Contacts of the helix formed by residues 303 - 315 (chain A) in PDB entry 1I4A
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 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 1.3 80.4 - - - +
304A GLY* 1.3 65.4 + - - +
306A TYR* 3.4 14.0 - - - +
307A ARG* 3.1 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER* 1.3 73.9 - - - +
305A ASP* 1.3 66.7 + - - -
306A TYR* 3.0 2.9 - - - -
307A ARG* 3.1 17.3 + - - +
308A LYS* 3.2 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 2.4 41.3 - - - +
34A ASP* 3.2 21.9 - - - +
37A ILE* 3.9 4.5 - - + +
75A PHE* 3.6 19.8 - - + -
304A GLY* 1.3 70.6 - - - -
306A TYR* 1.3 64.7 + - - +
308A LYS* 3.1 11.8 + - - +
309A VAL* 3.0 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.4 35.7 - - + -
75A PHE* 3.7 21.4 - - + +
78A VAL* 3.4 32.5 - - + -
264A ASP* 2.8 30.8 + - - +
267A LEU* 3.7 12.0 - - - +
268A ILE* 3.5 17.1 - - + +
302A THR* 3.7 27.8 - - + -
303A SER 3.4 11.7 - - - +
304A GLY* 5.1 0.2 - - - -
305A ASP* 1.3 78.2 - - - +
307A ARG* 1.3 59.1 + - - +
309A VAL* 2.9 23.2 - - - +
310A LEU* 3.1 18.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ILE* 4.4 0.7 - - + +
299A LYS* 3.0 48.7 + - - +
302A THR* 3.2 38.9 + - - +
303A SER* 3.1 25.8 + - - +
304A GLY 3.1 7.0 + - - +
306A TYR* 1.3 78.5 - - - +
308A LYS* 1.3 70.1 + - + +
310A LEU* 3.2 4.8 + - - +
311A LEU* 2.8 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 5.6 2.5 - - - +
37A ILE* 4.1 12.3 - - + -
295A TYR* 5.2 3.0 + - - -
304A GLY 3.2 11.6 + - - +
305A ASP* 3.1 20.1 + - - +
307A ARG* 1.3 94.1 - - + +
309A VAL* 1.3 61.8 + - - +
311A LEU* 3.4 19.9 + - - +
312A ILE* 3.1 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.5 7.5 - - + +
41A ALA* 4.6 7.9 - - + -
75A PHE* 4.3 10.1 - - + -
78A VAL* 3.5 28.7 - - + -
79A ILE* 4.4 7.0 - - + -
82A MET* 3.4 36.6 - - + -
305A ASP 3.0 12.2 + - - +
306A TYR* 2.9 25.4 - - - +
308A LYS* 1.3 76.3 - - - +
310A LEU* 1.3 58.5 - - + +
312A ILE* 3.2 10.5 + - - +
313A LEU* 2.9 32.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
78A VAL* 3.7 30.1 - - + -
267A LEU* 3.7 22.4 - - + -
268A ILE* 4.8 5.4 - - + -
271A MET* 3.9 30.2 - - + +
298A ILE* 3.8 21.9 - - + +
302A THR* 4.0 7.9 - - + +
306A TYR* 3.1 32.7 + - + +
307A ARG 3.2 8.0 + - - +
309A VAL* 1.3 84.9 - - + +
311A LEU* 1.3 61.3 + - - +
313A LEU* 3.2 12.3 + - + +
314A CYS* 3.0 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 3.5 71.9 - - + +
298A ILE* 3.7 17.9 - - + -
299A LYS* 3.9 13.5 - - + +
307A ARG* 2.8 39.9 + - + +
308A LYS* 3.9 21.8 - - - +
309A VAL 3.4 0.2 - - - -
310A LEU* 1.3 73.6 - - - +
312A ILE* 1.3 58.4 + - + +
314A CYS* 3.1 7.0 - - - +
315A GLY* 3.0 22.3 + - - -
316A GLY 4.1 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.5 32.3 - - + -
41A ALA* 3.7 30.7 - - + +
42A TYR* 3.6 36.8 - - + +
308A LYS* 3.1 19.0 + - + +
309A VAL 3.5 7.0 - - - +
310A LEU 3.2 0.6 - - - -
311A LEU* 1.3 74.1 - - + +
313A LEU* 1.3 65.7 + - + +
314A CYS 3.0 1.6 - - - -
315A GLY* 3.1 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ALA* 5.3 7.4 - - - +
48A ARG* 4.6 8.3 - - - +
78A VAL* 5.6 1.1 - - + -
82A MET* 4.3 31.6 - - + -
271A MET* 3.9 39.8 - - + +
272A VAL* 4.1 17.9 - - + -
275A ALA* 3.9 26.7 - - + +
279A MET* 3.5 13.9 - - - +
309A VAL* 2.9 24.1 + - + +
310A LEU* 3.2 15.2 + - + +
312A ILE* 1.3 76.9 - - + +
314A CYS* 1.3 63.2 + - - +
315A GLY* 4.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A MET* 3.6 13.4 - - + +
279A MET* 3.2 11.4 - - - +
280A LEU* 5.9 0.2 - - - +
283A ARG* 3.2 31.4 + - - -
294A LEU* 3.8 22.7 - - - -
295A TYR* 3.7 32.8 - - + -
298A ILE* 4.2 3.6 - - + -
310A LEU 3.0 12.4 + - - +
311A LEU* 3.1 15.3 - - - +
313A LEU* 1.3 78.3 - - - +
315A GLY* 1.3 57.2 + - - +
316A GLY 4.0 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 3.5 12.9 + - - -
311A LEU 3.0 8.1 + - - -
312A ILE* 3.1 13.8 + - - -
313A LEU 4.5 0.2 - - - -
314A CYS* 1.3 78.0 - - - +
316A GLY* 1.3 56.0 + - - +
----------------------------------------------------------
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