Contacts of the helix formed by residues 347 - 356 (chain D) in PDB entry 1JIQ
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 ARG 347 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C ARG* 3.8 21.2 - - - +
382C GLU* 3.0 39.6 + - - -
162D LEU* 5.6 6.3 - - - +
165D LEU* 3.8 29.9 - - + +
166D MET* 3.4 22.9 - - + +
169D GLU* 4.7 2.2 - - + +
344D TYR 4.7 0.6 + - - -
345D LEU 3.1 1.2 - - - -
346D HIS* 1.3 118.6 + - + +
348D PHE* 1.3 63.1 + - - +
349D ALA 3.5 1.6 - - - -
350D ALA* 3.5 23.4 + - + +
351D TYR* 3.1 18.0 + - - +
382D GLU* 5.1 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D MET* 3.8 20.6 - - + +
338D MET* 3.6 27.4 - - + -
340D PRO* 4.3 15.7 - - + -
345D LEU* 3.0 42.9 + - + +
346D HIS 3.5 0.4 - - - -
347D ARG* 1.3 74.7 - - - +
349D ALA* 1.3 67.3 + - - +
351D TYR* 3.2 5.4 + - - +
352D PHE* 3.2 46.3 + + - -
407D LEU* 4.2 18.2 - - + -
487D LEU* 4.5 6.7 - - + -
490D LEU* 4.7 14.4 - - + -
491D VAL* 4.0 18.8 - - + -
494D TYR* 4.1 18.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D MET* 3.7 41.3 - - + +
340D PRO* 5.3 2.8 - - + +
345D LEU 4.7 0.6 + - - -
346D HIS 5.1 2.3 + - - +
347D ARG* 4.5 0.2 - - - +
348D PHE* 1.3 80.9 - - - +
350D ALA* 1.3 64.0 + - - +
352D PHE* 3.1 3.7 + - - +
353D GLN* 3.1 24.9 + - - +
379D VAL* 4.0 3.2 - - + +
380D TRP* 4.2 12.1 - - - +
381D GLY 4.0 18.8 - - - +
382D GLU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C GLU* 4.1 9.9 - - + +
390C ALA* 5.2 0.9 - - - +
162D LEU* 4.0 15.7 - - + +
346D HIS 5.4 0.4 + - - -
347D ARG* 3.5 47.1 + - + +
348D PHE 3.3 0.4 - - - -
349D ALA* 1.3 79.0 - - - +
351D TYR* 1.3 62.9 + - - +
353D GLN* 3.1 29.7 + - - +
354D GLN 3.6 2.8 + - - -
381D GLY 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D GLY* 6.5 1.3 - - - -
162D LEU* 3.9 16.0 - - + +
163D GLY* 3.3 40.6 - - - -
166D MET* 3.9 20.0 - - + -
273D ARG* 3.3 25.9 + - + -
274D TYR* 4.7 1.6 - - - -
275D SER 5.3 0.3 + - - -
276D LEU* 3.5 21.6 + - + +
277D TRP* 4.9 0.2 + - - -
347D ARG 3.1 14.9 + - - +
348D PHE 3.4 8.3 - - - +
349D ALA 3.2 0.2 - - - -
350D ALA* 1.3 76.1 - - - +
352D PHE* 1.3 95.7 + + - +
354D GLN* 3.1 10.5 + - + +
355D GLY* 3.0 23.4 + - - -
491D VAL* 4.0 8.6 - - + +
495D GLU* 4.2 12.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D MET* 3.8 35.7 - - + -
348D PHE* 3.2 41.3 + + - -
349D ALA 3.1 7.0 + - - +
351D TYR* 1.3 102.7 - + - +
353D GLN* 1.3 60.4 + - - +
354D GLN 3.1 1.1 - - - -
355D GLY* 3.9 4.0 - - - +
356D ASP* 2.7 39.3 + - + +
379D VAL* 4.2 4.8 - - + +
491D VAL* 3.8 20.6 - - + -
494D TYR* 3.4 31.6 - + + -
495D GLU* 4.3 5.4 - - + -
498D ILE* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C TRP* 3.7 21.6 - - - +
381C GLY 5.1 2.8 + - - +
382C GLU* 3.9 16.0 - - - +
390C ALA* 3.7 7.2 - - + +
391C PHE* 3.8 32.9 - - + +
349D ALA 3.1 16.7 + - - +
350D ALA* 3.1 21.0 + - - +
352D PHE* 1.3 76.5 - - - +
354D GLN* 1.3 57.9 + - - +
357D MET* 3.0 36.7 - - - +
379D VAL* 2.8 32.5 + - - +
380D TRP* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C HIS 3.4 18.1 + - - -
390C ALA* 3.4 22.8 - - - +
158D GLY* 3.3 6.7 - - - +
159D GLY* 3.1 33.2 + - - +
162D LEU* 3.6 21.0 - - + +
272D GLY* 5.5 0.4 - - - -
273D ARG* 3.7 21.6 - - + +
350D ALA 3.6 2.0 + - - -
351D TYR* 3.1 10.3 + - + +
353D GLN* 1.3 77.6 - - - +
355D GLY* 1.3 66.9 + - - +
358D GLU* 2.9 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 355 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D ARG* 4.3 19.7 - - - +
274D TYR* 3.9 5.5 + - - -
351D TYR* 3.0 17.9 + - - -
352D PHE* 4.0 11.0 - - - -
354D GLN* 1.3 77.5 - - - +
356D ASP* 1.3 55.7 - - - +
359D SER* 2.6 28.9 + - - -
498D ILE* 3.6 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D HIS* 5.3 1.6 - - - -
338D MET* 5.7 1.6 - - - +
352D PHE* 2.7 26.4 + - + +
355D GLY* 1.3 71.5 - - - +
357D MET* 1.3 59.6 + - - +
359D SER* 3.1 5.0 + - - -
360D ASN* 2.9 36.2 + - - +
376D GLY* 4.9 0.2 - - - -
377D PRO* 3.8 24.2 - - - +
379D VAL* 3.6 24.5 - - + +
494D TYR* 6.2 0.3 - - - -
497D LYS* 4.7 12.8 + - - +
498D ILE* 3.5 27.5 - - + +
501D GLN* 4.7 5.5 + - - -
----------------------------------------------------------
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