Contacts of the helix formed by residues 295 - 305 (chain A) in PDB entry 4IRI
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 GLN 295 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLN 4.2 7.7 + - - +
294A ILE* 1.3 80.1 - - - +
296A LEU* 1.3 59.0 + - - +
297A TRP* 2.7 50.3 + - + +
298A GLN* 2.6 37.8 + - - +
299A PHE* 2.9 11.1 + - - +
334A TRP* 3.9 2.9 - - - -
381A ALA* 4.5 5.8 + - - +
15C A 3.8 27.5 + - - +
16C C 3.2 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN* 1.3 71.4 - - - +
297A TRP* 1.3 64.0 + - - +
299A PHE* 3.0 6.0 + - + +
300A LEU* 2.8 42.0 + - + +
334A TRP* 3.5 46.5 - - + +
348A LEU* 4.1 19.3 - - + +
351A ALA* 3.8 27.6 - - + -
352A LEU* 4.0 26.5 - - + +
355A TYR* 3.2 10.7 + - - +
16C C 3.0 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A GLN* 2.7 35.6 + - + +
296A LEU* 1.3 75.3 - - - +
298A GLN* 1.3 98.4 + - + +
300A LEU* 3.5 6.3 + - - +
301A LEU* 3.2 37.7 + - + +
355A TYR* 3.0 48.1 + + + -
360A ILE* 4.1 15.1 - - + +
373A PHE* 3.9 19.7 - - + -
378A ILE* 3.4 27.1 - - + -
381A ALA* 3.7 32.4 - - + +
382A LEU* 3.8 35.0 - - + -
16C C 4.0 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLN 4.7 1.0 - - - +
294A ILE* 3.5 20.3 - - + +
295A GLN* 2.6 44.2 + - - +
297A TRP* 1.3 114.6 - - + +
299A PHE* 1.3 55.1 + - - +
301A LEU* 3.4 8.0 + - - +
302A GLU* 3.1 24.3 + - - +
381A ALA 5.5 1.0 + - - -
382A LEU* 5.0 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 3.8 13.7 - - + -
295A GLN 2.9 8.0 + - - +
296A LEU* 3.5 14.4 - - + +
298A GLN* 1.3 77.2 - - - +
300A LEU* 1.3 75.7 + - + +
302A GLU* 3.1 19.1 + - - +
303A LEU* 3.1 47.6 + - + +
330A VAL* 4.4 4.9 - - + -
333A ARG* 4.0 14.8 - - + -
334A TRP* 3.6 57.2 - + + -
337A ARG* 4.0 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 2.8 33.5 + - + +
297A TRP 3.8 4.3 - - - +
299A PHE* 1.3 83.6 - - + +
301A LEU* 1.3 58.1 + - - +
303A LEU* 3.2 7.0 + - + +
304A LEU* 2.9 34.8 + - + +
313A ILE* 3.9 16.6 - - + +
322A PHE* 4.4 18.4 - - + -
324A MET* 4.4 8.3 - - + -
330A VAL* 3.9 28.7 - - + -
348A LEU* 5.4 0.4 - - + -
352A LEU* 3.9 29.2 - - + -
361A MET* 4.5 6.3 - - + -
373A PHE* 4.0 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TRP* 3.2 34.4 + - + +
298A GLN* 3.4 9.4 - - - +
299A PHE 3.1 0.4 - - - -
300A LEU* 1.3 76.1 - - - +
302A GLU* 1.3 56.0 + - - +
304A LEU* 3.1 2.4 + - + +
305A SER* 2.7 37.4 + - - -
315A TRP* 3.8 22.6 - - + -
373A PHE* 3.6 33.2 - - + -
378A ILE* 5.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ILE* 4.1 8.7 - - - +
298A GLN 3.1 10.8 + - - +
299A PHE* 3.2 19.3 - - - +
301A LEU* 1.3 77.4 - - - +
303A LEU* 1.3 69.2 + - + +
305A SER* 2.4 29.4 + - - +
306A ASP* 3.6 3.3 + - - +
309A ASN* 4.6 1.9 + - - -
337A ARG* 2.7 43.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 3.1 46.0 + - + +
300A LEU* 3.4 9.9 - - + +
302A GLU* 1.3 89.1 - - + +
304A LEU* 1.3 54.5 + - - +
306A ASP 2.9 27.0 + - - +
309A ASN* 3.0 24.1 + - - +
312A CYS* 4.5 13.5 - - - -
313A ILE* 3.7 26.2 - - + +
330A VAL* 4.5 13.9 - - + -
333A ARG* 3.7 30.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 2.9 25.6 + - + +
301A LEU* 3.6 4.9 - - + +
303A LEU* 1.3 75.2 - - - +
305A SER* 1.3 62.2 + - - +
306A ASP 3.2 5.8 + - - +
307A SER* 4.7 2.1 + - - -
313A ILE* 3.8 20.6 - - + -
314A THR* 3.5 15.0 - - - -
315A TRP* 3.5 73.1 + - + +
322A PHE* 3.8 15.0 - - + -
373A PHE* 3.5 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU 2.7 14.4 + - - -
302A GLU* 2.4 26.8 + - - +
304A LEU* 1.3 76.9 - - - +
306A ASP* 1.3 57.3 + - - +
307A SER 4.3 0.3 + - - -
315A TRP* 5.2 1.8 - - - +
----------------------------------------------------------
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