Contacts of the helix formed by residues 362 - 369 (chain A) in PDB entry 3PEI
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 GLY 362 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLY* 5.4 8.7 - - - -
270A MSE 3.3 31.5 - - - +
272A MSE 4.4 5.1 - - - -
361A THR* 1.3 68.1 - - - +
363A ALA* 1.3 65.3 + - - +
364A MSE 3.0 2.2 - - - -
365A ILE* 2.9 20.7 + - - +
366A ILE* 3.4 13.1 + - - +
495A K 4.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A THR* 3.9 5.1 - - - +
362A GLY* 1.3 77.0 - - - +
364A MSE 1.3 55.3 + - - +
366A ILE* 3.2 10.3 + - - +
367A SER* 2.8 33.0 + - - +
424A ARG 5.2 3.4 - - - +
427A GLY* 4.6 4.7 - - - +
428A SER* 3.3 28.0 - - - +
495A K 4.1 15.2 - - - -
514A CL 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A THR* 3.4 19.6 + - - +
362A GLY 3.0 0.4 - - - -
363A ALA* 1.3 78.6 - - - +
365A ILE* 1.3 58.3 + - - +
367A SER* 3.7 3.5 - - - -
368A LEU* 2.7 43.3 + - + +
369A GLY 3.5 3.6 + - - +
372A TYR 5.2 4.0 - - - +
374A GLY* 3.8 20.9 - - - +
376A PHE* 4.0 15.3 - - + -
400A LEU* 4.0 9.4 - - + -
428A SER* 3.3 37.7 + - - +
448A ASP* 3.4 48.2 - - + +
450A ALA* 4.4 4.0 - - + -
451A GLY* 4.8 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A MSE 3.9 32.5 - - + -
272A MSE 4.9 0.9 - - + -
362A GLY* 2.9 8.3 + - - +
364A MSE 1.3 77.3 - - - +
366A ILE* 1.3 62.2 + - + +
369A GLY* 2.8 27.7 + - - +
450A ALA* 4.0 23.8 - - + +
451A GLY* 3.6 24.0 - - - +
454A MSE 6.1 1.3 - - + -
455A GLY 4.5 7.6 - - - +
456A ASP* 3.6 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLY 3.4 10.7 + - - +
363A ALA* 3.2 9.3 + - - +
365A ILE* 1.3 81.7 - - + +
367A SER* 1.3 64.3 + - - +
369A GLY 4.8 0.2 + - - -
495A K 3.9 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 2.8 19.5 + - - +
364A MSE 3.7 11.5 - - - -
366A ILE* 1.3 80.6 - - - +
368A LEU* 1.3 76.8 - - - +
400A LEU* 5.2 8.8 - - - +
428A SER* 4.4 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A MSE 2.7 23.5 + - - +
367A SER* 1.3 89.9 - - - +
369A GLY* 1.3 64.2 + - - +
370A ASP 3.9 0.2 + - - -
371A ALA* 4.2 2.8 + - - +
372A TYR* 3.9 40.4 - - + +
374A GLY* 3.7 31.6 - - - +
398A TRP* 3.8 37.5 - - + -
400A LEU* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A MSE 3.5 5.0 + - - +
365A ILE* 2.8 29.2 + - - -
366A ILE 4.8 0.2 + - - -
367A SER 3.9 0.2 - - - -
368A LEU* 1.3 77.8 - - - +
370A ASP* 1.3 61.7 + - - -
372A TYR 3.8 8.0 - - - +
451A GLY* 3.7 16.0 - - - -
456A ASP* 4.1 15.3 - - - -
----------------------------------------------------------
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