Contacts of the helix formed by residues 326 - 342 (chain A) in PDB entry 2W3C
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 PRO 326 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 3.6 47.6 - - + +
277A VAL* 4.3 10.1 - - + -
324A GLY 4.0 3.3 - - - +
325A VAL* 1.4 86.3 - - + +
327A ALA* 1.3 66.0 + - - +
328A ASP* 3.2 16.6 - - - +
329A ILE* 3.1 13.0 + - + +
330A LEU* 3.1 17.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A VAL 3.4 3.2 + - - -
326A PRO* 1.3 72.5 - - - +
328A ASP* 1.3 57.3 + - - +
330A LEU* 3.4 12.6 + - + +
331A THR* 2.9 33.2 + - - +
378A PRO* 6.1 5.6 - - + -
381A LEU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.6 15.3 - - - +
281A HIS* 3.2 23.5 + - + +
326A PRO* 3.4 20.5 - - - +
327A ALA* 1.3 73.4 + - - +
329A ILE* 1.3 63.3 + - - -
330A LEU 3.2 0.2 - - - -
331A THR* 4.0 6.0 - - - -
332A GLU* 3.2 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 3.9 24.5 - - + +
277A VAL* 3.7 25.8 - - + +
280A LEU* 3.8 35.0 - - + -
281A HIS* 3.6 33.0 - - + +
284A LEU* 4.3 4.5 - - + +
319A ILE* 4.8 4.9 - - + -
325A VAL* 4.4 12.3 - - + -
326A PRO* 3.1 17.5 + - + +
328A ASP* 1.3 77.2 - - - +
330A LEU* 1.3 55.5 + - - +
332A GLU* 3.4 2.3 + - - +
333A THR* 2.5 45.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 4.1 8.1 - - + +
320A LEU* 3.8 30.5 - - + +
322A ALA 5.3 3.1 - - - +
325A VAL* 3.8 23.5 - - + +
326A PRO 3.1 11.9 + - - +
327A ALA* 3.4 15.0 - - + +
329A ILE* 1.3 74.6 - - - +
331A THR* 1.3 65.6 + - - +
333A THR* 3.3 6.1 + - - -
334A ILE* 3.1 32.4 + - + +
381A LEU* 4.5 15.0 - - + -
1630A PEG 4.0 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ALA* 2.9 18.9 + - - +
328A ASP* 4.0 7.6 - - - -
329A ILE 3.5 0.2 - - - -
330A LEU* 1.3 75.1 - - - +
332A GLU* 1.3 71.9 + - - +
334A ILE* 3.2 15.1 + - - +
335A ASN* 3.2 28.7 + - - +
380A VAL* 3.5 47.8 - - + +
381A LEU* 3.9 12.9 - - - +
384A ALA* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A HIS* 3.3 34.3 - - + +
284A LEU* 4.2 10.3 - - + -
288A ARG* 3.7 15.6 + - - +
328A ASP* 3.2 10.9 + - + +
329A ILE 4.1 1.8 - - - +
331A THR* 1.3 85.0 - - - +
333A THR* 1.3 55.3 + - - +
335A ASN* 3.0 29.2 + - - +
336A THR* 2.7 36.5 + - - -
380A VAL* 5.2 5.9 - - - +
598A GLN* 5.2 0.5 + - - -
1631A PEG 3.5 32.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 5.6 0.2 - - - +
284A LEU* 4.0 11.7 - - + +
316A LEU* 3.7 42.0 - - + +
319A ILE* 3.7 25.7 - - + +
320A LEU* 3.9 11.2 - - + -
329A ILE* 2.5 29.4 + - - +
330A LEU 3.7 5.8 - - - -
332A GLU* 1.3 75.2 - - - +
334A ILE* 1.3 58.1 + - - +
336A THR* 3.8 5.6 - - - -
337A VAL* 3.2 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 3.7 23.1 - - + -
330A LEU* 3.1 22.0 - - + +
331A THR* 3.2 7.0 + - - +
333A THR* 1.3 75.2 - - - +
335A ASN* 1.3 54.7 + - - +
336A THR 3.2 0.2 - - - -
337A VAL* 3.4 5.2 + - - +
338A SER* 2.5 36.7 + - - -
368A LEU* 4.6 3.6 - - + -
381A LEU* 3.5 31.2 - - + -
384A ALA* 3.1 29.6 - - + +
385A VAL* 4.3 13.9 - - + +
388A CYS* 3.8 18.0 - - + -
1630A PEG 4.4 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 3.6 22.0 - - - +
331A THR* 3.2 12.7 + - - +
332A GLU* 3.0 32.0 + - - +
334A ILE* 1.3 78.3 - - - +
336A THR* 1.3 61.2 + - - +
338A SER* 3.3 19.0 - - - -
339A GLU* 3.3 15.9 + - - +
384A ALA* 3.3 28.6 - - - +
387A TYR* 3.7 13.7 - - + +
598A GLN* 3.8 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU* 3.6 19.6 - - + +
287A VAL* 3.8 24.9 - - + -
288A ARG* 3.5 27.7 - - + +
316A LEU* 3.6 25.1 - - + -
332A GLU 2.7 23.3 + - - -
333A THR* 3.8 7.9 - - - -
335A ASN* 1.3 72.8 - - - +
337A VAL* 1.3 67.4 + - - +
339A GLU* 2.9 14.7 + - - +
340A VAL* 2.9 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 4.2 8.3 - - + -
316A LEU* 3.6 38.1 - - + -
317A CYS* 4.4 6.5 - - - -
320A LEU* 4.5 8.1 - - + -
333A THR 3.2 17.3 + - - +
334A ILE* 3.8 5.4 - - - +
336A THR* 1.3 76.7 - - - +
338A SER* 1.3 63.3 + - - +
340A VAL* 3.0 8.9 + - - -
341A ILE* 3.0 33.1 + - + +
351A PHE* 3.8 33.9 - - + -
388A CYS* 4.4 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE 2.5 29.4 + - - -
335A ASN* 3.3 13.3 - - - -
336A THR 3.1 0.2 - - - -
337A VAL* 1.3 72.2 - - - +
339A GLU* 1.3 56.4 + - - +
341A ILE* 3.4 3.4 - - - +
342A ARG 3.0 24.1 + - - -
384A ALA 4.0 0.5 + - - -
387A TYR* 3.7 13.4 - - - -
388A CYS* 3.2 27.3 + - - +
391A CYS* 3.1 35.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ARG* 2.7 65.9 + - + +
291A VAL* 3.7 25.5 - - + +
292A SER* 4.9 1.0 - - - -
293A PRO* 4.2 21.2 - - + +
304A GLN* 2.8 23.4 + - - -
335A ASN 3.8 4.7 - - - +
336A THR 2.9 8.0 + - - +
338A SER* 1.3 76.9 - - - +
340A VAL* 1.3 60.2 + - - +
341A ILE 3.3 0.2 - - - -
342A ARG* 3.9 7.7 + - - +
387A TYR* 3.1 28.3 + - + +
391A CYS* 5.2 0.2 - - - -
598A GLN* 4.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 4.0 26.0 - - + -
291A VAL* 4.0 9.6 - - + -
304A GLN* 3.1 16.6 - - + +
307A MET* 3.9 26.2 - - + -
313A LEU* 3.6 28.3 - - + -
316A LEU* 4.4 5.4 - - + -
336A THR* 2.9 20.1 + - + +
337A VAL* 3.0 8.0 + - - +
339A GLU* 1.3 78.1 - - - +
341A ILE* 1.3 57.4 + - - +
347A ASN* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLN* 4.0 0.4 - - - -
313A LEU* 3.4 30.5 - - + -
337A VAL* 3.0 20.1 + - + +
338A SER 3.4 6.3 - - - +
340A VAL* 1.3 77.0 - - - +
342A ARG* 1.3 70.8 + - - +
343A GLY 2.9 1.4 + - - -
344A CYS* 2.8 18.9 + - - +
347A ASN* 3.7 23.8 - - + +
348A GLN* 3.2 17.2 - - + +
351A PHE* 4.0 30.5 - - + -
388A CYS* 4.3 14.1 - - - +
391A CYS* 4.2 5.6 - - + -
392A PHE* 4.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.9 31.1 + - - +
300A THR* 5.4 0.5 - - - +
304A GLN* 3.0 20.2 + - - +
338A SER 3.0 17.1 + - - +
339A GLU* 4.2 9.4 - - - +
340A VAL 3.7 1.2 - - - -
341A ILE* 1.3 72.8 - - - +
343A GLY* 1.3 63.5 + - - +
387A TYR* 4.7 3.8 - - - -
391A CYS* 3.6 31.0 - - - +
394A TYR* 3.7 53.0 + - + +
597A PRO* 3.5 34.3 - - - +
611A HIS* 5.6 0.2 + - - -
612A GLU* 4.3 9.1 + - - -
615A LYS* 5.4 2.8 - - - +
----------------------------------------------------------
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