Contacts of the helix formed by residues 357 - 367 (chain A) in PDB entry 3ITX
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 ASP 357 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG 5.3 4.9 - - - +
355A LEU 3.3 5.2 + - - +
356A VAL* 1.3 71.2 - - - +
358A ARG* 1.3 57.0 + - - +
359A ALA* 3.2 11.8 + - - +
360A ALA* 2.9 32.4 + - + +
361A LEU* 3.0 27.4 + - - +
376A THR* 3.7 13.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASN* 2.9 40.5 + - - +
310A VAL* 3.5 29.4 - - + +
311A ASP* 4.0 16.9 + - - +
314A ALA* 4.2 25.4 - - + -
353A ALA* 2.8 27.5 + - - +
354A LEU 5.7 0.4 + - - -
356A VAL* 2.9 32.7 + - - +
357A ASP* 1.3 68.9 + - - +
359A ALA* 1.3 64.8 + - - +
361A LEU* 3.8 14.7 - - - +
362A SER* 3.0 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 3.2 8.4 + - - +
358A ARG* 1.3 80.0 - - - +
360A ALA* 1.3 62.0 + - - +
362A SER* 2.6 22.5 + - - -
363A GLY* 3.3 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASP* 2.9 32.4 + - + +
359A ALA* 1.3 76.2 - - - +
361A LEU* 1.3 64.1 + - - +
363A GLY* 3.1 3.7 + - - -
364A TYR* 3.0 46.2 + - + +
376A THR* 4.6 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ASN* 4.9 3.4 - - - +
311A ASP* 6.1 0.7 - - - +
356A VAL* 4.2 9.0 - - + -
357A ASP 3.0 17.0 + - - +
358A ARG* 3.8 19.5 - - - +
360A ALA* 1.3 77.1 - - - +
362A SER* 1.3 62.9 + - - +
364A TYR* 3.2 3.9 + - - -
365A GLN* 2.9 45.8 + - - +
373A ALA* 3.6 29.2 - - + +
376A THR* 4.0 11.4 - - + +
377A LEU* 4.0 23.3 - - + -
188C GLY* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ARG 3.0 14.7 + - - -
359A ALA* 2.6 25.5 + - - -
361A LEU* 1.3 76.2 - - - +
363A GLY* 1.3 60.9 + - - +
365A GLN* 3.3 13.1 + - - +
366A GLU* 3.0 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA 3.3 4.1 + - - -
360A ALA* 3.1 8.2 + - - -
362A SER* 1.3 83.5 + - - +
364A TYR* 1.3 61.6 + - - +
365A GLN 3.3 0.2 + - - -
366A GLU* 3.3 6.6 + - - +
367A ASP* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ALA* 3.0 34.7 + - + +
361A LEU* 3.9 3.6 - - - +
363A GLY* 1.3 77.0 - - - +
365A GLN* 1.3 61.0 + - - +
367A ASP* 2.9 13.4 - - - +
368A ASN* 3.2 0.9 + - - -
369A ASP* 2.8 62.8 + - + +
372A MET* 3.5 40.1 - - + +
373A ALA* 3.9 12.0 - - + +
376A THR* 3.4 27.1 - - - -
379A ARG* 5.4 1.7 + - - -
189C GLN 4.9 0.7 - - - +
407D ARG* 5.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 2.9 45.9 + - + +
362A SER* 3.7 12.5 - - - +
364A TYR* 1.3 76.3 - - - +
366A GLU* 1.3 65.5 + - - +
368A ASN* 3.2 14.2 + - - +
373A ALA* 4.9 0.2 - - + -
149C THR* 3.6 14.8 - - + +
188C GLY* 3.0 30.0 + - - +
189C GLN 3.8 16.0 - - - +
190C SER* 3.6 16.7 + - - -
191C ASN* 3.7 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A SER 3.0 17.0 + - - +
363A GLY* 3.7 6.3 - - - +
365A GLN* 1.3 77.4 - - - +
367A ASP* 1.3 58.2 + - + +
368A ASN* 3.9 0.7 + - - -
149C THR* 2.9 54.7 + - - +
150C ASN* 5.2 0.9 - - - -
198C ARG* 5.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A GLY 2.9 25.6 + - - +
364A TYR* 2.9 27.3 - - - +
366A GLU* 1.3 75.8 - - + +
368A ASN* 1.3 71.3 + - - +
369A ASP* 3.4 18.4 - - - +
143C TYR* 5.5 0.7 - - - -
----------------------------------------------------------
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