Contacts of the helix formed by residues 326 - 340 (chain B) in PDB entry 1PYD
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 MET 326 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B CYS* 3.7 31.0 - - + +
225B HIS* 3.8 20.9 - - + +
227B VAL* 3.8 26.2 - - + -
285B VAL* 4.7 2.0 - - - -
286B GLY 4.7 3.8 - - - +
309B PHE* 3.7 47.3 - - + +
310B HIS* 3.3 16.1 + - - +
311B SER* 3.9 16.5 + - - +
314B MET* 4.2 9.4 - - - -
324B VAL 3.7 2.0 + - - -
325B GLN* 1.4 69.3 - - - +
327B LYS* 1.3 64.8 - - + +
329B VAL* 3.7 3.1 - - - +
330B LEU* 2.8 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 4.2 23.6 - - + -
225B HIS 4.8 0.9 - - - +
226B ASP* 3.0 52.4 + - - +
227B VAL* 3.9 15.0 - - + -
230B GLU* 3.6 15.9 + - - +
325B GLN* 3.1 3.1 - - + +
326B MET* 1.3 84.7 - - + +
328B PHE* 1.3 69.9 + - + +
330B LEU* 3.8 2.4 - - - +
331B GLN* 3.1 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LEU* 3.8 37.9 - - + -
190B LYS 3.2 27.6 - - - -
191B PRO* 4.1 5.2 - - + -
192B ASN* 3.9 23.3 - - - +
197B GLU* 3.3 21.9 - - - +
325B GLN* 3.4 10.1 + - + -
326B MET 3.3 0.2 - - - -
327B LYS* 1.3 84.4 - - + +
329B VAL* 1.3 69.7 + - - +
331B GLN* 4.0 22.2 - - - +
332B LYS* 3.0 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 4.1 5.4 - - - +
197B GLU* 4.2 7.4 - - + -
200B VAL* 4.0 17.5 - - + -
201B ILE* 3.8 24.5 - - + +
204B ILE* 4.2 7.2 - - + -
309B PHE* 4.4 4.7 - - + -
314B MET* 4.2 11.2 - - - -
324B VAL* 3.8 27.1 - - + -
325B GLN 3.4 15.1 + - - +
326B MET* 3.2 8.1 + - - +
328B PHE* 1.3 79.1 - - - +
330B LEU* 1.3 58.3 + - - +
332B LYS* 3.6 1.2 - - - +
333B LEU* 2.8 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 3.3 41.7 - - + -
230B GLU* 3.9 20.9 - - + +
231B THR* 4.4 2.5 - - - +
234B LEU* 4.2 26.0 - - + -
285B VAL* 4.2 13.7 - - + -
309B PHE* 3.7 30.1 - - + -
326B MET* 2.8 21.5 + - + +
327B LYS 3.8 2.9 - - - +
329B VAL* 1.3 75.9 - - - +
331B GLN* 1.4 65.3 - - - +
333B LEU* 3.0 19.2 + - + +
334B LEU* 3.1 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 4.1 20.4 + - + +
327B LYS* 3.1 42.1 + - - +
328B PHE* 4.0 22.7 - - - +
329B VAL 3.4 0.2 - - - -
330B LEU* 1.4 79.2 - - - +
332B LYS* 1.3 70.7 + - + +
334B LEU* 3.3 26.4 + - + +
335B THR* 3.7 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN 5.9 1.0 - - - +
197B GLU* 2.6 33.7 + - - -
198B LYS* 6.2 1.1 - - - +
201B ILE* 4.2 17.9 - - + -
328B PHE* 3.0 31.5 + - + +
329B VAL 3.8 1.3 - - - +
331B GLN* 1.3 83.4 - - + +
333B LEU* 1.3 60.9 + - - +
335B THR* 2.6 31.2 + - + -
336B ASN* 2.8 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 4.3 11.4 - - + +
204B ILE* 3.4 36.8 - - + -
205B LEU* 3.6 26.9 - - + -
234B LEU* 5.8 2.9 - - + -
309B PHE* 4.0 26.7 - - + -
329B VAL* 2.8 26.2 + - + +
330B LEU* 3.0 15.5 + - + +
332B LYS* 1.3 76.4 - - - +
334B LEU* 1.3 53.9 + - + +
336B ASN* 2.8 6.4 + - - +
337B ILE* 2.7 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B GLU* 3.6 38.1 - - + +
233B LYS* 4.1 17.0 - - + +
234B LEU* 3.8 28.7 - - + +
237B LEU* 3.1 30.2 - - + +
330B LEU* 3.1 15.8 + - + +
331B GLN* 3.5 17.7 - - + +
332B LYS 3.3 0.4 - - - -
333B LEU* 1.3 75.5 - - + +
335B THR* 1.3 61.2 + - + +
336B ASN 3.5 0.2 + - - -
337B ILE* 4.2 3.6 + - + -
338B ALA 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLN 3.7 15.0 - - - +
332B LYS* 2.6 24.1 + - + +
334B LEU* 1.3 77.1 - - + +
336B ASN* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 5.3 5.3 - - - +
201B ILE* 3.7 14.1 - - - +
205B LEU* 3.6 28.9 - - + +
332B LYS 2.8 16.7 + - - +
333B LEU* 2.8 34.1 - - - +
334B LEU 5.0 0.2 - - - -
335B THR* 1.3 84.4 + - - +
337B ILE* 1.3 62.9 + - - +
338B ALA 3.5 2.5 - - - -
339B ASP* 3.3 23.2 + - - +
340B ALA* 3.5 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 5.2 1.8 - - + -
205B LEU* 4.3 14.6 - - + -
208B VAL* 4.2 27.8 - - + -
234B LEU* 3.4 31.9 - - + -
237B LEU* 4.0 20.2 - - + -
238B THR* 3.5 23.8 - - + -
240B PHE* 4.6 2.2 - - + -
283B LEU* 6.0 2.9 - - + -
333B LEU* 2.7 40.8 + - + +
334B LEU* 4.2 3.7 - - + -
336B ASN* 1.3 67.0 + - - +
338B ALA* 1.3 65.3 + - - +
339B ASP 3.1 2.2 - - - -
340B ALA* 3.2 3.5 + - - +
341B ALA* 3.0 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.5 45.2 - - + +
334B LEU 5.9 0.2 - - - +
336B ASN 3.5 0.8 + - - -
337B ILE* 1.3 80.4 - - - +
339B ASP* 1.3 57.7 + - + +
341B ALA* 3.2 4.4 + - - +
342B LYS* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASN* 3.3 12.9 + - - +
337B ILE 3.1 0.2 - - - -
338B ALA* 1.3 77.1 - - + +
340B ALA* 1.3 66.3 + - - +
341B ALA 3.0 1.3 - - - -
342B LYS* 2.9 52.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU* 3.8 45.3 - - + +
208B VAL* 3.9 8.9 - - + +
209B LYS* 3.7 30.3 - - + +
336B ASN 3.5 3.4 + - - +
337B ILE 3.2 8.7 + - - +
339B ASP* 1.3 78.0 + - - +
341B ALA* 1.3 57.6 + - - +
342B LYS* 5.3 1.6 - - - +
----------------------------------------------------------
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