Contacts of the helix formed by residues 325 - 334 (chain A) in PDB entry 1WDR
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 TYR 325 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 4.3 19.1 - - + -
297A SER 4.9 0.2 - - - -
299A ILE* 4.8 2.6 + - - +
311A GLU* 2.7 41.7 + - - +
316A TYR* 3.5 38.0 - + + +
318A ASN* 3.4 15.5 - - + -
323A ASP* 3.0 3.4 + - - +
324A GLY* 1.3 81.1 - - - +
326A ARG* 1.3 66.8 + - - +
327A PRO* 3.2 2.5 - - - -
328A ILE* 2.9 24.3 + - + +
329A ALA* 3.1 11.3 + - - +
339A LEU* 4.9 4.7 - - + +
341A PHE* 4.9 3.1 - + - -
362A LEU* 3.6 20.1 - - + +
365A GLN* 3.6 18.2 - - + +
366A VAL* 3.6 36.6 - - + -
369A GLY* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP* 2.9 17.4 + - - +
325A TYR* 1.3 74.5 - - - +
327A PRO* 1.3 58.7 - - - +
329A ALA* 3.2 5.3 + - - +
330A ARG* 2.8 30.3 + - - +
369A GLY* 3.8 25.3 - - - +
372A ARG* 4.1 15.5 - - - +
373A GLU* 2.8 42.8 + - + +
476A ALA* 3.3 31.6 + - + +
478A LYS* 3.0 28.5 + - - +
480A THR* 3.7 22.0 + - - +
2000A SO4 2.7 45.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 3.8 24.3 - - + +
322A ARG* 5.4 0.9 - - - +
323A ASP 3.1 25.6 - - - +
324A GLY* 3.9 4.9 - - - +
325A TYR 3.4 5.8 - - - +
326A ARG* 1.3 88.2 - - - +
328A ILE* 1.3 56.7 + - - +
330A ARG* 3.4 2.6 + - + +
331A MET* 3.0 28.2 + - - +
473A LEU* 3.5 29.6 - - - +
474A LEU* 4.3 3.4 - - + -
476A ALA* 3.7 7.2 - - + +
477A THR* 3.7 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 4.4 14.1 - - + -
270A LEU* 6.5 1.1 - - + -
271A LEU* 3.7 20.9 - - + -
294A ILE* 4.0 27.1 - - + -
296A VAL* 4.2 15.7 - - + -
316A TYR* 4.0 29.4 - - + -
324A GLY 3.9 17.9 - - - +
325A TYR* 2.9 18.6 + - + +
327A PRO* 1.3 72.6 - - - +
329A ALA* 1.3 67.6 + - - +
331A MET* 3.1 8.2 + - + +
332A LEU* 3.0 25.4 + - + +
339A LEU* 4.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR 3.1 11.3 + - - +
326A ARG* 3.2 8.5 + - - +
328A ILE* 1.3 76.3 - - - +
330A ARG* 1.3 61.9 + - - +
332A LEU* 3.1 12.8 + - - +
333A SER 3.1 9.9 + - - -
339A LEU* 4.2 9.3 - - + +
369A GLY 4.1 8.1 - - - +
370A GLY* 3.9 20.4 - - - +
373A GLU* 4.1 5.8 - - + -
375A ILE* 3.6 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ARG* 2.8 20.0 + - - +
327A PRO* 3.7 7.2 - - + +
328A ILE 3.3 0.2 - - - -
329A ALA* 1.3 74.8 - - - +
331A MET* 1.3 62.5 + - - +
333A SER* 2.7 27.9 + - - +
373A GLU* 2.8 39.5 + - - +
468A ILE* 4.0 14.8 - - + +
472A VAL* 3.0 40.4 + - - +
473A LEU* 3.8 17.3 - - + +
475A GLU* 3.7 21.4 + - - +
476A ALA* 3.7 10.7 - - + +
2000A SO4 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 4.5 15.7 - - + -
271A LEU* 4.0 15.9 - - + +
274A GLY* 4.0 9.2 - - - -
275A ASP* 3.7 51.4 - - + +
278A LEU* 3.9 14.8 - - + -
294A ILE* 4.6 1.3 - - + -
327A PRO 3.0 14.9 + - - +
328A ILE* 3.5 14.4 - - + +
330A ARG* 1.3 76.6 - - - +
332A LEU* 1.3 79.2 + - + +
333A SER 3.3 0.5 + - - -
334A ARG* 3.5 12.4 - - - +
335A HIS* 3.4 11.7 - - - -
468A ILE* 5.4 0.4 - - - -
473A LEU* 3.6 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 3.5 28.7 - - + -
294A ILE* 3.7 29.4 - - + -
328A ILE* 3.0 18.8 + - + +
329A ALA 3.1 6.9 + - - +
331A MET* 1.3 79.4 - - + +
333A SER* 1.3 67.3 + - - +
334A ARG 3.2 0.2 - - - -
335A HIS* 2.9 14.3 + - - +
336A HIS 3.1 8.7 + - - -
337A ALA* 3.2 27.4 + - + +
338A ILE 4.0 1.3 - - - +
339A LEU* 3.5 48.5 - - + +
375A ILE* 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ALA 3.1 6.4 + - - -
330A ARG* 2.7 25.3 + - - +
332A LEU* 1.3 77.8 - - - +
334A ARG* 1.3 62.7 + - - +
336A HIS* 3.0 24.0 + - - +
373A GLU* 4.4 9.8 + - - -
374A ASP 5.4 0.7 - - - -
375A ILE* 3.6 24.9 - - - +
468A ILE* 4.3 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASP* 2.9 40.5 + - - -
279A ASP* 2.8 34.6 + - - -
330A ARG 4.0 0.2 + - - -
331A MET* 3.5 14.8 + - - +
333A SER* 1.3 81.3 + - - +
335A HIS* 1.3 70.1 + - + +
336A HIS* 3.3 6.1 - - - -
464A SER* 3.3 11.7 + - - -
465A ALA* 2.8 67.2 + - + +
466A PRO* 3.3 16.2 + - - +
467A LYS* 3.5 26.3 - - - +
468A ILE* 4.1 22.2 - - + +
----------------------------------------------------------
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