Contacts of the helix formed by residues 315 - 340 (chain A) in PDB entry 1S0X
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 GLN 315 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASN 3.6 8.7 + - - +
314A LYS* 1.3 76.1 - - - +
316A ARG* 1.3 67.8 + - - +
317A GLU* 3.6 21.7 - - - +
318A VAL* 2.9 29.4 + - + +
319A MET* 3.0 12.5 + - - +
393A SER* 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS 3.9 0.8 + - - -
315A GLN* 1.3 74.4 + - - +
317A GLU* 1.3 64.2 + - - +
319A MET* 3.3 1.6 + - - +
320A TRP* 3.0 36.9 + - + +
393A SER* 3.3 25.4 + - - +
394A LEU 3.3 21.3 + - - +
395A GLY* 4.6 10.6 + - - +
396A CYS* 5.6 1.8 - - - -
487A LYS* 5.2 4.9 + - - +
490A ALA* 5.1 4.9 - - - +
491A PHE* 4.3 30.8 - - + +
494A ILE* 4.1 22.8 - - - +
495A TYR* 4.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLN* 3.6 26.0 - - - +
316A ARG* 1.3 75.9 + - - +
318A VAL* 1.3 62.5 + - + +
320A TRP* 3.6 1.9 + - - +
321A GLN* 3.1 28.1 + - - +
491A PHE* 3.7 26.0 - - + -
495A TYR* 3.7 33.1 + - + -
498A ILE* 4.2 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS* 4.1 28.9 - - + +
315A GLN* 2.9 30.6 + - + +
317A GLU* 1.3 84.1 - - + +
319A MET* 1.3 64.7 + - - +
321A GLN* 3.3 8.8 + - - +
322A LEU* 3.2 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR* 3.9 26.2 - - + +
314A LYS* 4.3 10.5 - - + +
315A GLN 3.0 13.6 + - - +
316A ARG 4.0 2.9 - - - +
318A VAL* 1.3 73.3 - - - +
320A TRP* 1.3 66.6 + - - +
322A LEU* 3.3 10.8 + - - +
323A CYS* 3.0 38.8 + - - -
381A PHE* 3.8 31.9 - - + -
390A VAL 3.4 25.6 - - - +
391A PHE* 4.0 8.3 - - + -
393A SER* 3.9 22.4 - - - -
394A LEU* 3.7 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ARG* 3.0 31.0 + - + +
317A GLU 3.7 0.4 - - - +
319A MET* 1.3 77.9 - - - +
321A GLN* 1.3 61.2 + - - +
323A CYS* 3.4 2.1 + - - +
324A ALA* 3.0 25.1 + - - +
394A LEU* 3.2 40.3 + - + +
396A CYS* 4.0 16.6 - - - -
484A HIS 5.0 0.7 - - - -
487A LYS* 3.9 15.9 - - + -
488A LEU* 3.7 35.4 - - + -
491A PHE* 3.5 41.6 - + + -
503A PHE* 4.0 19.8 - + + -
507A TYR* 3.8 16.4 - - - -
1001A C3S 3.2 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLU 3.1 18.4 + - - +
318A VAL* 3.3 7.6 + - - +
320A TRP* 1.3 76.7 - - - +
322A LEU* 1.3 60.6 + - - +
324A ALA* 3.3 3.5 + - - +
325A ILE* 2.9 58.6 + - + +
498A ILE* 5.2 2.5 - - + -
502A HIS* 3.0 47.0 + - + +
503A PHE* 3.7 17.2 - - + -
504A PRO* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A TYR* 3.8 33.0 - - + -
314A LYS* 4.6 11.0 - - + -
318A VAL* 3.2 12.6 + - + +
319A MET* 3.7 14.6 - - - +
321A GLN* 1.3 81.2 + - - +
323A CYS* 1.3 63.6 + - - +
325A ILE* 3.1 15.9 + - + +
326A LYS* 2.9 50.6 + - - +
381A PHE* 4.2 15.9 - - + -
382A ASP* 4.3 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A MET* 3.0 32.8 + - - +
320A TRP 3.9 1.8 - - - +
322A LEU* 1.3 76.7 - - - +
324A ALA* 1.3 57.5 + - - +
326A LYS* 3.3 3.3 + - - +
327A ILE* 2.8 32.9 + - - +
381A PHE* 4.2 6.3 - - - -
391A PHE* 3.9 32.8 - - - -
394A LEU* 4.1 11.7 - - + -
1001A C3S 3.5 39.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TRP* 3.0 17.7 + - + +
321A GLN 3.6 4.0 - - - +
323A CYS* 1.3 77.1 - - - +
325A ILE* 1.3 54.2 + - - +
327A ILE* 4.0 1.0 - - - +
328A THR* 2.6 38.6 + - - -
503A PHE* 4.0 19.3 - - + -
504A PRO* 4.1 12.1 - - + -
507A TYR* 4.0 29.5 - - + +
1001A C3S 3.9 2.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 2.9 49.8 + - - +
322A LEU* 3.1 13.9 + - + +
324A ALA* 1.3 75.3 - - - +
326A LYS* 1.3 73.2 + - + +
328A THR* 3.3 4.0 + - - -
329A GLU* 3.2 37.7 + - + +
502A HIS 5.3 0.2 - - - +
504A PRO* 3.9 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A LEU* 2.9 36.8 + - + +
323A CYS 3.8 1.1 - - - +
325A ILE* 1.3 83.0 - - - +
327A ILE* 1.3 60.4 + - - +
329A GLU* 3.3 41.4 + - - +
330A ALA 3.4 9.0 + - - -
381A PHE* 4.1 18.8 - - + -
382A ASP* 3.2 36.6 + - - +
1001A C3S 3.7 32.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A CYS 2.8 17.5 + - - +
324A ALA* 4.0 0.9 - - - +
326A LYS* 1.3 69.4 - - - +
328A THR* 1.3 68.1 + - - +
330A ALA* 3.3 4.2 + - - +
331A ILE* 3.0 42.0 + - + +
361A LEU* 3.9 23.3 - - + -
364A VAL* 4.8 8.5 - - + -
365A PHE* 5.2 6.1 - - + -
484A HIS* 5.1 5.4 - - + +
507A TYR* 4.1 20.6 - - + -
511A PHE* 4.9 0.2 - - + -
1001A C3S 3.8 62.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA 2.6 23.7 + - - -
325A ILE 3.6 4.9 - - - -
327A ILE* 1.3 79.8 - - - +
329A GLU* 1.3 62.9 + - - +
331A ILE* 3.3 8.2 + - + +
332A GLN* 3.0 31.8 + - - +
504A PRO* 3.6 21.4 - - + +
506A LEU* 4.0 29.2 - - + -
507A TYR* 3.4 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 4.3 23.8 + - - +
290A TYR* 5.4 1.4 + - - -
325A ILE* 3.2 26.6 + - + +
326A LYS* 3.4 38.3 + - - +
327A ILE 3.2 0.4 - - - -
328A THR* 1.3 76.3 - - - +
330A ALA* 1.3 62.5 + - - +
332A GLN* 3.2 23.6 + - - +
333A TYR* 3.2 22.7 - - + -
1001A C3S 6.1 0.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 4.8 3.7 + - - -
326A LYS 3.4 3.5 + - - +
327A ILE 3.3 7.9 + - - +
329A GLU* 1.3 77.9 - - - +
331A ILE* 1.3 62.5 + - - +
333A TYR* 3.2 13.2 + - - +
334A VAL* 3.2 22.3 + - - +
364A VAL* 4.2 21.1 - - + -
367A ARG* 4.9 0.5 + - - -
1001A C3S 3.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ILE* 3.0 26.6 + - + +
328A THR* 3.3 11.9 + - + +
330A ALA* 1.3 72.8 - - - +
332A GLN* 1.3 66.4 + - - +
334A VAL* 3.0 7.9 + - - +
335A VAL* 2.9 26.9 + - + +
360A SER* 4.0 18.2 - - - +
361A LEU* 4.5 5.8 - - + +
364A VAL* 3.8 17.0 - - + -
506A LEU* 4.0 12.3 - - + -
507A TYR* 5.4 1.1 - - + -
510A LEU* 3.6 24.7 - - + -
511A PHE* 3.6 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A THR* 3.0 30.1 + - - +
329A GLU* 3.2 17.9 + - - +
331A ILE* 1.3 77.3 - - - +
333A TYR* 1.3 65.8 + - + +
335A VAL* 3.4 8.5 + - - +
336A GLU* 3.3 24.9 + - - +
506A LEU* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 3.2 36.9 - - - +
288A CYS 4.6 2.0 - - - -
289A GLN* 3.5 60.1 + - + +
329A GLU* 3.2 25.5 + - + -
330A ALA* 3.2 9.3 + - - +
331A ILE 3.1 0.2 - - - -
332A GLN* 1.3 79.7 - - + +
334A VAL* 1.3 64.0 + - - +
336A GLU* 3.3 11.1 + - + +
337A PHE* 3.1 17.7 + - - +
367A ARG* 3.9 7.4 + - - +
1001A C3S 4.7 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ALA 3.2 13.1 + - - +
331A ILE* 3.0 10.4 + - - +
333A TYR* 1.3 75.5 - - - +
335A VAL* 1.3 65.2 + - - +
337A PHE* 3.2 9.5 + - + +
338A ALA* 3.0 21.3 + - - +
356A LEU* 5.2 2.0 - - + -
360A SER* 3.9 24.2 - - - +
363A VAL* 3.7 42.8 - - + -
364A VAL* 4.0 17.0 - - + -
367A ARG* 4.0 16.2 - - - +
428A LEU* 4.9 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 2.9 28.8 + - + +
332A GLN* 3.6 10.8 - - - +
333A TYR 3.3 0.2 - - - -
334A VAL* 1.3 77.9 - - - +
336A GLU* 1.3 64.7 + - - +
338A ALA* 3.3 7.8 + - - +
339A LYS* 3.1 36.9 + - + +
356A LEU* 4.4 29.4 - - + -
360A SER* 5.4 2.2 - - - -
506A LEU* 5.2 9.9 - - + -
510A LEU* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 3.7 15.9 - - + -
332A GLN 3.3 13.5 + - - +
333A TYR* 3.3 15.4 + - + +
334A VAL 3.2 0.4 - - - -
335A VAL* 1.3 75.4 - - - +
337A PHE* 1.3 67.3 + - - +
339A LYS* 3.4 42.8 + - - +
340A ARG* 3.6 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.9 13.9 - - + -
283A SER* 3.9 7.9 - - - -
284A HIS* 3.6 34.3 - - + -
287A THR* 3.4 25.7 - - - +
333A TYR 3.1 8.1 + - - +
334A VAL* 3.3 11.4 - - + +
336A GLU* 1.3 76.4 - - - +
338A ALA* 1.3 65.2 + - - +
340A ARG* 3.1 15.2 + - - +
341A ILE* 3.5 35.5 + - + +
363A VAL* 4.8 9.6 - - + -
367A ARG* 3.6 14.6 - - - +
421A ALA* 3.6 21.3 - - - -
424A SER* 3.7 24.9 - - - -
425A ALA 3.9 5.4 - - - -
428A LEU* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL 3.0 9.5 + - - +
335A VAL 3.3 8.7 + - - +
337A PHE* 1.3 74.8 - - - +
339A LYS* 1.3 65.0 + - + +
341A ILE* 2.8 30.2 + - - +
344A PHE* 3.6 26.9 - - + +
356A LEU* 3.8 28.3 - - + -
428A LEU* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 3.1 24.3 + - + +
336A GLU* 3.4 42.7 + - - +
337A PHE 3.3 0.2 - - - -
338A ALA* 1.3 76.3 - - + +
340A ARG* 1.3 62.2 + - + +
341A ILE 3.5 3.3 + - - +
344A PHE* 4.4 3.6 - - + -
345A MET* 3.3 44.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASN* 4.0 10.0 + - - +
283A SER* 3.7 33.5 + - - +
286A GLU* 3.0 42.4 + - - +
287A THR* 3.8 22.4 - - - +
336A GLU* 3.7 20.7 + - - +
337A PHE 3.1 8.2 + - - +
338A ALA 3.0 1.0 - - - -
339A LYS* 1.3 78.3 - - + +
341A ILE* 1.3 62.9 + - - +
342A ASP* 3.4 6.8 + - - +
----------------------------------------------------------
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