Contacts of the helix formed by residues 319 - 332 (chain B) in PDB entry 3Q36
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 THR 319 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B GLY 4.4 5.4 - - - +
318B LEU* 1.3 76.7 - - - +
320B LEU* 1.3 65.2 + - - +
321B GLU* 2.9 41.2 + - - +
322B GLN* 2.9 36.2 + - - +
323B ALA* 2.9 11.8 + - - +
353B PHE* 3.7 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B THR* 1.3 73.0 - - - +
321B GLU* 1.3 65.4 + - + +
323B ALA* 3.8 0.2 - - - +
324B LEU* 3.3 29.3 + - + +
349B ILE* 3.8 7.0 - - + +
350B ARG* 3.5 52.5 - - + +
353B PHE* 3.3 53.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
319B THR* 2.9 25.1 + - - +
320B LEU* 1.3 81.0 - - + +
322B GLN* 1.3 66.1 + - + +
324B LEU* 3.9 6.4 - - - +
325B GLN* 3.1 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ILE 3.0 25.3 + - - +
272B SER* 4.5 4.4 - - - +
273B LEU* 3.4 25.9 - - + +
317B GLY 4.1 1.4 - - - +
318B LEU* 3.3 17.1 - - + +
319B THR* 2.9 41.4 + - + +
321B GLU* 1.3 80.1 - - + +
323B ALA* 1.3 55.4 + - - +
325B GLN* 3.2 9.9 + - + +
326B PHE* 2.6 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 6.3 1.1 - - + -
318B LEU* 4.4 11.7 - - + +
319B THR 2.9 7.6 + - - +
320B LEU 3.8 4.3 - - - +
322B GLN* 1.3 74.1 - - - +
324B LEU* 1.3 56.7 + - - +
326B PHE* 2.8 26.4 + - - +
327B TRP* 2.8 29.0 + - + +
349B ILE* 3.9 10.1 - - + -
353B PHE* 3.7 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 3.3 29.7 + - + +
321B GLU* 3.9 5.2 - - - +
323B ALA* 1.3 77.6 - - - +
325B GLN* 1.3 54.2 + - - +
327B TRP* 4.9 2.5 - - - -
328B LYS* 2.7 45.8 + - + +
341B PHE* 4.8 8.7 - - + -
342B ASP* 5.6 1.3 - - - +
346B SER* 4.1 26.0 - - - +
349B ILE* 3.5 30.7 - - + +
350B ARG* 4.4 15.7 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
273B LEU* 3.2 26.7 - - + +
321B GLU 3.1 16.0 + - - +
322B GLN* 3.3 10.1 - - - +
323B ALA 3.1 0.4 - - - -
324B LEU* 1.3 76.5 - - - +
326B PHE* 1.3 55.5 + - - +
328B LYS* 4.6 3.9 - - - +
329B GLN* 3.1 54.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.4 17.7 - - + -
276B ILE* 3.7 25.8 - - + -
292B HIS* 3.9 8.1 - + - -
295B LEU* 3.4 31.4 - - + -
296B ARG* 4.1 22.4 - - - -
309B TYR* 3.7 19.3 - + - -
313B LEU* 3.4 29.6 - - + -
318B LEU* 4.7 4.3 - - + -
322B GLN 2.6 17.1 + - - +
323B ALA* 2.8 13.5 + - - +
325B GLN* 1.3 68.9 - - - +
327B TRP* 1.3 78.0 + + - +
329B GLN* 4.1 3.3 - - - +
330B GLU* 3.4 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.6 30.1 - - + -
301B LEU* 3.8 23.6 - - + -
306B ARG* 3.9 21.5 - - + -
309B TYR* 3.9 14.4 - + - -
310B GLY* 3.5 34.6 + - - -
313B LEU* 4.5 6.3 - - + +
323B ALA* 2.8 35.6 + - - +
324B LEU 4.3 0.2 - - - +
326B PHE* 1.3 80.5 - + - +
328B LYS* 1.3 70.2 + - - +
330B GLU* 2.8 15.7 + - - +
331B PHE* 2.8 40.6 + + + -
341B PHE* 3.8 18.8 - - + -
349B ILE* 3.6 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 2.7 27.7 + - + +
325B GLN* 4.1 4.7 - - - +
327B TRP* 1.3 76.7 - - - +
329B GLN* 1.3 57.9 + - - +
330B GLU 2.8 4.2 + - - -
331B PHE* 2.9 1.4 + - - +
332B ILE* 2.9 48.3 + - + +
338B PRO* 3.7 13.0 + - - +
341B PHE* 3.1 32.1 - - + -
342B ASP* 2.7 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 5.3 3.8 - - - +
325B GLN* 3.1 42.9 + - - +
326B PHE* 4.2 3.0 - - - +
328B LYS* 1.3 78.6 - - - +
330B GLU* 1.3 58.4 + - - +
332B ILE* 4.0 11.7 - - + +
333B LYS* 3.2 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.5 42.2 - - + +
296B ARG* 3.4 46.9 + - - -
299B HIS* 3.2 47.3 + - - +
326B PHE* 3.4 17.0 + - + +
327B TRP* 2.8 13.1 + - - +
329B GLN* 1.3 71.4 - - - +
331B PHE* 1.3 67.8 + - - +
332B ILE 3.2 1.1 - - - -
333B LYS* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.8 7.6 - - + -
299B HIS 3.5 14.4 - - - +
300B HIS* 3.8 30.1 - + - -
301B LEU 4.2 3.8 - - - -
306B ARG* 4.1 16.6 - - - -
327B TRP* 2.8 42.5 + + + +
328B LYS 3.6 6.1 - - - +
330B GLU* 1.3 77.7 - - - +
332B ILE* 1.3 57.7 + - + +
333B LYS 3.3 0.2 - - - -
334B GLY* 3.2 13.5 + - - -
336B MET* 2.9 34.6 + - + +
341B PHE* 3.7 28.5 - + + -
345B TYR* 3.7 40.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LYS* 2.9 50.2 + - + +
329B GLN* 4.3 9.0 - - + +
331B PHE* 1.3 75.2 - - + +
333B LYS* 1.3 61.7 + - + +
334B GLY 2.9 5.6 - - - -
335B LYS* 3.2 17.8 + - - +
336B MET* 3.9 22.0 - - + +
338B PRO* 4.2 25.4 - - + -
341B PHE* 5.4 2.7 - - + -
----------------------------------------------------------
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