Contacts of the helix formed by residues 372 - 392 (chain B) in PDB entry 4JYH
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 372 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 3.9 21.8 - - + +
329A CYS* 6.4 1.3 - - - -
345A GLN* 4.4 13.5 - - - +
349A LEU* 3.8 31.6 - - - -
371A LEU* 3.8 21.1 - - + -
372A MET* 3.9 4.0 - - - -
374A ILE* 4.0 19.7 - - + -
378A ARG* 6.0 2.5 - - - +
368B PRO 2.9 20.6 + - - +
369B LYS* 4.1 7.4 - - - +
371B LEU* 1.3 73.8 - - - +
373B LYS* 1.3 56.0 + - - +
374B ILE 3.0 6.1 - - - +
375B THR* 3.0 40.1 - - + +
376B ASP* 3.7 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP* 3.0 30.6 + - - -
342A ASP* 5.7 1.4 + - - -
305B PHE* 3.9 19.3 - - + -
308B GLN* 4.0 20.9 - - - -
309B LEU* 4.3 7.6 - - + -
312B LEU* 3.9 30.4 - - + +
314B MET* 6.1 0.4 - - - -
322B LEU* 4.7 10.1 - - + -
369B LYS* 3.4 22.8 + - - +
370B ILE* 3.1 15.8 + - + +
372B MET* 1.3 76.2 + - - +
374B ILE* 1.3 63.4 + - - +
375B THR 3.1 0.4 - - - -
376B ASP* 3.1 28.1 + - - +
377B LEU* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 3.6 15.5 - - + -
375A THR* 4.2 11.9 - - + +
260B ASP* 5.0 1.5 - - - +
322B LEU* 3.6 34.5 - - + +
325B ILE* 3.8 28.0 - - + -
326B CYS* 4.4 27.6 - - + +
332B ARG* 6.2 1.3 - - - +
371B LEU* 3.2 21.8 - - + +
373B LYS* 1.3 77.3 - - - +
375B THR* 1.3 64.5 + - - +
377B LEU* 3.2 12.4 + - + +
378B ARG* 3.0 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 3.8 3.7 - - - +
374A ILE* 3.6 24.8 - - + +
375A THR* 3.4 25.4 + - - +
378A ARG* 3.2 42.8 - - + +
372B MET* 3.0 33.8 + - + +
374B ILE* 1.3 80.1 - - - +
376B ASP* 1.3 59.5 + - - +
378B ARG* 3.2 16.3 + - - +
379B SER* 3.4 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP* 3.1 28.4 - - - +
378A ARG* 3.3 29.0 + - - +
305B PHE* 3.5 19.0 - - + -
308B GLN* 4.1 2.0 - - - +
372B MET 4.3 6.3 - - - +
373B LYS* 3.1 37.0 + - - +
375B THR* 1.3 76.6 - - - +
377B LEU* 1.3 64.1 + - - +
378B ARG 3.3 0.3 + - - -
379B SER* 3.4 4.9 + - - -
380B ILE* 3.3 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASP* 3.4 41.3 - - + +
261B ILE* 5.5 0.2 - - - -
263B ILE* 3.6 27.7 - - + +
264B LEU* 3.9 29.8 - - + +
305B PHE* 3.6 22.2 - - + -
322B LEU* 5.5 2.9 - - + -
326B CYS* 5.0 9.0 - - + -
373B LYS 3.1 17.2 + - - +
374B ILE* 3.2 18.6 + - + +
376B ASP* 1.3 77.1 - - - +
378B ARG* 1.3 52.3 + - - +
380B ILE* 3.3 4.4 + - - +
381B SER* 2.7 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR* 3.3 42.8 - - + +
378A ARG* 4.7 1.3 - - + -
379A SER* 3.6 24.8 + - - -
256B ALA* 3.2 26.7 + - - +
260B ASP* 3.3 22.5 + - - -
332B ARG* 2.9 35.9 - - - +
374B ILE* 3.0 12.9 + - - +
375B THR 3.3 10.3 - - - +
376B ASP 3.1 0.2 - - - -
377B LEU* 1.3 75.2 - - - +
379B SER* 1.3 59.6 + - - +
381B SER* 3.3 13.8 + - - -
382B ALA* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 3.0 54.8 + - - +
382A ALA* 4.3 2.6 - - - +
301B LEU* 5.7 1.6 - - - -
375B THR 3.4 0.8 + - - -
376B ASP 3.4 8.4 + - - -
378B ARG* 1.3 78.5 - - - +
380B ILE* 1.3 65.2 + - - +
382B ALA* 3.2 5.6 + - - +
383B LYS* 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.6 27.8 - - + +
298B LEU* 4.9 4.0 - - + +
301B LEU* 4.3 36.6 - - + +
302B VAL* 3.9 26.0 - - + -
305B PHE* 3.7 41.1 - - + -
376B ASP* 3.3 16.2 - - + +
377B LEU* 3.3 3.5 + - - +
378B ARG 3.3 0.2 - - - -
379B SER* 1.3 76.6 - - - +
381B SER* 1.3 52.4 + - - +
383B LYS* 3.5 1.7 + - - +
384B GLY* 2.6 33.6 + - - -
501B JYH 5.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ALA 4.8 0.3 + - - -
259B LEU* 3.5 22.5 - - - +
260B ASP* 3.1 33.0 + - - -
263B ILE* 3.6 13.6 - - - +
377B LEU 2.7 22.1 + - - -
378B ARG* 3.7 14.6 + - - -
380B ILE* 1.3 72.8 - - - +
382B ALA* 1.3 62.0 + - - +
384B GLY 4.2 0.2 - - - +
385B ALA* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER* 4.4 17.0 - - - +
382A ALA* 3.5 23.3 - - + -
383A LYS* 4.8 17.5 + - + +
378B ARG* 2.8 20.3 + - - +
379B SER 3.4 5.6 - - - +
381B SER* 1.3 73.2 - - - +
383B LYS* 1.3 63.5 + - - +
384B GLY 3.0 4.6 + - - -
385B ALA* 3.2 18.1 + - - +
386B GLU* 3.7 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 5.6 2.8 + - - -
382A ALA* 4.4 22.4 - - + +
385A ALA* 6.3 2.0 - - - -
298B LEU* 3.7 24.4 - - + +
301B LEU* 3.9 27.7 - - + +
379B SER* 3.0 21.8 + - - +
380B ILE* 4.0 2.5 - - - +
382B ALA* 1.3 75.0 - - - +
384B GLY* 1.3 61.9 + - - +
386B GLU* 3.4 9.8 + - - +
387B ARG* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 3.8 13.9 - - - -
298B LEU* 3.7 14.4 - - - -
380B ILE 2.6 23.2 + - - -
381B SER 3.6 2.5 - - - -
382B ALA 3.0 0.8 - - - -
383B LYS* 1.3 71.9 - - - +
385B ALA* 1.3 65.0 + - - +
387B ARG* 3.0 6.2 + - - +
388B VAL* 3.0 24.3 + - - +
501B JYH 4.1 6.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 5.8 5.2 - - - +
259B LEU* 3.7 6.2 - - + +
381B SER 3.1 13.1 + - - +
382B ALA* 3.2 10.1 + - - +
384B GLY* 1.3 74.5 - - - +
386B GLU* 1.3 65.2 + - - +
388B VAL* 3.2 13.5 + - - +
389B ILE* 3.1 27.2 + - + +
407B MET* 5.6 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 5.8 2.3 + - - +
386A GLU* 3.7 33.5 - - + +
382B ALA 3.7 7.0 + - - +
383B LYS* 3.4 13.4 + - - +
384B GLY 3.1 1.0 - - - -
385B ALA* 1.3 79.1 - - - +
387B ARG* 1.3 64.2 + - - +
389B ILE* 3.2 21.3 + - + +
390B THR* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ARG 4.4 9.1 + - - -
213B LEU* 5.2 0.2 - - - +
294B GLY* 3.0 27.0 + - - +
295B PHE 3.8 14.2 + - - +
296B GLY* 4.0 16.1 - - - +
297B PRO* 3.6 20.4 - - - +
298B LEU* 3.4 27.6 - - + -
383B LYS 3.3 2.4 + - - +
384B GLY 3.0 10.3 + - - +
386B GLU* 1.3 79.4 - - - +
388B VAL* 1.3 56.4 + - - +
390B THR* 3.2 29.8 + - - +
391B LEU* 2.9 63.2 + - + +
394B GLU* 3.4 15.5 + - - -
501B JYH 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 4.4 6.5 - - + -
384B GLY 3.0 19.9 + - - +
385B ALA* 3.2 11.2 + - - +
387B ARG* 1.3 75.4 - - - +
389B ILE* 1.3 65.1 + - + +
391B LEU* 3.7 14.8 + - - +
392B LYS* 3.7 19.3 + - + +
399B MET* 4.0 18.3 - - + +
403B ILE* 4.5 4.0 - - + -
407B MET* 4.0 29.4 - - + -
501B JYH 4.1 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ALA* 3.1 16.5 + - + +
386B GLU* 3.4 25.4 - - - +
387B ARG 3.1 0.4 - - - -
388B VAL* 1.3 79.5 - - + +
390B THR* 1.3 65.7 - - - +
391B LEU 3.3 0.5 + - - -
392B LYS* 3.3 36.7 + - - +
393B MET* 4.0 7.6 + - + +
407B MET* 6.1 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLU* 3.1 13.7 + - - +
387B ARG* 3.2 31.3 + - - +
389B ILE* 1.3 80.3 - - - +
391B LEU* 1.3 62.4 + - - +
393B MET* 3.0 24.4 + - + +
394B GLU* 3.7 18.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 4.3 8.3 - - + -
218B TRP* 3.7 16.2 - - + -
294B GLY* 3.8 18.4 - - - +
387B ARG* 2.9 51.1 + - + +
388B VAL* 3.8 2.0 - - - +
389B ILE 3.2 0.6 - - - -
390B THR* 1.3 72.2 - - - +
392B LYS* 1.3 56.8 + - - +
393B MET 2.9 5.2 - - - -
394B GLU* 2.8 27.7 + - - +
395B ILE* 2.8 26.5 + - + +
399B MET* 3.7 14.4 - - + -
501B JYH 3.3 38.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B VAL* 3.7 16.4 - - + +
389B ILE* 3.3 27.5 + - - +
390B THR 3.3 0.6 - - - -
391B LEU* 1.3 75.7 - - - +
393B MET* 1.3 64.5 + - + +
394B GLU 3.3 0.8 + - - -
395B ILE* 4.1 16.9 + - - +
397B GLY 5.0 4.7 - - - +
399B MET* 3.3 34.3 - - + +
404B GLN* 3.9 27.4 + - + +
----------------------------------------------------------
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