Contacts of the helix formed by residues 362 - 384 (chain A) in PDB entry 4BSN
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 GLU 362 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 3.9 31.6 - - + +
316A GLN* 5.6 0.7 - - - +
360A VAL* 3.3 4.2 + - + -
361A GLU* 1.3 85.7 - - - +
363A THR* 1.3 73.0 + - - +
364A GLU* 4.3 8.3 - - + +
365A ILE* 3.5 21.1 - - + +
366A PHE* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 1.3 81.5 - - - +
364A GLU* 1.3 71.3 + - + +
366A PHE* 4.2 1.6 - - - +
367A LYS* 3.7 23.7 + - - +
449A ASP* 4.6 16.8 - - - +
453A LEU* 6.1 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 4.8 17.8 + - - +
362A GLU* 3.6 7.1 - - + +
363A THR* 1.3 86.0 - - + +
365A ILE* 1.3 65.9 + - - +
367A LYS* 3.1 25.6 + - - +
368A ILE* 3.1 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 4.8 8.5 - - + +
319A ILE* 3.7 22.2 - - + +
320A GLN* 4.7 14.1 + - + +
323A SER* 4.3 15.0 - - - +
357A VAL* 3.7 29.4 - - + +
360A VAL* 3.7 34.1 - - + +
362A GLU* 3.5 26.8 - - + +
364A GLU* 1.3 80.0 - - - +
366A PHE* 1.3 64.8 + - - +
368A ILE* 3.2 10.6 + - + +
369A CYS* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A SER* 4.2 16.6 - - - -
360A VAL 4.7 7.6 - - - +
362A GLU 3.3 20.3 + - - +
363A THR 4.2 2.5 - - - +
364A GLU 3.2 0.6 - - - -
365A ILE* 1.3 81.2 - - - +
367A LYS* 1.3 57.8 + - - +
369A CYS* 3.2 14.5 - - - -
370A LEU* 2.9 43.3 + - + +
373A TRP* 5.9 3.1 - + - -
419A LEU* 5.5 8.3 - - + -
420A MET* 5.7 1.8 - - + -
423A ARG* 3.6 54.3 - - + -
453A LEU* 5.0 15.7 - - + -
457A MET* 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A THR* 3.7 17.2 + - - +
364A GLU* 3.1 27.0 + - - +
366A PHE* 1.3 78.2 - - - +
368A ILE* 1.3 58.6 + - + +
370A LEU* 3.8 10.7 - - + +
371A GLU* 3.1 38.6 + - - +
449A ASP* 3.5 24.1 + - - +
453A LEU* 4.9 24.6 - - + +
456A ASN* 6.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLN* 3.8 37.7 - - + +
323A SER* 3.6 15.3 - - - +
324A LEU* 3.8 42.0 - - + +
327A CYS* 3.8 13.6 - - + +
364A GLU* 3.1 27.9 + - - +
365A ILE* 3.5 9.4 - - + +
366A PHE 3.2 0.2 - - - -
367A LYS* 1.3 79.4 - - + +
369A CYS* 1.3 59.4 + - - +
371A GLU* 3.3 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SER* 3.3 18.3 + - - +
354A MET* 3.6 23.1 - - - -
357A VAL 4.9 1.8 - - - -
358A SER* 3.7 33.2 - - - +
365A ILE* 3.1 15.7 + - - -
366A PHE* 3.2 33.0 - - - -
368A ILE* 1.3 73.6 - - - +
370A LEU* 1.3 60.1 + - - +
371A GLU 3.1 1.6 - - - -
372A TYR* 3.1 19.9 + - - +
373A TRP* 3.0 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PHE* 2.9 28.8 + - + +
367A LYS* 3.8 9.6 - - + +
369A CYS* 1.3 72.6 - - - +
371A GLU* 1.3 65.6 + - - +
372A TYR 3.0 1.6 - - - -
373A TRP* 3.9 14.1 - - + -
374A ASN* 3.0 23.0 + - - +
420A MET* 4.9 6.3 - - - -
453A LEU* 3.8 17.0 - - + -
456A ASN* 3.7 44.0 - - + +
457A MET* 3.5 41.5 - - + -
460A THR* 4.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A CYS* 4.1 6.7 - - - -
331A LYS* 4.3 19.7 - - + +
367A LYS* 3.1 25.9 + - - +
368A ILE* 3.3 15.3 - - - +
370A LEU* 1.3 77.3 - - - +
372A TYR* 1.3 60.0 + - - +
374A ASN* 4.2 8.7 + - - +
375A HIS* 3.8 16.5 + - - +
456A ASN* 4.1 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU 4.6 0.4 - - - -
327A CYS* 3.7 39.3 - - + -
330A LEU* 3.3 45.1 - - + +
331A LYS* 4.5 6.7 - - + -
334A ASP* 5.8 0.8 - - + +
351A LEU* 3.4 20.4 - - + +
354A MET* 4.1 21.5 - - + -
369A CYS* 3.1 10.8 + - - +
370A LEU 3.0 0.6 - - - -
371A GLU* 1.3 76.5 - - - +
373A TRP* 1.3 73.1 + + - +
374A ASN 3.2 1.8 - - - -
375A HIS* 3.1 12.2 + + - +
376A LEU* 2.8 63.2 + - + +
409A TYR* 4.0 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.3 17.3 - - + -
354A MET* 4.0 10.3 - - + +
355A LEU* 3.6 44.0 - - + -
358A SER* 2.8 30.7 + - - -
366A PHE* 5.9 3.6 - + - -
369A CYS* 3.0 28.0 + - + +
370A LEU* 3.2 11.0 + - + +
372A TYR* 1.3 92.5 - + - +
374A ASN* 1.3 57.6 + - - +
376A LEU* 3.6 19.9 - - + +
377A ALA* 3.0 31.9 + - - +
412A MET* 5.5 2.5 - - + -
416A VAL* 3.6 38.6 - - + -
419A LEU* 4.7 5.5 - - + +
420A MET* 4.3 13.0 - - + -
460A THR* 3.5 14.1 - - + +
464A LEU* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU 3.0 16.6 + - - +
371A GLU* 4.2 10.6 + - - +
373A TRP* 1.3 77.1 - - - +
375A HIS* 1.3 60.7 + - - +
377A ALA* 3.5 1.7 + - - +
378A ALA* 3.0 33.8 + - - +
456A ASN* 3.0 25.4 - - - +
459A GLU* 3.4 30.5 + - - +
460A THR* 3.2 24.2 + - - +
463A TYR* 4.3 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU 4.3 1.1 - - - -
331A LYS* 3.5 55.2 + - + +
334A ASP* 3.9 15.0 - - - -
371A GLU 3.8 10.5 + - - +
372A TYR* 3.1 15.3 + + - +
374A ASN* 1.3 80.9 - - - +
376A LEU* 1.3 70.6 + - - +
378A ALA* 3.3 5.9 + - - +
379A GLU* 3.1 44.8 + - + +
382A ARG* 5.1 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 4.2 3.6 - - + -
372A TYR* 2.8 56.9 + - + +
373A TRP* 3.6 28.0 - - + +
375A HIS* 1.3 83.2 + - - +
377A ALA* 1.3 70.4 - - + +
378A ALA 3.3 0.2 + - - -
379A GLU* 3.5 6.6 + - - +
380A LEU* 3.3 24.7 + - + +
409A TYR* 3.6 27.6 - - + -
413A LEU* 4.4 22.9 - - + -
416A VAL* 5.1 2.2 - - + -
464A LEU* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A TRP 3.0 18.6 + - - +
374A ASN 4.0 3.1 - - - +
376A LEU* 1.3 79.7 - - - +
378A ALA* 1.3 61.4 + - - +
380A LEU* 3.3 12.2 - - - +
381A TYR* 3.1 25.8 + - - +
460A THR* 3.9 6.7 - - + +
463A TYR* 3.7 23.2 - - + +
464A LEU* 3.7 25.8 - - + +
467A LEU* 5.0 0.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
374A ASN* 3.0 22.9 + - - +
375A HIS* 3.6 9.2 - - + +
376A LEU 3.2 0.4 - - - -
377A ALA* 1.3 78.5 - - - +
379A GLU* 1.3 63.0 + - - +
381A TYR* 3.4 2.9 + - - +
382A ARG* 3.1 51.2 + - - +
459A GLU* 5.6 0.2 - - - +
463A TYR* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS 5.2 0.7 - - - +
334A ASP* 3.7 13.0 - - - +
335A GLN* 3.7 21.7 + - - -
375A HIS* 3.1 33.7 + - + +
376A LEU* 4.1 4.3 - - - +
377A ALA 3.4 0.2 - - - -
378A ALA* 1.3 77.8 - - - +
380A LEU* 1.3 59.0 + - + +
382A ARG* 3.1 27.4 + - - +
383A GLU* 3.1 23.2 + - - +
405A ARG* 2.8 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.3 26.5 - - + +
377A ALA* 3.3 18.6 - - - +
379A GLU* 1.3 73.6 - - + +
381A TYR* 1.3 60.0 + - - +
383A GLU* 3.6 13.5 - - - +
384A SER* 3.1 30.7 + - - +
405A ARG* 4.1 26.6 - - + +
406A ARG* 4.6 8.7 - - + -
409A TYR* 4.1 34.1 - - + -
413A LEU* 4.4 15.0 - - + -
467A LEU* 3.6 29.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA 3.1 21.0 + - - +
378A ALA 3.5 7.0 - - - +
379A GLU 3.1 0.2 - - - -
380A LEU* 1.3 75.5 - - - +
382A ARG* 1.3 76.9 + - + +
383A GLU 3.1 1.8 - - - -
384A SER 4.1 1.6 - - - -
385A PRO* 3.2 43.6 - - + +
463A TYR* 3.6 41.5 - + + -
466A HIS* 4.0 42.1 + + + -
467A LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A HIS* 4.9 6.9 + - - -
378A ALA* 3.1 39.8 + - - +
379A GLU* 3.1 38.3 + - - +
381A TYR* 1.3 90.3 - - + +
383A GLU* 1.3 60.7 + - - +
385A PRO* 4.7 6.5 - - - +
463A TYR* 5.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU 3.1 11.3 + - - +
380A LEU* 3.6 11.9 - - - +
381A TYR 3.1 0.2 - - - -
382A ARG* 1.3 81.9 - - - +
384A SER* 1.3 70.7 + - - +
385A PRO* 3.8 5.4 - - - +
386A PHE* 5.2 2.1 - - - -
403A PRO* 3.3 22.7 - - - +
404A PRO* 3.3 12.7 - - + +
405A ARG* 3.1 43.4 + - + +
406A ARG* 3.7 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU 3.1 10.0 + - - +
381A TYR* 3.3 7.9 - - - +
383A GLU* 1.3 84.4 + - - +
385A PRO* 1.3 61.0 - - - +
386A PHE* 3.2 13.2 - - - +
388A THR* 6.5 0.2 - - - -
403A PRO* 3.6 23.3 - - - -
406A ARG* 2.5 65.0 + - - -
467A LEU* 4.3 0.5 - - - +
----------------------------------------------------------
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