Contacts of the helix formed by residues 329 - 334 (chain A) in PDB entry 2WO6
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 329 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLN* 3.0 19.3 + - - -
327A TYR 3.6 2.0 + - - -
328A ARG* 1.3 76.3 - - - +
330A PRO* 1.3 76.4 - - - +
331A GLU* 3.7 16.5 - - - -
332A VAL* 3.3 15.9 + - - +
333A LEU* 3.1 21.9 + - - +
342A ILE* 3.5 12.2 - - - +
345A TRP* 3.6 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 1.3 85.4 - - - +
331A GLU* 1.3 69.9 + - - +
333A LEU* 3.4 11.2 + - + +
334A LEU* 2.9 45.3 + - + +
345A TRP* 3.6 34.5 - - + -
370A MET* 4.5 7.2 - - + -
373A ILE* 4.8 2.9 - - + -
380A PRO* 5.6 0.4 - - + -
384A ILE* 6.4 0.7 - - + -
462A TYR* 3.6 40.6 - - + +
467A ARG* 3.9 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 3.7 11.4 - - - +
330A PRO* 1.3 79.3 - - - +
332A VAL* 1.3 56.5 + - - +
334A LEU* 3.4 3.1 + - - -
335A GLY 3.2 5.4 + - - -
336A MET* 2.7 57.0 + - + +
337A PRO 4.2 7.0 - - - +
338A TYR* 4.1 9.9 - - + -
339A ASP* 5.3 0.5 + - - +
341A ALA* 4.4 0.3 - - - +
342A ILE* 3.6 20.3 + - + +
384A ILE* 6.1 0.9 - - + -
462A TYR 4.3 2.8 - - - +
464A PRO* 3.8 26.0 - - + +
467A ARG* 2.6 46.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR 4.6 1.8 - - - +
320A GLN 3.3 26.8 - - - +
322A ILE* 3.7 34.8 - - + +
323A GLN* 3.7 8.5 - - - +
328A ARG* 3.8 11.4 - - + -
329A SER* 3.3 22.1 + - - +
330A PRO 3.2 0.2 - - - -
331A GLU* 1.3 74.1 - - - +
333A LEU* 1.3 67.5 + - - +
334A LEU 3.0 1.8 - - - -
335A GLY* 2.9 14.6 + - - +
336A MET 4.6 3.4 - - - +
338A TYR* 3.8 31.9 - - + -
342A ILE* 4.2 1.8 - - + -
366A GLU* 4.8 0.2 - - - +
390A LYS* 4.1 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 3.7 19.7 - - - +
329A SER 3.1 21.9 + - - +
330A PRO 3.8 3.8 - - - +
332A VAL* 1.3 76.4 - - - +
334A LEU* 1.3 59.2 + - - +
366A GLU* 3.6 53.8 - - + +
369A GLN* 4.1 14.1 - - + -
370A MET* 3.9 22.9 - - + -
373A ILE* 3.5 32.5 - - + -
390A LYS* 3.0 21.5 + - - -
394A PHE* 3.5 16.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PRO* 2.9 29.3 + - + +
331A GLU 3.8 3.8 - - - +
332A VAL 3.0 0.4 - - - -
333A LEU* 1.3 77.9 - - - +
335A GLY* 1.3 61.3 + - - +
336A MET* 4.0 4.9 - - + -
370A MET* 3.8 15.0 - - + -
380A PRO* 5.1 4.0 - - + -
384A ILE* 4.2 16.2 - - + -
385A LEU* 3.9 29.4 - - + -
388A ALA* 3.6 25.1 - - + -
389A PRO* 3.3 6.9 - - - +
390A LYS* 3.0 28.6 + - - -
391A ALA* 3.9 10.1 - - - -
394A PHE* 3.9 24.9 - - + -
395A PHE* 4.4 0.9 - - + -
----------------------------------------------------------
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