Contacts of the helix formed by residues 305 - 314 (chain E) in PDB entry 1OUQ
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 SER 305 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E GLY 3.2 4.8 + - - -
304E VAL* 1.3 74.8 - - - +
306E ILE* 1.3 67.0 + - - +
307E PRO* 3.2 17.5 - - - +
308E GLU* 2.9 36.0 + - - +
309E ILE* 3.1 10.4 + - - +
300F ALA 4.0 2.3 + - - -
303F GLY* 3.9 26.0 - - - -
304F VAL 4.8 0.7 - - - -
305F SER* 6.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304E VAL 5.2 3.1 - - - +
305E SER* 1.3 69.9 - - - +
307E PRO* 1.4 63.6 - - + +
309E ILE* 3.3 12.1 + - + +
310E MET* 2.7 48.6 + - + +
318E VAL* 4.2 9.9 - - + -
321E VAL* 5.3 7.2 - - + -
322E MET* 4.1 33.9 - - + -
325E ILE* 5.1 8.1 - - + -
331E GLU* 4.7 12.3 - - - +
306F ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E SER* 3.2 18.2 - - - +
306E ILE* 1.4 90.0 - - + +
308E GLU* 1.3 71.6 + - + +
310E MET* 3.2 6.4 + - + +
311E GLN* 2.9 25.9 + - - +
300F ALA* 4.6 20.9 - - + +
304F VAL 4.0 17.0 - - - +
305F SER* 5.6 0.7 - - - -
306F ILE* 3.6 31.0 - - + +
309F ILE* 5.0 6.1 - - + -
321F VAL* 5.8 2.9 - - + -
322F MET* 4.1 11.0 - - + +
325F ILE* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E MET* 5.6 0.2 - - - -
304E VAL* 3.3 23.3 - - + +
305E SER* 2.9 30.4 + - - +
307E PRO* 1.3 77.2 - - - +
309E ILE* 1.3 59.0 + - - +
311E GLN* 3.2 11.5 - - - +
312E ALA* 2.8 29.5 + - - +
300F ALA* 3.4 25.1 - - + +
301F ARG* 4.2 18.0 - - - +
303F GLY* 4.6 3.8 - - - -
327F ASN* 5.5 4.3 - - - +
328F LEU* 5.1 8.0 - - - +
333F GLY* 5.6 0.5 - - - -
334F ALA* 5.1 16.9 + - + +
337F ARG* 5.0 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 309 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E ALA* 4.6 7.2 - - - +
299E MET* 3.8 29.6 - - + +
300E ALA* 4.0 26.9 - - + +
304E VAL* 3.4 36.6 - - + +
305E SER 3.1 5.9 + - - +
306E ILE* 3.5 13.2 - - + +
308E GLU* 1.3 76.9 - - - +
310E MET* 1.3 65.8 + - - +
311E GLN 2.8 2.1 + - - -
312E ALA* 2.9 12.3 + - - +
313E GLY 3.0 10.6 + - - -
315E TRP* 3.9 9.3 - - + -
321E VAL* 3.9 22.4 - - + -
325E ILE* 5.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 310 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ILE* 2.7 43.4 + - + +
307E PRO 3.6 4.7 - - - +
309E ILE* 1.3 73.4 - - - +
311E GLN* 1.3 56.0 + - - +
314E GLY 3.1 4.0 + - - -
315E TRP* 2.7 59.2 + - + +
316E THR 3.6 8.1 - - - +
317E ASN 2.7 30.5 - - - +
318E VAL* 3.9 13.0 - - - -
321E VAL* 4.3 17.3 - - + -
306F ILE* 4.9 2.2 - - - -
318F VAL* 4.5 9.6 - - + -
322F MET* 3.5 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206E THR 4.2 14.9 - - - +
207E ALA* 4.5 3.8 - - - -
208E GLY 4.9 5.2 + - - -
211E LYS* 4.9 1.4 + - - +
307E PRO 2.9 14.5 + - - +
308E GLU* 3.2 11.0 - - - +
309E ILE 2.8 0.8 + - - -
310E MET* 1.3 76.7 - - - +
312E ALA* 1.3 82.6 + - + +
313E GLY 3.2 0.7 + - - -
314E GLY* 3.2 13.8 + - - -
315E TRP 5.4 0.2 - - - -
322F MET* 4.1 15.9 - - + -
325F ILE* 4.4 12.0 - - + +
326F ARG* 4.4 7.3 + - - -
327F ASN* 3.6 40.7 + - - +
328F LEU 5.9 0.4 + - - -
332F THR* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E LEU* 4.0 9.9 - - + +
211E LYS* 2.6 32.2 + - - +
299E MET* 3.9 25.1 - - + -
308E GLU 2.8 15.8 + - - +
309E ILE 2.9 3.8 + - - +
311E GLN* 1.3 88.7 - - - +
313E GLY* 1.3 55.9 + - - +
334F ALA* 4.4 15.0 - - + -
335F MET* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 313 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E LEU* 3.7 18.0 - - - +
207E ALA* 4.5 3.8 - - - +
211E LYS* 3.8 8.7 + - - -
292E ARG* 3.3 20.1 + - - -
309E ILE 3.0 10.5 + - - -
312E ALA* 1.3 80.4 - - - +
314E GLY* 1.3 58.5 + - - +
315E TRP* 3.2 26.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 314 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E ARG* 5.0 8.0 + - - -
206E THR* 3.4 23.4 + - - +
207E ALA* 4.0 19.8 + - - +
292E ARG* 5.0 2.5 - - - -
310E MET 3.1 6.1 + - - -
311E GLN 3.2 9.9 + - - -
313E GLY* 1.3 77.8 - - - +
315E TRP* 1.3 66.6 + - - +
117H A 4.5 6.9 + - - -
----------------------------------------------------------
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