Contacts of the helix formed by residues 334 - 360 (chain B) in PDB entry 2G9Y
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 ASN 334 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B LEU* 5.2 0.6 - - - +
270B GLY 2.9 29.9 + - - +
271B PRO 3.8 10.9 + - - -
272B LYS* 4.0 5.7 - - - +
329B GLN* 2.9 31.4 + - - +
332B ALA* 4.1 8.5 - - + +
333B ALA* 1.3 77.6 - - - +
335B PRO* 1.3 58.0 - - - +
336B CYS* 3.5 9.9 + - - +
337B GLY* 2.9 25.9 + - - -
338B GLN* 2.9 28.1 + - - +
402B TYR* 4.0 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PRO 4.3 2.9 - - - +
273B ALA 4.5 1.6 - - - +
333B ALA 3.3 12.3 - - - +
334B ASN* 1.3 82.5 - - - +
336B CYS* 1.3 54.1 + - - +
338B GLN* 3.3 2.4 + - + -
339B ILE* 2.7 42.7 + - - +
388B GLN* 3.5 35.7 - - + +
390B LEU* 3.7 21.3 - - + -
400B MET* 3.9 19.3 - - + -
402B TYR* 3.5 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B TRP* 3.4 13.6 - - + +
269B LEU 3.6 19.7 - - - +
270B GLY* 3.7 17.3 - - - -
271B PRO 5.6 0.2 + - - -
284B VAL* 4.1 6.3 - - - -
286B CYS* 2.0 58.6 - - + -
334B ASN* 3.3 1.8 + - - -
335B PRO* 1.3 78.6 - - - +
337B GLY* 1.3 58.5 + - - +
339B ILE* 4.6 0.9 - - - -
340B GLY 2.9 24.1 + - - -
388B GLN* 4.7 2.4 + - - -
390B LEU* 4.0 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B VAL* 5.1 1.8 - - - -
268B TRP* 3.6 18.1 + - - -
329B GLN* 3.5 27.6 - - - -
334B ASN* 2.9 12.7 + - - -
336B CYS* 1.3 76.1 - - - +
338B GLN* 1.3 62.4 + - - +
340B GLY* 3.9 0.5 - - - -
341B GLU* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.7 18.6 + - - +
60B ALA* 4.7 2.2 - - - +
326B ILE* 3.8 27.8 - - + +
329B GLN* 3.2 14.1 - - + +
330B ASP* 3.1 29.9 - - - +
334B ASN 2.9 16.5 + - - +
335B PRO 3.6 2.9 - - - +
337B GLY* 1.3 77.7 - - - +
339B ILE* 1.3 64.5 + - - +
341B GLU* 3.4 3.3 + - - +
342B THR* 3.0 26.6 + - - +
374B SER* 3.2 17.6 + - - -
400B MET* 3.4 17.3 - - - +
402B TYR* 2.8 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA 4.1 6.1 - - - +
61B ALA* 3.7 32.3 - - + +
64B TYR* 3.7 31.6 - - + -
65B ALA* 4.8 0.2 - - + -
268B TRP* 3.7 20.6 - - + -
286B CYS* 5.3 0.4 - - - -
335B PRO* 2.7 30.4 + - + +
336B CYS* 4.1 3.4 - - - +
338B GLN* 1.3 76.3 - - - +
340B GLY* 1.3 63.6 + - - +
342B THR* 3.0 10.0 + - - -
343B VAL* 3.0 23.7 + - + +
390B LEU* 4.2 8.5 - - + -
398B MET* 4.4 0.2 - - + -
400B MET* 4.1 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ARG* 3.4 14.7 - - - -
268B TRP* 3.6 34.5 - - - -
336B CYS 2.9 15.7 + - - -
337B GLY 3.9 0.9 - - - -
338B GLN 3.3 0.2 - - - -
339B ILE* 1.3 77.6 - - - +
341B GLU* 1.3 61.5 + - - +
343B VAL* 3.3 2.2 + - - +
344B ASP* 2.9 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 4.7 9.0 + - - +
264B MET 5.5 0.5 - - - +
265B PRO 4.6 2.6 - - - +
266B VAL* 3.6 22.4 - - + +
267B ARG* 2.9 30.5 + - - +
323B GLY* 5.1 4.3 - - - +
325B SER* 3.5 33.1 + - - +
326B ILE* 3.6 26.9 - - + +
337B GLY 3.1 17.6 + - - +
338B GLN 3.8 1.8 - - - +
339B ILE 3.2 0.2 - - - -
340B GLY* 1.3 75.5 - - - +
342B THR* 1.3 59.2 + - - +
344B ASP* 3.4 18.0 - - - +
345B LEU* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 4.0 14.7 - - + +
57B GLU* 4.6 8.2 + - - +
58B ILE* 4.8 2.5 - - - -
61B ALA* 3.4 26.8 - - + +
72B PHE* 4.5 5.4 - - + -
75B ILE* 3.7 18.8 - - + +
326B ILE* 3.5 22.8 - - - +
338B GLN* 3.0 16.0 + - - +
339B ILE* 3.0 9.2 + - - -
341B GLU* 1.3 75.1 - - - +
343B VAL* 1.3 61.8 + - - +
344B ASP 3.1 0.2 - - - -
345B LEU* 3.3 2.6 + - - +
346B ASP* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 5.2 0.4 - - + -
65B ALA* 3.7 30.7 - - + -
66B GLU* 6.1 0.4 - - - +
72B PHE* 4.5 13.0 - - + -
267B ARG* 4.1 22.9 - - - +
268B TRP* 4.0 16.4 - - + -
339B ILE* 3.0 19.3 + - + +
340B GLY* 3.5 9.0 - - - +
342B THR* 1.3 75.2 - - - +
344B ASP* 1.3 64.0 + - - +
346B ASP* 3.3 10.8 + - + +
347B GLU* 3.2 24.9 + - + +
958B SO4 5.1 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B THR* 4.2 9.9 - - - +
267B ARG* 3.2 30.1 + - - +
298B THR* 4.6 3.5 - - - -
299B LEU* 3.4 38.6 + - - +
300B ALA 4.6 1.4 + - - -
323B GLY* 5.7 0.5 - - - -
340B GLY 2.9 14.4 + - - +
341B GLU* 3.4 24.9 - - - +
343B VAL* 1.3 73.9 - - - +
345B LEU* 1.3 64.5 + - - +
347B GLU* 3.1 16.9 + - - +
348B ALA* 3.4 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.4 24.2 - - + -
49B ILE 4.2 3.6 - - - +
50B GLY* 3.4 31.4 - - - +
53B MET* 3.6 26.2 - - + -
75B ILE* 4.5 2.7 - - + -
299B LEU* 3.9 22.4 - - + +
321B VAL 4.8 1.6 - - - +
323B GLY* 4.0 15.0 - - - +
326B ILE* 4.1 3.6 - - + -
341B GLU 3.1 12.0 + - - +
342B THR* 3.3 8.5 + - - +
344B ASP* 1.3 79.8 - - - +
346B ASP* 1.3 60.0 + - - +
348B ALA* 3.0 5.0 + - - +
349B VAL* 2.9 38.0 + - + +
366B VAL* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 5.3 1.9 - - - +
72B PHE* 3.2 29.3 - - + +
73B LYS 4.4 1.9 + - - -
74B GLY 3.0 10.9 + - - -
75B ILE* 2.9 43.1 + - + -
342B THR 3.0 13.4 + - - +
343B VAL* 3.4 12.8 - - - +
344B ASP 3.2 0.4 - - - -
345B LEU* 1.3 77.6 - - - +
347B GLU* 1.3 57.2 + - - +
349B VAL* 3.3 3.0 + - - +
350B GLN* 2.8 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ARG* 2.6 44.4 + - - -
298B THR* 5.3 3.8 - - - +
300B ALA* 4.0 19.6 - - + +
343B VAL* 3.2 19.1 - - + +
344B ASP* 3.1 9.1 + - - +
346B ASP* 1.3 74.7 - - - +
348B ALA* 1.3 66.8 + - - +
350B GLN* 3.1 26.5 + - - +
351B ARG* 3.1 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.0 11.2 - - + +
299B LEU* 3.8 25.6 - - + -
300B ALA* 4.0 14.3 - - - +
303B THR* 3.6 26.1 - - - +
321B VAL* 4.5 0.2 - - + -
344B ASP 3.4 2.0 + - - +
345B LEU 3.0 9.3 + - - +
347B GLU* 1.3 79.6 - - - +
349B VAL* 1.3 62.9 + - - +
351B ARG* 3.3 6.1 + - - +
352B ALA* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 22.7 - - + -
74B GLY* 3.3 30.7 - - - +
75B ILE* 3.7 12.8 - - + +
345B LEU* 2.9 27.3 + - + +
346B ASP 3.5 7.4 - - - +
348B ALA* 1.3 74.7 - - - +
350B GLN* 1.3 59.6 + - - +
352B ALA* 3.2 3.3 + - - +
353B LEU* 2.9 37.8 + - + +
364B VAL* 5.5 0.2 - - + -
366B VAL* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LYS* 3.7 42.1 + - + +
74B GLY* 3.5 19.7 - - - +
346B ASP* 2.8 38.7 + - - +
347B GLU* 3.1 17.5 + - - +
349B VAL* 1.3 77.0 - - - +
351B ARG* 1.3 58.5 + - + +
353B LEU* 3.4 4.5 + - - +
354B GLU* 2.9 49.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA* 3.4 39.0 + - + +
301B GLN* 4.3 7.7 - - - +
303B THR* 4.4 11.2 - - + -
304B ASP* 2.8 42.1 + - - +
307B ILE* 4.5 3.4 - - + +
347B GLU* 3.1 13.5 + - - +
348B ALA 3.5 7.0 - - - +
350B GLN* 1.3 77.6 - - - +
352B ALA* 1.3 64.7 + - - +
354B GLU* 3.2 20.9 + - - +
355B PHE* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.0 24.6 - - + +
48B LEU* 3.9 26.5 - - + -
303B THR* 4.7 3.1 - - + +
307B ILE* 4.3 6.0 - - - +
348B ALA 3.0 13.4 + - - +
349B VAL 3.4 8.1 - - - +
351B ARG* 1.3 77.9 - - - +
353B LEU* 1.3 56.7 + - - +
355B PHE* 3.4 4.7 + - - +
356B ALA* 2.9 30.0 + - - +
364B VAL* 4.2 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.2 18.5 - - + +
73B LYS 4.5 2.2 - - - +
74B GLY* 3.6 27.8 - - - +
77B ALA* 3.9 18.4 - - + -
78B LEU* 4.0 11.4 - - + -
349B VAL* 2.9 29.1 + - + +
350B GLN* 3.9 3.6 - - - +
352B ALA* 1.3 71.5 - - - +
354B GLU* 1.3 61.2 + - + +
356B ALA* 3.7 2.3 - - - +
357B LYS* 2.9 31.7 + - - +
364B VAL* 3.9 26.7 - - + -
422B TYR* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLN* 2.9 46.1 + - - +
351B ARG* 3.2 21.6 + - - +
353B LEU* 1.3 76.8 - - - +
355B PHE* 1.3 65.4 + - - +
357B LYS* 3.4 11.1 + - - +
358B LYS* 3.5 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASN* 4.1 2.2 - - - -
46B ILE* 4.2 13.0 - - + -
307B ILE* 3.4 33.0 - - + -
311B SER* 4.2 13.9 - - - -
317B PHE* 4.0 32.3 - + - -
351B ARG 3.0 16.5 + - - +
352B ALA 3.7 1.8 - - - +
354B GLU* 1.3 77.4 - - - +
356B ALA* 1.3 62.9 + - - +
358B LYS* 3.1 19.4 - - + +
359B GLU* 2.9 48.7 + - + +
362B THR* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA 2.9 18.1 + - - +
353B LEU* 3.7 4.7 - - - +
354B GLU 3.3 0.4 - - - -
355B PHE* 1.3 83.3 - - - +
357B LYS* 1.3 57.0 + - - +
359B GLU* 4.5 0.2 - - - -
360B GLY* 3.0 27.9 + - - -
362B THR* 3.9 20.4 + - + +
364B VAL* 3.4 26.0 - - + -
422B TYR* 4.0 18.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 3.1 43.4 - - + +
4B MET 4.6 2.0 - - - +
5B PRO* 5.6 1.1 - - - -
6B VAL* 3.9 30.8 + - + +
8B GLU* 4.4 14.3 + - - -
353B LEU 2.9 20.9 + - - +
354B GLU* 3.9 6.5 - - - +
355B PHE 3.3 0.4 - - - -
356B ALA* 1.3 74.2 - - - +
358B LYS* 1.3 60.7 + - + +
360B GLY* 4.1 4.9 + - - -
422B TYR* 3.6 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 4.8 6.3 - - - +
354B GLU 3.5 10.9 + - - +
355B PHE* 3.1 30.7 - - + +
357B LYS* 1.3 78.4 - - + +
359B GLU* 1.3 68.2 + - + +
360B GLY* 3.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LYS* 3.4 30.1 + - - +
44B ASN* 3.6 7.6 - - - +
355B PHE* 2.9 41.5 + - + +
356B ALA 4.2 0.4 - - - +
358B LYS* 1.3 80.0 - - + +
360B GLY* 1.3 57.5 + - - +
361B ASN* 2.5 51.2 + - - +
362B THR* 2.8 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 6.0 1.8 - - - -
4B MET* 4.1 10.6 - - - +
40B LYS* 3.0 29.3 + - - -
356B ALA 3.0 15.5 + - - -
357B LYS 4.1 6.0 + - - -
358B LYS 3.3 4.0 - - - -
359B GLU* 1.3 74.3 - - - +
361B ASN* 1.3 61.1 + - - +
362B THR 3.6 2.0 - - - -
422B TYR* 5.8 1.6 - - - -
424B PRO* 5.2 0.2 - - - -
----------------------------------------------------------
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