Contacts of the helix formed by residues 373 - 392 (chain A) in PDB entry 2ZJ4
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 CYS 373 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A AGP 3.8 24.1 + - - +
372A ALA* 1.3 78.1 - - - +
374A GLY* 1.3 69.7 + - - +
375A THR 3.3 0.5 + - - -
376A SER* 3.1 19.2 + - - -
377A TYR* 3.2 3.1 + - - -
399A LEU* 4.8 3.6 - - - -
400A ALA* 3.8 17.5 - - - -
401A SER* 4.9 3.1 - - - -
419A LEU 4.8 0.2 + - - -
425A THR* 3.8 15.0 - - + -
427A ASP* 4.1 12.6 - - - -
428A THR* 3.5 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A AGP 3.4 15.7 - - - -
373A CYS* 1.3 71.7 - - - +
375A THR* 1.3 62.9 + - - -
377A TYR* 3.1 10.2 + - - +
378A HIS* 3.0 26.0 + - - -
399A LEU* 4.5 7.7 - - - +
556A LEU* 4.1 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A AGP 3.0 28.8 + - - -
374A GLY* 1.3 73.6 - - - -
376A SER* 1.3 62.1 + - - +
378A HIS* 3.1 4.0 + - - +
379A ALA* 3.1 18.0 + - - +
473A SER* 4.2 9.2 - - - +
477A TYR* 3.6 26.9 - - + -
480A GLN* 4.7 2.0 - - - +
553A GLU* 2.6 39.8 + - - +
556A LEU* 3.4 6.6 - - - +
557A LYS* 2.9 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A AGP 2.7 28.9 + - - -
372A ALA* 3.6 4.5 - - - -
373A CYS 3.1 11.2 + - - -
375A THR* 1.3 76.4 - - - +
377A TYR* 1.3 61.7 + - - +
379A ALA* 3.2 8.8 + - - +
380A GLY 3.5 0.2 + - - -
419A LEU* 3.2 48.3 + - - +
420A SER* 3.6 0.9 - - - -
421A GLN* 3.7 0.5 + - - +
480A GLN* 2.8 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ALA* 3.4 21.6 - - - +
373A CYS 3.2 10.8 + - - -
374A GLY 3.1 11.2 + - - +
376A SER* 1.3 75.6 - - - +
378A HIS* 1.3 81.7 + + - +
380A GLY* 3.1 12.8 + - - -
381A VAL* 3.2 31.9 + - + +
397A VAL* 3.5 34.2 + - + +
398A GLU 3.9 18.6 - - - -
399A LEU* 3.6 44.9 - - + +
419A LEU* 5.2 0.4 - - - -
552A LEU* 4.8 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY* 3.0 21.5 + - - -
375A THR* 3.1 8.9 + - - +
377A TYR* 1.3 91.2 - + - +
379A ALA* 1.3 56.4 + - - +
381A VAL* 3.2 6.3 + - - -
382A ALA* 2.9 29.8 + - - +
477A TYR* 3.8 9.4 - - + -
549A ALA* 3.6 8.7 - - + +
552A LEU* 3.5 41.4 + - + +
553A GLU* 2.9 44.6 - - + +
556A LEU* 3.7 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A THR 3.1 7.9 + - - +
376A SER 3.2 10.5 + - - +
378A HIS* 1.3 74.7 - - - +
380A GLY* 1.3 58.9 + - - +
382A ALA* 3.4 5.7 + - - +
383A THR* 2.9 30.9 + - - +
419A LEU* 4.6 4.0 - - + -
477A TYR* 3.6 18.3 - - + +
480A GLN* 3.8 39.0 - - + +
481A PHE* 4.5 6.2 - - - +
484A LEU* 4.0 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.8 22.0 - - - +
376A SER 3.5 4.8 + - - -
377A TYR 3.1 8.2 + - - -
379A ALA* 1.3 74.5 - - - +
381A VAL* 1.3 64.2 + - - +
382A ALA 3.1 1.1 - - - -
383A THR* 3.2 3.6 + - - -
384A ARG* 3.0 25.5 + - - +
397A VAL* 4.0 13.4 - - - +
419A LEU* 3.7 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 3.2 47.6 + - + +
378A HIS* 3.2 9.4 + - - +
380A GLY* 1.3 76.9 - - - +
382A ALA* 1.3 60.6 + - - +
383A THR 3.5 0.7 + - - -
384A ARG* 3.7 17.3 + - - +
385A GLN 5.0 1.0 + - - -
397A VAL* 3.9 9.4 - - + -
546A TYR 5.6 0.2 - - - +
548A TYR* 4.0 29.4 - - + -
549A ALA* 3.9 17.6 + - + +
552A LEU* 4.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A HIS 2.9 16.7 + - - +
379A ALA* 3.6 8.1 - - - +
380A GLY 3.1 0.6 - - - -
381A VAL* 1.3 78.3 - - - +
383A THR* 1.3 60.8 + - - +
384A ARG 3.6 0.2 - - - -
385A GLN 5.4 0.6 + - - -
386A VAL* 5.5 0.7 - - - +
477A TYR* 3.5 14.4 - - - +
481A PHE* 3.8 29.1 - - + -
546A TYR* 4.8 22.8 - - - +
549A ALA* 3.4 18.8 - - + +
642A CYS 5.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ALA 2.9 17.4 + - - +
380A GLY* 3.2 4.4 + - - -
382A ALA* 1.3 80.9 - - - +
384A ARG* 1.3 66.2 + - - +
385A GLN 3.4 2.2 - - - -
386A VAL* 3.4 12.7 + - + +
387A LEU* 2.9 32.6 + - - +
481A PHE* 3.7 44.2 - - + +
484A LEU* 3.3 28.7 - - + +
485A VAL* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLY 3.0 16.1 + - - +
381A VAL* 3.8 12.3 - - - +
382A ALA 3.6 2.0 - - - -
383A THR* 1.3 76.4 - - - +
385A GLN* 1.3 59.3 + - - +
387A LEU* 3.2 7.8 + - - +
388A GLU* 2.9 49.1 + - - +
395A VAL* 3.0 46.9 + - + +
396A MET* 4.5 9.4 - - - +
397A VAL* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A VAL 5.0 0.8 + - - -
382A ALA 5.4 0.6 - - - +
383A THR 3.4 0.4 - - - -
384A ARG* 1.3 80.0 - - - +
386A VAL* 1.3 58.0 + - - +
388A GLU* 3.3 17.6 + - + +
389A GLU* 2.9 27.6 + - + +
545A GLY* 4.4 8.3 - - - -
546A TYR* 3.5 62.4 + - + +
597A THR* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ALA 5.5 0.2 - - - +
383A THR* 3.4 25.2 - - + +
385A GLN* 1.3 76.9 - - - +
387A LEU* 1.3 69.1 + - + +
389A GLU* 3.9 19.3 - - - +
390A LEU* 3.1 45.2 + - + +
485A VAL* 4.5 19.5 - - + -
488A ALA* 4.4 8.4 - - + +
505A ILE* 4.5 2.7 - - + -
546A TYR* 4.6 4.3 - - + -
642A CYS* 4.1 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.3 7.9 - - + -
370A LEU* 3.7 36.6 - - + -
383A THR* 2.9 34.7 + - - +
384A ARG* 3.2 4.9 + - - +
386A VAL* 1.3 75.2 - - + +
388A GLU* 1.3 61.0 + - - +
391A THR* 2.6 39.9 + - + -
395A VAL* 4.0 13.5 - - + -
484A LEU* 4.0 15.5 - - + +
487A PHE* 3.7 34.8 - - + -
488A ALA* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 2.9 41.1 + - - +
385A GLN* 3.3 24.3 + - - +
387A LEU* 1.3 75.8 - - - +
389A GLU* 1.3 57.0 + - - +
392A GLU* 2.8 32.6 + - - +
393A LEU 3.9 15.0 - - - +
394A PRO* 5.3 1.5 - - + +
395A VAL* 3.8 22.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 2.9 19.3 + - + +
386A VAL* 3.6 11.7 - - - +
387A LEU 3.3 0.2 - - - -
388A GLU* 1.3 76.7 - - - +
390A LEU* 1.3 69.3 + - + +
392A GLU* 3.8 13.3 - - - +
498A MET* 3.9 8.0 - - - +
501A ARG* 2.8 51.3 + - - +
546A TYR* 3.8 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A VAL* 3.1 23.1 + - + +
389A GLU* 1.3 110.0 - - + +
391A THR* 1.3 63.3 + - - +
392A GLU 3.5 0.2 - - - -
485A VAL* 6.1 0.9 - - + -
488A ALA* 3.8 41.3 - - + +
489A LEU* 4.3 7.0 - - + +
492A CYS* 3.4 26.7 + - - +
495A ARG* 2.8 23.7 + - - -
498A MET* 3.7 14.0 - - + +
501A ARG* 4.2 14.1 - - + -
502A ARG* 5.6 0.9 - - + -
505A ILE* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.2 17.9 - - + +
387A LEU* 2.6 37.3 + - + +
390A LEU* 1.3 76.0 - - - +
392A GLU* 1.3 65.6 + - - +
393A LEU* 3.0 45.9 + - - +
395A VAL* 4.6 0.3 - - - +
487A PHE* 4.7 0.2 - - + -
488A ALA* 5.0 3.1 - - - -
491A MET* 3.9 37.8 - - + +
495A ARG* 3.8 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU 2.8 17.5 + - - +
389A GLU 3.8 14.9 - - - +
391A THR* 1.3 77.9 - - - +
393A LEU* 1.3 65.0 + - + +
394A PRO* 4.2 2.6 - - - +
495A ARG* 3.9 18.9 + - - +
498A MET* 3.8 19.9 - - + +
----------------------------------------------------------
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