Contacts of the helix formed by residues 346 - 360 (chain D) in PDB entry 1JLH
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 346 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ARG* 3.7 24.5 - - - +
381C GLU* 3.3 35.5 + - - +
161D LEU* 4.8 8.0 - - + +
164D LEU* 3.9 29.3 - - + +
165D MET* 3.3 21.7 - - + +
168D GLU* 4.7 1.8 - - + -
343D TYR 4.8 0.6 + - - -
344D LEU 3.1 1.0 - - - -
345D HIS* 1.3 116.5 + - + +
347D PHE* 1.3 63.1 + - - +
348D ALA 3.5 1.8 - - - -
349D ALA* 3.4 27.3 + - + +
350D TYR* 3.1 17.2 + - - +
381D GLU* 5.1 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D MET* 3.9 22.8 - - + +
337D MET* 3.6 26.2 - - + -
339D PRO* 4.2 18.6 - - + -
344D LEU* 2.9 40.4 + - + +
345D HIS 3.5 0.2 - - - -
346D ARG* 1.3 74.5 - - - +
348D ALA* 1.3 68.7 + - - +
350D TYR* 3.2 13.5 + - - +
351D PHE* 3.2 39.4 + + - -
406D LEU* 4.2 15.0 - - + -
486D LEU* 4.5 7.9 - - + -
489D LEU* 4.7 14.1 - - + -
490D VAL* 4.3 17.5 - - + -
493D TYR* 4.1 17.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D MET* 3.7 40.8 - - + +
339D PRO* 5.2 3.9 - - + +
344D LEU 4.6 0.6 + - - -
345D HIS 5.1 2.8 + - - +
347D PHE* 1.3 79.2 - - - +
349D ALA* 1.3 64.4 + - - +
351D PHE* 3.3 2.8 + - - +
352D GLN* 3.0 23.0 + - - +
378D VAL* 4.3 5.2 - - + +
379D TRP 4.3 2.5 - - - -
380D GLY* 4.0 27.8 - - - +
381D GLU* 5.5 0.7 - - - -
382D PRO* 6.3 0.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
381C GLU* 4.4 7.2 - - - +
389C ALA* 5.4 2.1 - - - +
161D LEU* 3.9 14.7 - - + +
345D HIS 5.4 0.8 + - - +
346D ARG* 3.4 50.1 + - - +
347D PHE 3.2 0.4 - - - -
348D ALA* 1.3 79.2 - - - +
350D TYR* 1.3 63.9 + - - +
352D GLN* 3.1 27.3 - - - +
353D GLN* 3.7 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D GLY* 6.3 2.0 - - - -
161D LEU* 3.7 17.2 - - + +
162D GLY* 3.2 39.9 - - - -
165D MET* 3.9 20.9 - - + -
272D ARG* 3.4 27.5 + - + -
273D TYR* 4.8 1.2 - - - -
275D LEU* 3.4 21.5 + - + +
346D ARG 3.1 14.3 + - - +
347D PHE 3.2 8.7 + - - +
349D ALA* 1.3 77.4 - - - +
351D PHE* 1.3 95.3 + + - +
352D GLN 3.1 0.2 - - - -
353D GLN* 3.2 11.5 + - - +
354D GLY* 3.1 22.1 + - - -
490D VAL* 4.0 10.0 - - + +
494D GLU* 4.4 9.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D MET* 3.7 34.5 - - + -
347D PHE* 3.2 47.1 + + - +
348D ALA 3.3 2.4 + - - +
350D TYR* 1.3 96.5 - + - +
352D GLN* 1.3 60.2 + - - +
353D GLN 3.1 1.8 - - - -
354D GLY* 3.7 5.4 - - - +
355D ASP* 2.8 37.4 + - + +
378D VAL* 4.2 3.6 - - + +
490D VAL* 3.5 30.7 - - + -
493D TYR* 3.3 32.3 - + + -
494D GLU* 4.2 9.4 - - + -
497D ILE* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C TRP* 3.9 18.8 - - - +
380C GLY 5.1 3.5 + - - +
381C GLU* 3.9 15.4 - - - +
389C ALA* 4.5 1.9 - - + +
390C PHE* 3.6 32.1 - - + +
348D ALA 3.0 11.7 + - - +
349D ALA* 3.1 22.8 - - - +
350D TYR 3.1 0.2 - - - -
351D PHE* 1.3 77.0 - - - +
353D GLN* 1.3 56.5 + - - +
356D MET* 2.9 47.6 + - - +
378D VAL* 2.7 36.6 + - - +
379D TRP* 3.9 11.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
388C HIS 3.5 14.9 + - - +
389C ALA* 3.2 34.3 - - + +
157D GLY* 3.4 22.3 + - - -
158D GLY* 3.1 20.9 + - - +
161D LEU* 3.7 20.1 - - + +
272D ARG* 3.8 16.0 + - + +
349D ALA 3.7 2.4 + - - +
350D TYR* 3.2 11.0 + - - +
352D GLN* 1.3 77.3 - - - +
354D GLY* 1.3 68.1 + - - +
355D ASP 3.1 1.3 - - - -
357D GLU* 2.8 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ARG* 4.1 21.3 - - - +
273D TYR* 3.9 3.9 + - - -
350D TYR* 3.1 15.4 + - - -
351D PHE* 3.5 8.0 + - - -
353D GLN* 1.3 78.7 - - - +
355D ASP* 1.3 55.4 + - - +
358D SER* 2.6 30.1 + - - -
497D ILE* 3.6 14.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
335D HIS* 5.3 1.7 - - - -
337D MET* 5.8 1.9 - - - +
351D PHE* 2.8 25.2 + - + +
354D GLY* 1.3 71.3 - - - +
356D MET* 1.3 59.6 + - - +
358D SER* 3.1 2.8 + - - -
359D ASN* 2.8 39.5 + - - +
375D GLY* 4.8 0.5 - - - -
376D PRO* 4.0 21.2 - - - +
378D VAL* 3.5 23.9 - - + +
496D LYS* 4.6 11.6 + - - +
497D ILE* 3.6 28.9 - - + +
500D GLN* 4.5 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 356 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C TRP* 3.7 28.9 - - + -
390C PHE* 3.8 18.6 - - + +
393C LEU* 3.8 40.6 + - + +
352D GLN* 2.9 40.3 + - - +
355D ASP* 1.3 80.3 - - - +
357D GLU* 1.3 58.5 + - - +
359D ASN 5.1 0.2 - - - -
360D GLY* 2.8 30.1 + - - +
375D GLY* 6.0 0.2 - - - -
376D PRO 3.5 16.8 - - - +
377D ILE* 3.9 11.2 - - + -
378D VAL* 3.5 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C GLN 5.5 0.7 - - - +
388C HIS* 4.0 16.8 - - - +
389C ALA 3.5 15.0 + - - +
390C PHE* 5.3 0.2 - - - +
392C GLN* 3.5 28.5 + - + +
272D ARG* 2.9 33.8 + - - +
352D GLN 4.1 0.2 + - - -
353D GLN* 2.8 39.9 + - + +
356D MET* 1.3 75.2 - - - +
358D SER* 1.3 60.1 + - - +
361D LYS* 3.4 13.5 + - - -
510D ASP 3.9 0.3 - - - +
511D GLN* 4.1 14.4 - - + +
514D VAL* 4.5 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 358 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ARG* 2.7 22.0 + - - +
273D TYR* 2.7 15.5 + - - -
354D GLY 2.6 26.3 + - - -
355D ASP 3.1 3.2 + - - -
357D GLU* 1.3 80.0 - - - +
359D ASN* 1.3 65.2 + - - +
360D GLY 3.6 0.2 - - - -
361D LYS* 2.8 25.3 + - - +
497D ILE* 3.6 15.9 - - - -
508D SER* 3.3 19.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 359 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ASP* 2.8 19.7 + - - +
358D SER* 1.3 76.8 - - - +
360D GLY* 1.3 55.5 + - - +
361D LYS* 2.9 13.0 + - - -
374D THR* 3.4 4.5 + - - -
375D GLY* 2.9 27.5 + - - -
497D ILE* 3.1 34.0 + - - +
500D GLN* 3.9 7.5 + - - +
501D GLY* 3.7 3.8 - - - +
504D TRP* 3.5 29.9 - - + -
506D ILE* 3.8 12.7 - - + +
508D SER* 2.6 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 360 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C GLN* 3.0 34.0 + - - +
393C LEU* 3.8 26.9 - - - -
396C GLN 3.5 2.6 - - - +
397C GLY* 3.8 9.2 - - - -
356D MET* 2.8 25.9 + - - +
357D GLU 4.5 0.2 - - - -
358D SER 3.6 1.2 - - - -
359D ASN* 1.3 70.9 - - - +
361D LYS* 1.3 56.5 + - - -
374D THR* 4.7 1.3 - - - -
375D GLY 5.1 0.2 - - - -
----------------------------------------------------------
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