300A GLY 3.8 0.4 - - - -
330A LYS* 3.6 33.1 - - - +
338A HIS* 6.2 2.7 - - - +
263C VAL* 3.3 10.3 - - - +
264C CYS* 3.3 1.9 - - - -
265C GLY* 3.0 27.5 + - - +
508C SER 5.8 0.8 + - - -
510C THR 4.5 3.1 - - - +
511C GLY* 3.9 39.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TRP* 2.6 49.4 + - + +
296A PHE 3.6 0.5 + - - -
298A LYS* 1.3 83.6 - - + +
300A GLY* 1.3 61.8 + - - +
301A HIS* 2.6 38.2 + - - -
336A GLN 4.6 1.6 - - - +
337A SER* 3.7 17.9 - - - -
240C LEU* 4.0 10.4 - - - +
263C VAL* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PHE 3.1 4.1 + - - -
297A GLU 4.1 0.8 + - - -
298A LYS 3.8 0.2 - - - -
299A THR* 1.3 79.8 - - - +
301A HIS* 1.3 61.7 + - - +
238C PHE 3.5 22.2 - - - -
239C LYS* 3.4 12.3 - - - +
240C LEU* 3.1 29.7 + - - +
263C VAL* 3.5 16.8 - - - +
----------------------------------------------------------
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