Contacts of the helix formed by residues 372 - 384 (chain A) in PDB entry 4I6J
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 HIS 372 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A MET* 4.1 14.1 - - + +
261A SER* 3.3 36.9 - - - +
262A LEU* 3.6 29.0 + - + +
364A GLN* 5.1 0.6 + - - -
370A TRP* 3.4 28.0 - + + -
371A ILE* 1.3 73.6 - - - +
373A HIS* 1.3 93.6 + + - +
374A LEU* 3.1 34.4 + - + +
375A ALA* 2.8 21.4 + - + +
376A ARG 2.9 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A TRP* 5.0 1.0 - - - -
371A ILE 3.6 1.4 + - - -
372A HIS* 1.3 98.0 + + - +
374A LEU* 1.3 88.5 + - + +
376A ARG* 3.0 21.3 + - - +
377A HIS* 3.0 38.8 + - - -
426B PRO 4.5 1.1 - - - +
427B THR* 3.6 59.1 - - + +
428B TRP* 4.0 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A MET* 3.5 45.8 - - + -
262A LEU* 5.4 2.9 - - + -
357A TRP* 5.4 1.6 - - + -
372A HIS* 3.1 16.4 + - + +
373A HIS* 1.3 95.5 + - + +
375A ALA* 1.3 60.4 + - - +
377A HIS* 3.4 25.5 + - + +
378A ALA 3.3 15.6 + - - -
431A TYR* 5.3 1.8 - - + +
436A PHE* 3.8 35.0 - - + -
440A THR* 5.4 3.4 - - + +
395B GLU* 5.2 10.3 - - - +
425B MET* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LEU* 4.5 15.6 - - + +
357A TRP* 4.7 4.5 - - + -
361A ILE* 3.4 38.3 - - + +
364A GLN* 5.9 0.2 - - - +
371A ILE* 4.6 2.2 - - + -
372A HIS* 2.8 21.6 + - - +
374A LEU* 1.3 73.1 - - - +
376A ARG* 1.3 65.9 + - - +
378A ALA* 3.2 7.2 + - - +
379A VAL* 3.0 26.9 + - - +
446A TYR* 5.0 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A SER* 5.2 0.4 - - - -
370A TRP* 3.4 17.6 - - - +
371A ILE* 2.8 43.0 + - + +
372A HIS 2.9 13.5 + - - +
373A HIS* 3.0 16.3 + - - +
375A ALA* 1.3 77.2 - - - +
377A HIS* 1.3 52.7 + - - +
379A VAL* 3.9 3.0 - - - +
380A ALA* 2.7 39.3 + - + +
399A PHE* 4.4 14.9 - - + -
403A LEU* 3.4 19.8 - - - +
405A ASP* 2.6 44.3 + - - -
418A LEU* 5.3 0.2 - - - -
427B THR 5.7 0.4 - - - -
428B TRP* 3.1 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A HIS* 3.0 25.9 + - - -
374A LEU* 3.7 23.5 - - + +
375A ALA 3.3 0.2 - - - -
376A ARG* 1.3 77.3 - - - +
378A ALA* 1.3 58.0 + - - +
381A CYS* 2.8 35.0 + - - +
418A LEU* 3.5 36.4 - - + +
431A TYR* 3.5 36.1 - - + -
425B MET* 3.6 17.5 - - + +
426B PRO 3.1 27.0 + - - -
428B TRP 4.0 11.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TRP* 3.4 35.4 - - + +
358A ILE* 3.9 7.4 - - + +
361A ILE* 5.1 1.3 - - + -
374A LEU 3.3 10.2 + - - +
375A ALA* 3.2 9.7 + - - +
377A HIS* 1.3 79.9 - - - +
379A VAL* 1.3 59.9 + - + +
381A CYS* 3.9 1.6 - - - +
382A PHE* 3.0 28.9 + - - +
431A TYR* 4.3 17.0 - - + +
436A PHE* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TRP* 3.2 42.8 + - + +
358A ILE* 4.1 19.3 - - + +
361A ILE* 3.4 39.9 - - + -
362A MET* 3.6 19.5 - - + -
375A ALA 3.0 9.8 + - - +
376A ARG* 4.1 1.3 - - - +
378A ALA* 1.3 79.4 - - - +
380A ALA* 1.3 66.1 + - - +
382A PHE* 3.4 0.9 + - - +
383A LEU* 3.3 11.6 + - - +
399A PHE* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ARG 2.7 23.7 + - - +
377A HIS 4.0 1.6 - - - +
379A VAL* 1.3 73.8 - - - +
381A CYS* 1.3 58.0 + - - +
383A LEU* 3.3 3.3 + - - +
384A THR* 2.7 32.4 + - - -
399A PHE* 5.5 1.1 - - + -
415A TRP* 3.5 39.4 - - + -
418A LEU* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A HIS 2.8 23.5 + - - +
378A ALA 3.9 3.1 - - - +
380A ALA* 1.3 74.1 - - - +
382A PHE* 1.3 65.0 + - - +
383A LEU 3.1 0.7 + - - -
384A THR* 3.2 11.5 + - - -
385A ARG* 3.5 26.0 + - - -
386A GLY* 2.9 42.5 + - - -
418A LEU* 4.6 6.5 - - + +
429A HIS 4.8 1.3 - - - -
430A CYS* 5.3 0.4 - - - -
431A TYR* 3.7 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TRP* 3.8 17.7 - + - -
353A THR* 3.8 24.7 - - + -
355A PHE* 3.8 37.5 - + - -
358A ILE* 4.0 19.1 - - + -
378A ALA 3.0 18.2 + - - +
379A VAL* 3.7 5.6 - - - +
380A ALA 3.3 0.2 - - - -
381A CYS* 1.3 75.7 - - - +
383A LEU* 1.3 56.6 + - - +
387A ASP* 3.2 45.6 + - + +
388A LEU* 2.8 50.8 + - + +
431A TYR 5.6 2.9 + - - +
433A PRO* 3.9 13.7 - - + -
488A ILE* 4.5 2.7 - - + -
489A VAL* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.3 9.9 - - + -
348A TRP* 3.6 47.3 - - + +
379A VAL 3.3 9.5 + - - +
380A ALA 3.7 7.6 - - - +
381A CYS 3.1 0.6 - - - -
382A PHE* 1.3 82.3 - - - +
384A THR* 1.3 52.1 + - + +
388A LEU* 3.4 22.9 - - + +
389A TRP 3.2 4.0 + - - -
390A VAL* 2.7 58.6 + - + +
391A SER 4.6 3.1 - - - +
395A GLY* 3.7 23.8 - - - +
415A TRP* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TRP* 3.9 11.0 - - + -
380A ALA 2.7 26.1 + - - +
381A CYS* 3.2 3.9 + - - -
383A LEU* 1.3 74.8 - - - +
385A ARG* 1.3 68.2 + - - +
386A GLY 3.4 1.9 + - - -
387A ASP 3.9 1.2 + - - -
389A TRP* 2.8 30.7 + - - -
390A VAL 3.4 19.7 - - - +
391A SER 4.2 0.4 - - - +
392A TRP* 3.7 23.1 - - + +
415A TRP* 4.4 7.7 - - + -
419A SER* 3.6 37.0 + - - -
----------------------------------------------------------
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