Contacts of the helix formed by residues 331 - 354 (chain B) in PDB entry 5WYF
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 GLY 331 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE 3.4 2.0 + - - -
328B GLU 3.0 16.2 + - - -
329B TYR 3.4 1.4 + - - -
330B GLU* 1.3 77.6 - - - +
332B LEU* 1.3 59.7 + - - +
333B VAL* 3.4 3.4 - - - -
334B GLU* 3.5 13.9 + - - +
335B LYS* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN 4.0 6.7 - - - +
59B VAL* 4.0 28.5 - - + -
326B VAL* 4.2 10.5 - - + +
327B ILE* 3.0 28.8 + - + +
330B GLU* 3.8 17.9 - - + +
331B GLY* 1.3 74.4 - - - +
333B VAL* 1.3 66.2 + - - +
335B LYS* 3.7 21.8 - - + +
336B SER* 2.9 24.6 + - - -
413B LEU* 4.3 20.7 - - + +
414B VAL* 3.8 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLY* 4.0 20.6 - - - -
260B GLY* 3.5 11.6 - - - +
261B LYS* 3.4 34.1 - - - -
262B MET* 3.5 18.8 - - + +
327B ILE* 3.9 23.9 + - + +
331B GLY 3.4 0.6 - - - -
332B LEU* 1.3 79.8 - - - +
334B GLU* 1.3 62.3 + - - +
336B SER* 3.1 10.6 + - - -
337B ALA 3.1 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLY 5.2 0.7 - - - -
331B GLY* 3.5 13.5 + - - +
332B LEU 3.3 0.2 - - - -
333B VAL* 1.3 79.8 - - - +
335B LYS* 1.3 59.0 + - - +
337B ALA* 3.2 10.1 + - + +
338B THR* 2.9 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU 5.1 3.6 - - - +
331B GLY 3.1 17.7 + - - +
332B LEU* 3.7 19.7 - - + +
334B GLU* 1.3 76.9 - - - +
336B SER* 1.3 54.9 + - - +
338B THR* 4.3 5.6 - - - -
339B ASP* 2.6 70.0 + - - +
365B LEU* 5.2 0.2 - - - -
413B LEU 2.9 24.6 + - - +
414B VAL* 3.6 8.2 - - - +
415B ILE* 2.7 27.4 + - - +
416B PRO* 5.6 1.1 - - - -
417B ARG 5.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLY 3.1 18.6 + - - -
258B ARG 3.0 15.1 + - - -
260B GLY 3.4 1.2 + - - -
332B LEU 2.9 12.6 + - - -
333B VAL 3.3 7.0 - - - -
335B LYS* 1.3 76.4 - - - +
337B ALA* 1.3 58.5 + - - +
340B GLY* 2.8 24.6 + - - -
364B GLY* 3.3 11.4 - - - -
365B LEU* 2.9 30.2 + - - +
413B LEU* 3.7 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B THR 5.1 0.2 - - - -
260B GLY* 3.5 28.7 - - - +
333B VAL 3.1 6.9 + - - +
334B GLU* 3.2 12.3 + - + +
336B SER* 1.3 76.1 - - - +
338B THR* 1.3 56.3 + - - +
340B GLY* 3.7 0.3 - - - -
341B ALA* 2.9 30.5 + - - +
364B GLY* 4.3 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 2.9 31.4 + - - +
335B LYS* 3.7 6.7 - - - -
337B ALA* 1.3 70.9 - - - +
339B ASP* 1.3 74.9 + - - +
340B GLY 3.2 0.3 + - - -
341B ALA* 3.2 7.7 + - - +
342B TYR* 3.0 20.4 + - - +
417B ARG* 4.6 7.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
335B LYS* 2.6 59.3 + - - +
338B THR* 1.3 79.6 - - - +
340B GLY* 1.3 52.3 + - - +
342B TYR* 3.3 4.0 + - - +
343B ALA* 2.7 35.5 + - - +
365B LEU* 3.6 24.6 - - + +
415B ILE 4.1 2.8 - - - +
417B ARG* 3.0 31.2 + - - +
420B LEU* 4.1 12.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
336B SER 2.8 15.7 + - - -
337B ALA 3.7 0.4 - - - -
339B ASP* 1.3 75.3 - - - +
341B ALA* 1.3 59.5 + - - +
343B ALA* 3.5 1.7 + - - -
344B LYS* 2.9 29.6 + - - +
362B MET* 3.4 8.5 - - - +
364B GLY* 3.1 30.3 - - - -
365B LEU* 4.0 6.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA 2.9 17.4 + - - +
338B THR* 3.6 5.6 - - - +
340B GLY* 1.3 73.7 - - - +
342B TYR* 1.3 64.2 + - - +
344B LYS* 3.4 8.4 + - - +
345B GLN* 3.1 29.1 + - + +
364B GLY 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B THR* 3.0 12.8 + - + +
339B ASP 3.4 9.0 - - - +
341B ALA* 1.3 74.9 - - - +
343B ALA* 1.3 68.9 + - - +
345B GLN* 3.1 9.9 + - + +
346B ARG* 2.8 58.7 + - + +
417B ARG* 3.4 44.4 - - - +
420B LEU* 4.2 6.5 - - + -
421B ASP* 2.5 33.3 + - - -
424B LEU* 4.1 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASP 2.7 19.7 + - - +
340B GLY 4.0 3.4 - - - +
342B TYR* 1.3 78.3 - - - +
344B LYS* 1.3 62.9 + - - +
346B ARG* 3.3 6.8 + - - +
347B PHE* 3.0 32.6 + - + -
362B MET* 4.1 9.6 - - + -
365B LEU* 4.6 2.9 - - + -
409B PHE* 4.0 31.6 - - + -
420B LEU* 4.8 8.1 - - + -
424B LEU* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLY 2.9 19.3 + - - +
341B ALA* 3.4 10.1 - - - +
343B ALA* 1.3 75.3 - - - +
345B GLN* 1.3 65.6 + - - +
347B PHE* 3.2 3.5 + - - +
348B LEU* 2.9 48.0 + - + +
360B VAL* 4.0 25.1 - - + +
362B MET* 3.9 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ALA 3.1 11.9 + - - +
342B TYR* 3.1 11.7 + - + +
344B LYS* 1.3 87.8 - - - +
346B ARG* 1.3 64.0 + - + +
348B LEU* 3.4 26.0 + - - +
349B GLU* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TYR* 2.8 68.0 + - + +
343B ALA 3.7 7.6 - - - +
344B LYS 3.3 0.2 - - - -
345B GLN* 1.3 77.8 - - + +
347B PHE* 1.3 56.5 + - - +
349B GLU* 3.4 14.4 + - - +
350B MET* 3.1 37.0 + - - +
421B ASP* 3.3 16.4 + - - +
424B LEU* 3.9 40.5 + - + +
425B GLN* 4.7 13.7 + - - +
428B ASP* 5.1 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA* 3.0 25.4 + - + +
344B LYS 3.9 2.7 - - - +
346B ARG* 1.3 73.9 - - - +
348B LEU* 1.3 61.2 + - - +
349B GLU 3.2 0.2 - - - -
350B MET* 3.3 26.7 + - + +
351B GLN* 2.9 28.1 + - - +
357B ILE* 4.5 2.5 - - + +
360B VAL* 3.9 19.0 - - + +
362B MET* 3.5 21.1 - - + -
369B ILE* 3.8 32.1 - - + -
407B LEU* 5.7 1.6 - - + -
409B PHE* 3.8 25.6 - + + -
424B LEU* 3.6 27.6 - - + -
427B LEU* 3.8 28.3 - - + -
431B PHE* 4.9 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LYS* 2.9 33.0 + - + +
345B GLN* 3.8 33.9 - - - +
347B PHE* 1.3 76.2 - - - +
349B GLU* 1.3 60.6 + - - +
351B GLN* 3.4 27.2 + - - +
352B GLN* 3.4 24.8 + - - +
360B VAL* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLN 3.0 17.1 + - - +
346B ARG* 3.7 16.7 + - - +
347B PHE 3.2 0.4 - - - -
348B LEU* 1.3 72.4 - - - +
350B MET* 1.3 67.9 + - - +
352B GLN* 3.0 37.6 + - + +
353B ARG* 3.1 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ARG* 3.1 24.2 + - - +
347B PHE* 3.3 26.4 + - + +
349B GLU* 1.3 77.3 - - - +
351B GLN* 1.3 56.9 + - - +
353B ARG* 3.0 27.5 + - - +
354B HIS* 2.9 37.1 + - + -
357B ILE* 4.0 4.9 - - + -
424B LEU* 4.2 13.7 - - - +
427B LEU* 3.8 2.0 - - + -
428B ASP* 3.2 33.2 - - - +
431B PHE* 3.1 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE 2.9 13.7 + - - +
348B LEU* 3.5 34.1 - - - +
349B GLU 3.2 0.2 - - - -
350B MET* 1.3 74.3 - - - +
352B GLN* 1.3 62.5 + - - +
354B HIS 3.7 14.4 + - - +
355B PRO* 4.4 4.4 - - + +
357B ILE* 2.6 48.6 + - + +
358B GLY 3.2 23.4 + - - -
359B ASP* 3.7 4.8 - - - +
360B VAL* 4.0 4.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.4 15.0 + - - +
349B GLU* 3.0 33.9 - - + +
351B GLN* 1.3 78.1 - - - +
353B ARG* 1.3 64.4 + - + +
354B HIS 3.7 0.2 - - - -
355B PRO* 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B GLU* 3.1 41.9 + - - +
350B MET* 3.0 16.1 + - - +
352B GLN* 1.3 84.3 - - + +
354B HIS* 1.3 66.2 + - + +
355B PRO* 4.0 6.3 - - - +
428B ASP* 2.8 43.4 + - - -
432B THR* 5.2 1.0 + - - -
1007B CD 2.3 30.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B MET* 2.9 30.7 + - + +
351B GLN 3.7 6.0 - - - +
352B GLN 3.7 0.2 - - - -
353B ARG* 1.3 91.9 + - + +
355B PRO* 1.4 61.3 - - - +
356B MET* 3.1 9.0 - - + -
357B ILE* 3.0 31.5 + - + +
428B ASP* 2.6 26.8 + - - -
431B PHE* 3.6 35.1 - + + +
432B THR* 3.2 27.1 - - - -
435B GLU* 3.2 15.3 + - - +
1007B CD 2.9 22.5 - - - -
----------------------------------------------------------
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