Contacts of the helix formed by residues 315 - 334 (chain B) in PDB entry 3OX4
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 315 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LYS* 4.6 0.4 - - - -
314B LEU* 1.3 76.0 - - - +
316B ASP* 1.3 55.8 + - - -
317B LYS 3.3 2.5 - - - -
318B GLU* 3.2 18.8 + - - -
319B GLY* 2.7 32.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
297B ALA* 3.8 7.9 - - + +
298B GLY* 3.4 33.8 - - - +
301B LYS* 3.5 25.0 + - - +
315B GLY* 1.3 71.0 - - - -
317B LYS* 1.3 57.9 + - - +
320B ALA* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 4.3 10.5 - - + +
315B GLY 3.3 0.6 - - - -
316B ASP* 1.3 77.6 - - - +
318B GLU* 1.3 63.9 + - + +
320B ALA* 3.5 2.3 + - - +
321B GLU* 3.0 29.2 + - + +
----------------------------------------------------------
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 LEU* 4.1 25.0 - - + +
315B GLY* 3.2 22.4 + - - +
317B LYS* 1.3 79.7 - - + +
319B GLY* 1.3 67.4 + - - +
321B GLU* 3.2 7.3 + - - +
322B ALA* 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LYS* 4.0 17.7 - - - -
311B ILE* 3.5 10.7 - - - +
314B LEU* 3.9 17.7 - - - +
315B GLY 2.7 21.0 + - - -
316B ASP 3.8 0.4 - - - -
318B GLU* 1.3 73.1 - - - +
320B ALA* 1.3 56.7 + - - +
322B ALA* 3.3 1.0 + - - +
323B THR* 2.9 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA* 4.7 7.4 - - + -
297B ALA* 3.6 30.7 - - + +
300B LEU* 4.0 16.1 - - + +
301B LYS* 4.3 2.3 - - - +
316B ASP 2.8 18.4 + - - +
317B LYS* 3.7 4.0 - - - +
319B GLY* 1.3 75.5 - - - +
321B GLU* 1.3 63.6 + - - +
323B THR* 3.0 10.0 + - - -
324B ILE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA* 5.2 4.0 - - - +
317B LYS* 3.0 19.8 + - + +
318B GLU* 3.2 6.7 + - - +
320B ALA* 1.3 76.5 - - - +
322B ALA* 1.3 61.9 + - - +
324B ILE* 3.5 14.8 + - - +
325B GLN* 3.1 17.9 + - + +
328B ARG* 3.1 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 3.7 3.6 - - + +
311B ILE* 3.7 24.0 - - + -
314B LEU* 4.4 6.1 - - + -
318B GLU 2.9 16.1 + - - +
319B GLY 3.6 4.5 - - - +
320B ALA 3.2 0.2 - - - -
321B GLU* 1.3 74.4 - - - +
323B THR* 1.3 65.8 + - - +
325B GLN* 3.5 7.3 + - - +
326B ALA* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 3.6 32.3 - - + -
300B LEU* 3.3 27.0 + - + +
304B GLY* 3.4 23.4 - - - -
307B MET* 4.7 3.1 - - - -
309B LEU* 3.5 9.8 - - + +
311B ILE* 3.4 4.7 - - - +
319B GLY 2.9 17.8 + - - -
320B ALA* 3.0 9.5 + - - -
322B ALA* 1.3 77.3 - - - +
324B ILE* 1.3 65.4 + - + +
326B ALA* 2.9 14.4 + - - +
327B VAL* 3.0 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO* 3.7 17.5 - - + +
289B LEU* 3.6 24.2 - - + +
290B ALA* 3.5 33.2 - - + +
293B ALA* 4.3 11.2 - - + -
300B LEU* 4.4 5.8 - - + -
320B ALA 2.9 20.2 + - - +
321B GLU* 3.8 15.0 - - - +
323B THR* 1.3 78.4 - - + +
325B GLN* 1.3 57.0 + - - +
327B VAL* 3.2 11.4 + - - +
328B ARG* 3.0 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B GLU* 3.1 18.9 + - + +
322B ALA* 3.7 7.9 - - - +
323B THR 3.2 0.2 - - - -
324B ILE* 1.3 73.8 - - - +
326B ALA* 1.3 60.4 + - - +
328B ARG* 3.1 35.9 + - - +
329B ASP* 2.7 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B MET* 5.1 9.4 - - + +
309B LEU* 3.6 27.6 - - + -
322B ALA 3.0 13.3 + - - +
323B THR 2.9 12.2 + - - +
325B GLN* 1.3 77.1 - - - +
327B VAL* 1.3 56.1 + - - +
329B ASP* 3.4 8.5 + - - +
330B LEU* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B MET* 4.2 11.5 - - + +
196B LEU* 4.6 6.5 - - + -
200B PHE* 3.8 32.8 - - + -
285B LEU* 3.7 30.7 - - + -
286B PRO* 4.2 13.7 - - + -
289B LEU* 4.1 8.7 - - + -
307B MET* 4.7 7.4 - - + -
323B THR 3.0 17.5 + - - +
324B ILE* 3.2 8.7 + - - +
326B ALA* 1.3 75.5 - - - +
328B ARG* 1.3 66.5 + - - +
330B LEU* 3.2 6.3 + - - +
331B ALA* 2.9 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B PRO* 3.7 28.9 + - + +
287B HIS* 5.9 6.1 + - - -
290B ALA* 4.7 8.1 - - - +
321B GLU* 3.1 27.9 + - - -
324B ILE* 3.0 41.9 + - - +
325B GLN* 3.1 38.0 + - - +
327B VAL* 1.3 78.1 - - - +
329B ASP* 1.3 57.2 + - - +
331B ALA* 3.3 6.9 + - - +
332B ALA* 3.0 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLN* 2.7 49.6 + - - +
326B ALA* 3.8 6.6 - - - +
328B ARG* 1.3 72.9 - - - +
330B LEU* 1.3 61.4 + - - +
332B ALA* 3.4 6.8 + - - +
333B SER* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B MET* 4.2 13.2 - - - -
196B LEU* 4.2 25.6 - - + -
223B ILE* 4.8 6.3 - - + +
224B ALA* 5.0 10.3 - - - +
227B LEU* 4.5 11.4 - - + -
228B LYS* 4.5 22.4 - - + +
307B MET* 4.6 12.3 - - + -
326B ALA 2.9 18.7 + - - +
327B VAL* 3.2 5.4 + - - +
329B ASP* 1.3 75.1 - - - +
331B ALA* 1.3 62.9 + - - +
333B SER* 2.6 28.5 + - - +
334B ILE* 3.2 19.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B MET* 4.2 15.7 - - + +
282B ALA 5.0 4.3 - - - +
286B PRO* 6.2 2.5 - - + -
327B VAL* 2.9 17.4 + - + +
328B ARG* 3.6 7.6 - - - +
330B LEU* 1.3 77.6 - - - +
332B ALA* 1.3 61.3 + - - +
334B ILE* 3.3 3.9 + - - -
335B GLY 3.3 4.3 + - - -
336B ILE* 2.9 55.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ARG 3.0 17.0 + - - +
329B ASP* 3.7 7.4 - - - +
331B ALA* 1.3 75.2 - - - +
333B SER* 1.3 62.7 + - - +
334B ILE 3.1 1.4 + - - -
335B GLY* 3.1 13.1 + - - +
336B ILE 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 4.4 4.3 + - - -
228B LYS* 3.8 32.8 + - - +
329B ASP 2.9 14.2 + - - -
330B LEU* 2.6 33.5 + - - +
332B ALA* 1.3 77.6 - - - +
334B ILE* 1.3 59.7 + - - +
335B GLY 3.5 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS* 3.3 22.0 + - - +
186B GLY* 6.0 0.3 - - - -
189B ALA* 3.6 30.7 - - + +
193B MET* 3.9 27.4 - - + -
227B LEU* 3.9 19.7 - - + -
228B LYS* 4.2 20.4 - - + +
231B CYS* 3.8 26.7 - - + -
330B LEU* 3.4 16.6 - - + +
331B ALA 3.5 7.6 - - - +
332B ALA 3.1 0.4 - - - -
333B SER* 1.3 90.1 + - - +
335B GLY* 1.3 59.7 + - - +
336B ILE* 4.0 4.0 - - + -
----------------------------------------------------------
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