Contacts of the helix formed by residues 309 - 316 (chain A) in PDB entry 1PG3
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 TRP 309 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 3.2 50.1 - + + -
166A PHE* 3.8 24.2 - + - -
262A LEU* 4.1 4.0 - - + -
263A TYR 5.4 2.5 - - - -
305A ALA* 5.4 0.2 - - + -
306A ASP* 3.1 33.5 + - + +
308A GLY* 1.3 84.5 - - - +
310A VAL* 1.3 69.1 + - + +
311A THR* 4.2 10.1 - - - +
312A GLY* 2.8 12.9 + - - +
313A HIS* 3.1 12.3 + - - -
525A HIS* 3.5 36.7 + + + -
526A ARG 6.0 4.5 - - - -
590A LEU* 4.2 4.0 - - + -
801A EDO 4.2 9.2 - - - -
990A COA 4.2 19.5 + - - -
999A PRX 5.7 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 5.2 6.5 - - + -
262A LEU* 3.4 25.9 - - + +
276A HIS* 5.2 0.7 - - - +
309A TRP* 1.3 72.9 - - - +
311A THR* 1.3 60.8 + - - +
313A HIS* 3.0 6.2 + - + +
314A SER* 2.8 33.9 + - - +
414A TRP* 3.5 30.7 - - + -
416A THR* 3.7 40.5 + - + +
419A GLY* 4.7 3.8 - - - +
999A PRX 3.7 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 311 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A CYS* 3.9 3.0 - - - -
305A ALA* 3.3 26.2 - - + -
309A TRP* 3.1 3.6 - - - +
310A VAL* 1.3 78.6 - - - +
312A GLY* 1.3 57.1 + - - +
315A TYR* 2.7 32.6 + - + -
316A LEU 3.6 0.9 + - - -
355A TYR* 3.7 30.3 - - + -
386A VAL* 4.1 4.6 - - + +
414A TRP* 3.7 16.2 - - + -
990A COA 3.5 14.2 - - - -
999A PRX 3.3 27.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ALA* 4.0 4.6 - - - +
306A ASP 3.3 24.5 + - - -
307A VAL* 4.1 8.3 - - - -
309A TRP 2.8 5.8 + - - -
311A THR* 1.3 79.8 - - - +
313A HIS* 1.3 63.6 + - - +
316A LEU* 2.9 34.4 + - - +
317A LEU* 3.4 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A MET* 3.8 14.6 - - + +
159A HIS* 3.8 15.3 + + - -
161A VAL* 3.6 31.6 + - + +
260A PHE* 3.6 36.5 - + + -
262A LEU* 3.6 26.0 - - + +
281A TYR* 3.5 10.3 - - - +
307A VAL 2.9 29.4 + - - -
308A GLY 4.2 1.1 - - - -
309A TRP 3.3 7.1 + - - -
310A VAL* 3.0 7.7 + - - +
312A GLY* 1.3 78.3 - - - +
314A SER* 1.3 58.5 + - - +
317A LEU* 4.2 1.0 - - - +
318A TYR* 3.2 36.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TYR* 2.7 23.8 + - - -
285A ALA* 4.3 4.9 - - - +
310A VAL* 2.8 20.4 + - - +
313A HIS* 1.3 74.8 - - - +
315A TYR* 1.3 87.7 + - - +
316A LEU 3.7 0.4 - - - -
319A GLY* 2.9 30.6 + - - +
414A TRP* 3.9 2.4 - - - -
419A GLY 2.7 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA* 3.8 7.9 - - - -
288A THR* 2.7 29.1 + - - -
289A PHE* 3.8 22.4 - + + -
293A PHE* 4.0 4.7 - + - -
301A TYR* 2.6 43.0 + - - +
303A CYS* 3.1 6.1 - - - +
311A THR 2.7 18.7 + - - +
314A SER* 1.3 95.9 - - - +
316A LEU* 1.3 58.1 + - - +
320A PRO* 3.9 7.6 - - - -
355A TYR* 3.9 12.3 - + + -
414A TRP* 3.5 22.4 - + - -
419A GLY 4.5 0.2 + - - -
420A GLY* 3.1 6.9 - - - -
421A PHE* 3.0 62.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 3.6 32.1 - - + -
303A CYS* 3.7 18.4 - - + +
305A ALA 3.7 8.7 - - - +
307A VAL* 4.2 12.6 - - + -
311A THR 3.6 0.2 + - - -
312A GLY* 2.9 24.1 + - - +
315A TYR* 1.3 79.0 - - - +
317A LEU* 1.3 67.7 + - + +
320A PRO* 3.3 3.1 - - - +
327A THR* 2.7 39.6 + - + +
328A LEU 3.4 29.4 - - - +
329A MET* 4.2 17.9 - - + -
----------------------------------------------------------
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