Contacts of the helix formed by residues 348 - 361 (chain D) in PDB entry 1JXQ
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 TRP 348 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B TRP* 4.6 28.1 - + - +
351B GLU* 6.0 1.7 - - + +
352B THR* 5.9 0.2 + - - -
334D PHE* 3.8 14.8 - + + -
336D GLY* 2.8 26.5 + - - +
337D PHE 4.0 11.7 - - - +
338D VAL* 3.8 20.2 - - + +
346D GLY 3.6 2.4 + - - -
347D SER* 1.3 71.2 - - - +
349D TYR* 1.3 60.3 + - - +
351D GLU* 3.9 5.8 - - + +
352D THR* 2.9 57.1 + - - -
376D ALA* 3.3 29.8 - - + -
377D VAL* 3.7 27.4 - - + -
380D LYS* 3.3 49.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D PHE* 5.2 0.7 - + - -
282D ILE 5.2 1.8 - - - -
283D GLN* 3.0 33.9 - - + +
330D SER* 3.3 21.0 + - - -
332D SER* 3.5 27.7 - - - +
334D PHE* 4.2 13.8 - - + -
336D GLY 4.4 0.8 + - - -
347D SER* 3.0 9.4 + - - +
348D TRP* 1.3 84.0 - - - +
350D VAL* 1.3 70.7 + - + +
352D THR* 3.0 5.1 + - - -
353D LEU* 2.8 60.6 + - + +
370D LEU* 5.2 1.7 - - - +
373D VAL* 3.7 25.4 - - + +
377D VAL* 4.2 7.9 - - + -
387D PRO* 3.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D ASP* 3.1 40.2 - - + +
188D LYS* 4.0 17.7 - - + +
189D LEU* 4.4 25.6 - - + +
235D LEU* 5.3 1.1 - - + -
283D GLN* 4.5 12.3 - - + -
347D SER* 3.2 21.9 + - - +
349D TYR* 1.3 89.3 - - + +
351D GLU* 1.3 57.6 + - - +
353D LEU* 3.8 5.3 - - - +
354D ASP* 2.7 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE 4.9 0.3 - - - +
338B VAL 3.2 22.6 - - - +
339B SER* 3.8 7.6 + - - -
340B TRP* 2.9 44.3 + - - +
348B TRP* 6.3 0.9 - - + -
380B LYS* 5.5 1.7 + - - -
188D LYS* 3.0 37.4 + - - +
338D VAL* 4.1 8.3 - - + -
347D SER 3.1 11.1 + - - +
348D TRP* 3.9 7.4 - - + +
350D VAL* 1.3 83.4 - - - +
352D THR* 1.3 61.9 + - - +
354D ASP* 3.8 1.6 - - - +
355D ASP* 2.9 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D TRP* 2.9 54.2 + - + -
349D TYR* 3.4 4.0 - - - -
351D GLU* 1.3 77.9 - - - +
353D LEU* 1.3 59.7 + - - +
355D ASP* 3.4 5.4 + - - +
356D ILE* 2.9 41.8 + - + +
373D VAL* 4.3 12.3 - - + +
376D ALA* 3.8 27.6 - - + -
377D VAL* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D LEU* 4.7 16.8 - - + -
192D ARG* 5.1 3.1 - - + -
193D PHE* 6.1 2.5 - - + -
281D PHE* 4.5 19.5 - - + -
349D TYR* 2.8 52.9 + - + +
350D VAL* 3.8 4.9 - - - +
352D THR* 1.3 74.7 - - - +
354D ASP* 1.3 67.5 + - - +
356D ILE* 3.2 1.2 + - - -
357D PHE* 2.9 62.4 + - + -
370D LEU* 4.6 9.0 - - + -
373D VAL* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 2.5 37.3 + - - -
341B ARG* 4.1 7.5 + - - -
188D LYS* 3.7 23.5 - - + +
189D LEU* 5.2 4.0 - - + -
192D ARG* 2.5 62.7 + - - +
350D VAL 2.7 23.7 + - - +
351D GLU* 3.8 6.9 - - - +
353D LEU* 1.3 78.8 - - + +
355D ASP* 1.3 57.5 + - - +
357D PHE* 3.9 0.2 - - - +
358D GLU* 3.0 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 3.9 32.7 - - + +
380B LYS* 3.2 35.0 + - - +
351D GLU* 2.9 22.8 + - + +
352D THR* 3.6 7.4 - - - +
353D LEU 3.1 0.2 - - - -
354D ASP* 1.3 75.8 + - - +
356D ILE* 1.3 65.7 + - + +
358D GLU* 3.3 5.4 + - - +
359D GLN* 3.1 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D THR* 2.9 28.9 + - + +
353D LEU 3.7 2.9 - - - +
355D ASP* 1.3 75.1 - - + +
357D PHE* 1.3 62.0 + - + +
359D GLN* 3.0 2.9 + - - -
360D TRP* 2.8 43.0 + - + +
369D LEU* 3.9 33.4 - - + +
372D ARG* 3.5 20.9 - - + +
373D VAL* 3.4 37.9 - - + +
376D ALA* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ARG* 3.6 31.8 + - - +
193D PHE* 5.1 3.8 - + - -
196D LEU* 4.1 15.0 - - + -
281D PHE* 4.5 9.6 - + - -
353D LEU* 2.9 45.6 + - + +
354D ASP 3.9 0.2 - - - +
356D ILE* 1.3 76.9 - - + +
358D GLU* 1.3 64.2 + - - +
361D ALA* 2.9 39.0 + - + +
366D LEU* 4.4 9.0 - - + -
369D LEU* 3.7 36.6 - - + -
370D LEU* 3.9 20.0 - - + -
373D VAL* 4.8 2.0 - - + -
400D PHE* 3.9 22.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B TRP* 3.5 41.0 - - + -
341B ARG* 5.4 0.9 + - - -
192D ARG* 2.9 30.0 + - - +
195D SER* 5.5 0.2 + - - -
354D ASP 3.0 19.2 + - - +
355D ASP* 3.4 8.3 - - - +
357D PHE* 1.3 77.2 - - - +
359D GLN* 1.3 66.3 + - + +
361D ALA 5.1 0.2 + - - -
362D HIS* 5.2 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LYS 4.4 13.0 - - - +
381B GLY* 5.9 0.2 - - - -
355D ASP* 3.1 26.8 + - - +
356D ILE* 3.0 2.0 + - - -
357D PHE 3.0 0.8 - - - -
358D GLU* 1.3 85.5 - - + +
360D TRP* 1.3 91.3 + - + +
362D HIS* 3.2 20.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ILE* 3.8 22.2 - - + -
383B TYR* 6.5 0.2 - + - -
356D ILE* 2.8 30.5 + - + +
359D GLN* 1.3 102.7 + - + +
361D ALA* 1.3 63.0 + - - +
362D HIS* 2.8 13.6 + - - -
363D SER* 2.8 14.4 + - - -
364D GLU* 2.8 55.4 + - - +
369D LEU* 3.4 16.6 - - + -
372D ARG* 2.9 43.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 361 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ARG* 6.0 0.2 - - - +
196D LEU* 4.3 23.6 - - + -
357D PHE* 2.9 27.0 + - + +
360D TRP* 1.3 76.9 - - - +
362D HIS* 1.3 60.1 + - - +
363D SER 3.3 0.4 + - - -
364D GLU 3.7 9.1 + - - +
369D LEU* 3.6 25.0 - - + +
399D PHE* 5.2 2.6 - - - +
400D PHE* 4.1 17.5 + - + +
402D THR* 3.5 13.4 + - + +
----------------------------------------------------------
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