Contacts of the helix formed by residues 315 - 328 (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 ASP 315 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLU 3.7 0.4 + - - -
314B MET* 1.3 74.8 - - - +
316B ASP* 1.3 61.9 + - - +
317B THR* 3.4 9.9 + - - -
318B GLU* 2.9 32.9 + - - +
319B THR* 2.9 31.5 + - - -
355B TYR* 2.5 27.5 + - - -
359B ARG* 3.5 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 4.4 15.4 - - + +
188B HIS* 3.4 33.6 + - + +
189B GLN* 4.8 12.9 - - + +
192B PHE* 4.5 9.2 - - - +
194B SER* 4.3 23.7 - - - -
315B ASP* 1.3 76.9 - - - +
317B THR* 1.3 57.4 + - - +
319B THR* 4.3 2.7 - - - -
320B GLY* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B THR* 3.5 37.7 - - + +
184B ILE* 4.0 1.2 - - - +
185B ARG* 3.3 32.0 - - + +
315B ASP* 3.1 4.9 + - - -
316B ASP* 1.3 79.4 - - - +
318B GLU* 1.3 58.3 + - - +
320B GLY* 3.3 1.0 + - - -
321B LEU* 2.9 33.4 + - + +
355B TYR* 3.3 40.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B MET* 3.0 40.2 - - + +
315B ASP* 2.9 22.6 + - - +
317B THR* 1.3 76.4 - - - +
319B THR* 1.3 57.3 + - - +
321B LEU* 3.8 6.8 - - - +
322B LEU* 3.0 30.0 + - - +
352B LEU* 4.4 10.6 - - + +
355B TYR* 3.7 17.3 - - + -
356B ILE* 3.9 17.8 - - + +
359B ARG* 3.1 18.9 + - - +
360B ARG* 3.1 30.8 + - - -
370B ILE* 4.5 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B HIS* 3.3 31.6 - - + +
192B PHE* 5.6 0.4 - - + -
264B LEU* 4.6 9.9 - - + -
265B ARG* 6.1 2.2 - - + -
268B THR* 4.3 22.4 - - + +
314B MET* 3.3 25.3 - - + +
315B ASP 2.9 19.0 + - - -
316B ASP* 4.0 2.2 - - - -
318B GLU* 1.3 76.9 - - - +
320B GLY* 1.3 55.8 + - - +
322B LEU* 3.4 4.9 + - - +
323B SER* 2.8 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 3.6 10.8 - - - -
188B HIS* 3.8 25.5 - - - -
235B PHE* 3.5 10.1 - - - -
316B ASP 3.0 17.7 + - - -
317B THR 3.8 0.7 - - - -
319B THR* 1.3 73.7 - - - +
321B LEU* 1.3 60.2 + - - +
323B SER* 3.3 0.9 + - - -
324B ALA* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 5.9 0.4 - - + -
181B THR* 4.2 12.8 - - + -
184B ILE* 3.4 28.2 - - + +
317B THR* 2.9 35.6 + - + +
318B GLU* 3.8 4.7 - - - +
320B GLY* 1.3 75.6 - - - +
322B LEU* 1.3 56.7 + - - +
324B ALA* 3.4 3.8 + - - +
325B ILE* 3.0 35.2 + - - +
348B LEU* 4.1 24.9 - - + +
351B ALA* 4.1 16.8 - - + +
352B LEU* 3.8 39.7 - - + +
355B TYR* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.5 22.9 - - + -
309B LEU* 6.2 0.4 - - + -
314B MET* 4.4 21.1 - - + -
318B GLU 3.0 17.2 + - - +
319B THR* 3.7 5.6 - - - +
320B GLY 3.2 0.2 - - - -
321B LEU* 1.3 74.6 - - - +
323B SER* 1.3 65.7 + - - +
324B ALA 3.1 1.6 - - - -
325B ILE* 3.2 7.1 + - + +
326B CYS* 3.0 23.3 + - + +
352B LEU* 4.7 7.4 - - + -
370B ILE* 4.1 26.9 - - + +
371B LEU* 4.3 11.0 - - + +
373B LYS* 4.7 11.7 - - + -
374B ILE* 3.6 35.2 - - + +
377B LEU* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B HIS* 4.9 5.0 - - - -
235B PHE* 4.2 16.8 - - - -
261B ILE* 3.7 27.5 - - - +
264B LEU* 3.2 21.1 - - - +
265B ARG* 5.6 2.8 + - - +
319B THR* 2.8 26.2 + - - +
320B GLY* 3.7 4.9 - - - -
322B LEU* 1.3 76.2 - - - +
324B ALA* 1.3 57.5 + - - +
326B CYS* 3.4 7.8 + - - +
327B LEU* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ILE* 4.4 4.7 - - + -
235B PHE* 4.2 1.5 - - + -
239B LEU* 3.8 33.0 - - + -
320B GLY 3.0 16.1 + - - +
321B LEU* 3.6 9.0 - - - +
322B LEU 3.1 0.2 - - - -
323B SER* 1.3 76.8 - - - +
325B ILE* 1.3 59.4 + - - +
327B LEU* 3.3 0.8 + - - -
328B ILE* 2.9 35.9 + - - +
348B LEU* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A MET* 6.5 0.9 - - + -
321B LEU 3.0 19.0 + - - +
322B LEU* 3.2 9.2 + - + +
324B ALA* 1.3 75.6 - - - +
326B CYS* 1.3 63.2 + - - +
328B ILE 3.5 4.7 - - - +
329B CYS* 4.3 1.4 - - - +
345B GLN* 3.4 32.1 + - + +
348B LEU* 3.7 35.4 - - + +
349B LEU* 3.8 27.4 - - + -
352B LEU* 3.6 31.0 - - + -
371B LEU* 4.2 5.8 - - + -
374B ILE* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ALA* 4.0 9.9 - - - -
260B ASP* 3.7 33.2 - - - -
261B ILE* 4.6 6.3 - - + -
322B LEU* 3.0 13.6 + - + +
323B SER* 3.5 13.2 - - - +
325B ILE* 1.3 79.6 - - - +
327B LEU* 1.3 61.3 + - - +
329B CYS* 3.6 5.0 - - - +
332B ARG* 3.0 31.2 + - - +
374B ILE* 4.4 27.6 - - + +
377B LEU* 5.0 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 5.6 1.6 - - + +
235B PHE* 5.3 4.3 - - + -
236B ALA* 3.5 32.3 - - + +
239B LEU* 3.9 17.9 - - + -
242B PHE* 3.9 15.3 - - + -
253B LEU* 3.3 51.6 - - - +
254B LEU* 3.6 19.7 - - + +
257B ALA* 3.6 15.5 - - + +
258B CYS* 5.3 0.4 - - - +
261B ILE* 4.3 9.4 - - + -
323B SER 3.1 16.5 + - - +
324B ALA* 3.9 3.4 - - - +
326B CYS* 1.3 77.1 - - - +
328B ILE* 1.3 59.2 + - + +
329B CYS* 2.8 9.6 + - - +
332B ARG* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 4.1 22.0 - - + -
240B PRO 6.2 0.2 - - - +
242B PHE* 3.6 37.0 - - + -
245B LEU* 5.1 2.7 - - + -
253B LEU* 4.4 4.9 - - + -
324B ALA 2.9 17.0 + - - +
325B ILE 3.5 3.3 - - - +
327B LEU* 1.3 74.1 - - + +
329B CYS* 1.3 58.0 + - - +
341B VAL* 3.5 31.4 - - + +
344B LEU* 3.8 14.4 - - + -
345B GLN* 2.9 40.9 + - + +
348B LEU* 4.1 11.0 - - + -
----------------------------------------------------------
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