Contacts of the helix formed by residues 298 - 311 (chain A) in PDB entry 2G9Y
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 THR 298 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG* 3.7 37.2 - - - +
293A ASN 5.7 1.1 - - - +
296A VAL 4.4 4.5 - - - +
297A PRO* 1.3 76.8 - - - +
299A LEU* 1.3 61.3 + - - +
300A ALA* 3.5 8.7 + - - +
301A GLN* 2.7 46.1 + - - +
302A MET* 2.9 29.4 + - - +
344A ASP* 4.7 2.7 - - - -
347A GLU* 5.2 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.9 15.9 - - + -
148A THR* 4.0 13.6 - - + +
298A THR* 1.3 75.4 - - - +
300A ALA* 1.3 58.5 + - - +
302A MET* 3.3 8.4 + - + +
303A THR* 2.8 33.1 + - - -
321A VAL* 3.4 23.1 - - + -
322A GLU 3.9 10.3 - - - +
323A GLY* 3.9 24.5 - - - -
344A ASP* 3.4 32.1 + - - +
345A LEU* 4.1 17.0 - - + -
348A ALA* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A THR* 3.2 7.2 + - - +
299A LEU* 1.3 78.3 - - - +
301A GLN* 1.3 58.1 + - - +
303A THR* 3.5 2.4 + - - -
304A ASP* 3.0 28.4 + - - +
344A ASP* 4.8 2.4 + - - -
347A GLU* 3.9 29.8 - - + +
348A ALA* 4.0 12.7 - - - +
351A ARG* 3.1 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ALA* 5.3 5.3 - - - +
243A LEU* 5.3 2.0 - - + +
294A ASP* 5.7 0.7 - - - +
296A VAL 4.1 1.7 - - - +
297A PRO* 3.2 15.4 - - + +
298A THR* 2.7 52.8 + - - +
299A LEU 3.2 0.2 - - - -
300A ALA* 1.3 76.3 - - + +
302A MET* 1.3 65.2 + - - +
304A ASP* 3.3 5.8 + - - +
305A LYS* 3.0 25.9 + - - +
351A ARG* 4.8 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.9 10.3 - - + +
147A SER 4.0 12.3 - - - +
148A THR* 4.5 3.1 - - + -
204A LEU* 3.6 33.8 - - + +
243A LEU* 4.4 4.3 - - + -
259A PHE* 3.8 30.5 - - - -
264A MET* 3.9 26.7 - - + +
297A PRO* 3.9 15.9 - - + -
298A THR 2.9 21.9 + - - +
299A LEU* 3.8 24.7 - - + +
301A GLN* 1.3 76.8 - - - +
303A THR* 1.3 57.2 + - - +
305A LYS* 3.9 2.9 - - - +
306A ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 5.5 0.9 - - + -
48A LEU* 5.3 0.7 - - + -
146A VAL* 4.9 1.1 - - - +
299A LEU 2.8 23.3 + - - -
300A ALA* 3.6 8.3 - - - -
302A MET* 1.3 78.2 - - - +
304A ASP* 1.3 56.9 + - - +
306A ALA* 3.3 5.8 + - - +
307A ILE* 3.0 52.6 + - + +
319A LEU* 4.4 2.6 - - + +
321A VAL* 3.6 38.1 - - + +
348A ALA* 3.7 23.8 - - - +
351A ARG* 4.3 5.4 - - + -
352A ALA* 4.6 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA 3.0 13.6 + - - +
301A GLN* 3.3 5.1 + - - +
303A THR* 1.3 76.8 - - - +
305A LYS* 1.3 62.1 + - - +
307A ILE* 3.4 9.7 + - - +
308A GLU* 3.0 23.6 + - - +
351A ARG* 2.8 56.7 + - - +
355A PHE* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 5.1 1.8 - - + -
243A LEU* 3.3 47.1 - - + -
244A ASN* 3.3 19.1 + - - +
246A VAL* 3.0 26.6 + - - -
255A LEU* 5.4 0.2 - - + -
301A GLN 3.0 16.8 + - - +
302A MET* 3.9 7.2 - - - +
304A ASP* 1.3 76.8 - - - +
306A ALA* 1.3 63.0 + - - +
308A GLU* 2.9 34.6 + - - +
309A LEU* 3.0 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 4.2 5.2 - - + -
202A VAL* 4.0 28.0 - - + -
204A LEU* 4.9 0.6 - - - +
302A MET 3.0 18.4 + - - +
303A THR* 3.6 4.5 - - - +
304A ASP 3.3 0.2 - - - -
305A LYS* 1.3 74.5 - - - +
307A ILE* 1.3 55.0 + - - +
309A LEU* 3.3 2.9 + - - +
310A LEU* 2.7 44.7 + - + +
319A LEU* 4.0 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.8 23.6 - - + -
303A THR* 3.0 36.9 + - + +
304A ASP* 3.7 10.3 - - - +
306A ALA* 1.3 75.4 - - - +
308A GLU* 1.3 58.8 + - - +
310A LEU* 4.6 3.8 - - - -
311A SER* 2.8 36.7 + - - +
317A PHE* 4.6 6.0 - - + -
319A LEU* 3.9 15.7 - - + -
351A ARG 4.2 9.6 - - - +
352A ALA* 4.2 0.7 - - - -
355A PHE* 3.4 52.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL 4.4 1.7 - - - +
247A THR* 5.1 2.8 - - - +
304A ASP 3.0 14.0 + - - +
305A LYS* 2.9 44.1 + - - +
307A ILE* 1.3 77.7 - - - +
309A LEU* 1.3 71.4 + - + +
311A SER* 3.0 20.1 + - - -
312A LYS* 3.8 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A VAL* 4.2 8.1 - - + -
204A LEU* 6.5 0.2 - - + -
246A VAL* 3.9 12.3 - - + +
247A THR 3.7 9.0 - - - +
248A GLU* 3.5 37.5 - - - +
249A ALA* 4.0 27.6 + - + +
255A LEU* 3.5 30.7 - - + -
305A LYS* 3.0 29.1 + - + +
306A ALA* 3.9 2.0 - - - +
308A GLU* 1.3 94.5 - - + +
310A LEU* 1.3 62.8 + - - +
312A LYS* 3.7 15.3 - - - +
313A ASN 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 3.8 10.5 - - + +
143A THR 3.3 35.9 - - - +
144A GLY* 3.8 13.9 - - - +
201A ASP* 4.0 5.2 - - + -
202A VAL* 3.8 17.7 - - + -
249A ALA 5.9 0.4 - - - +
306A ALA* 2.7 35.9 + - + +
307A ILE 4.1 1.1 - - - +
309A LEU* 1.3 71.2 - - - +
311A SER* 1.3 56.8 + - - +
312A LYS 3.0 10.6 + - - -
313A ASN* 3.1 21.5 + - - +
317A PHE* 3.7 27.9 - - + -
319A LEU* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 5.9 0.2 - - - -
307A ILE* 2.8 26.9 + - - +
308A GLU* 3.0 13.5 + - - -
310A LEU* 1.3 68.1 - - - +
312A LYS* 1.3 63.8 + - - +
313A ASN 3.0 10.9 + - - +
314A GLU* 5.2 0.7 - - - -
317A PHE* 3.8 19.4 - - - -
355A PHE* 4.3 17.8 - - - -
----------------------------------------------------------
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