Contacts of the helix formed by residues 353 - 363 (chain A) in PDB entry 3DTC
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 353 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLY 3.6 3.4 + - - -
352A ILE* 1.3 75.9 - - - +
354A GLY* 1.3 68.6 + - - +
355A LEU* 3.4 16.1 + - - +
356A ALA* 3.0 32.5 + - + +
357A VAL* 2.9 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 3.5 25.2 - - - -
352A ILE 3.2 4.8 + - - -
353A ASP* 1.3 74.1 + - - +
355A LEU* 1.3 62.7 + - - +
357A VAL* 2.9 20.4 + - - +
358A ALA 2.9 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 3.5 29.5 - - + +
353A ASP* 3.4 13.8 + - - +
354A GLY* 1.3 74.6 - - - +
356A ALA* 1.3 57.4 + - - +
358A ALA* 3.3 8.4 + - + +
359A TYR* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 4.1 13.2 - - + -
353A ASP* 3.0 29.7 + - + +
355A LEU* 1.3 73.8 - - - +
357A VAL* 1.3 61.5 + - - +
359A TYR* 3.7 4.9 - - - +
360A GLY* 2.8 27.0 + - - -
366A LEU* 4.0 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 4.1 5.6 - - + +
314A ALA* 3.9 22.9 - - + +
349A PHE* 3.6 39.3 - - + +
352A ILE* 3.6 29.2 - - + +
353A ASP 2.9 16.5 + - - +
354A GLY* 2.9 9.5 + - - +
356A ALA* 1.3 75.4 - - - +
358A ALA* 1.3 59.9 + - - +
361A VAL* 2.8 37.9 + - + +
366A LEU* 3.6 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR* 3.5 35.4 - - + +
321A ILE* 3.6 29.2 - - + +
354A GLY 2.9 7.0 + - - +
355A LEU* 3.5 13.2 - - + +
357A VAL* 1.3 77.9 - - - +
359A TYR* 1.3 57.1 + - - +
362A ALA* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU 3.0 17.0 + - - +
356A ALA* 3.7 6.7 - - - +
358A ALA* 1.3 76.3 - - - +
360A GLY* 1.3 55.5 + - - +
362A ALA* 4.7 2.9 - - - -
363A MET* 2.7 71.8 + - + +
365A LYS* 3.3 33.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA 2.8 13.7 + - - -
359A TYR* 1.3 80.3 - - - +
361A VAL* 1.3 61.3 + - - +
363A MET 3.5 0.3 - - - -
364A ASN 3.3 2.3 + - - -
365A LYS* 3.1 38.1 + - - -
366A LEU* 3.3 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TYR 5.1 3.6 - - - +
314A ALA 5.6 1.6 - - - +
316A MET 4.1 8.1 - - - +
318A PRO* 3.8 25.1 - - + +
321A ILE* 3.8 20.6 - - + -
333A TRP* 4.2 13.5 - - + +
349A PHE* 3.9 28.0 - - + -
357A VAL* 2.8 30.0 + - + +
360A GLY* 1.3 69.7 - - - +
362A ALA* 1.3 58.9 + - - +
364A ASN* 2.7 27.4 + - - -
366A LEU* 4.0 16.7 - - + +
367A ALA* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A PRO* 4.3 8.8 - - - +
321A ILE* 4.0 19.1 - - + -
322A ARG* 2.9 45.5 + - + +
358A ALA 2.9 22.3 + - - +
359A TYR* 3.9 2.9 - - - +
361A VAL* 1.3 74.3 - - - +
363A MET* 1.3 67.0 + - - +
364A ASN* 2.8 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 6.1 3.1 - - - -
359A TYR* 2.7 57.3 + - + +
360A GLY 3.5 1.3 - - - -
362A ALA* 1.3 77.9 - - - +
364A ASN* 1.3 53.3 + - - +
365A LYS* 2.5 56.5 + - + +
----------------------------------------------------------
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