Contacts of the helix formed by residues 436 - 453 (chain A) in PDB entry 1OPL
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 SER 436 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ILE* 3.8 8.2 - - - +
406A LEU* 4.1 9.6 - - - -
409A GLY* 5.9 2.0 - - - -
410A ASP 3.7 16.2 - - - -
411A THR* 4.5 7.9 - - - -
428A GLU* 4.9 3.0 + - - -
435A PHE* 1.3 78.3 - - - +
437A ILE* 1.3 66.0 + - - +
438A LYS* 2.9 27.6 + - - +
439A SER* 2.8 21.4 + - - -
440A ASP* 3.3 7.6 + - - -
499A PRO* 5.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET* 4.5 5.4 - - + -
373A LEU 4.8 0.4 - - - -
374A GLU* 3.8 43.7 - - + +
378A PHE 3.8 20.6 - - - +
379A ILE* 3.7 11.7 - - + +
406A LEU* 4.9 0.8 - - - +
408A THR* 4.5 24.0 - - + +
409A GLY* 5.2 6.2 - - - +
436A SER* 1.3 76.3 - - - +
438A LYS* 1.3 76.9 + - + +
440A ASP* 3.1 19.1 + - - +
441A VAL* 3.0 24.9 + - + +
505A PHE* 3.8 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 5.2 1.0 + - - -
436A SER* 2.9 13.5 + - - +
437A ILE* 1.3 90.2 - - + +
439A SER* 1.3 63.3 + - - +
441A VAL* 3.2 8.0 + - + +
442A TRP 3.2 13.3 + - - -
499A PRO* 3.4 43.7 - - + +
500A SER* 4.8 6.9 + - - +
502A ARG* 2.9 43.7 + - + +
503A PRO 3.6 18.1 + - - +
504A SER* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ARG* 5.6 0.2 - - - +
424A TRP 4.9 1.2 - - - +
426A ALA* 3.8 14.2 + - - +
428A GLU* 3.8 6.0 + - - -
429A SER* 3.6 22.0 - - - -
435A PHE* 3.4 18.1 - - - +
436A SER* 2.8 34.1 + - - -
438A LYS* 1.3 77.9 - - - +
440A ASP* 1.3 64.5 + - - +
442A TRP* 3.3 4.2 + - - +
443A ALA* 3.1 20.3 + - - +
502A ARG* 3.9 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET* 3.8 11.8 - - + +
379A ILE* 3.5 11.5 - - - +
380A HIS* 2.8 32.6 + - - +
381A ARG* 2.9 30.1 + - - +
383A LEU* 3.8 6.9 - - + +
436A SER 3.3 7.7 + - - +
437A ILE* 3.1 15.2 + - - +
439A SER* 1.3 77.6 + - - +
441A VAL* 1.3 58.5 + - - +
443A ALA* 3.2 8.5 + - - +
444A PHE* 2.8 25.3 + - - +
505A PHE* 3.5 19.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 5.0 0.9 - - - +
437A ILE* 3.0 18.9 + - + +
438A LYS* 3.5 15.9 - - + +
439A SER 3.2 0.2 - - - -
440A ASP* 1.3 77.8 - - - +
442A TRP* 1.3 63.9 + - - +
444A PHE* 3.1 10.9 + - - +
445A GLY 3.1 9.5 + - - -
494A CYS* 3.5 33.8 - - - +
502A ARG* 3.9 10.1 - - + -
503A PRO* 3.4 29.4 - - + +
504A SER* 4.7 0.9 - - - -
505A PHE* 3.6 31.6 - - + +
508A ILE* 3.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LYS 4.9 1.6 + - - -
424A TRP 4.0 8.4 - - - -
425A THR 3.8 8.1 + - - +
426A ALA* 3.7 24.9 - - + -
427A PRO* 3.5 28.7 - - + -
438A LYS 3.2 10.4 + - - +
439A SER 3.5 8.5 - - - +
440A ASP 3.2 0.2 - - - -
441A VAL* 1.3 77.6 - - - +
443A ALA* 1.3 65.3 + - - +
445A GLY 3.0 10.9 + - - -
446A VAL* 3.3 19.4 + - + +
459A TYR* 4.4 7.3 + - - -
471A LEU* 3.8 29.3 - - + +
476A ARG* 3.8 19.1 - - - -
494A CYS 3.5 11.4 + - - +
495A TRP* 3.2 56.9 + + + -
496A GLN 3.6 7.4 - - - -
502A ARG* 3.6 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ARG 6.3 1.1 - - - -
383A LEU* 3.7 32.2 - - + +
424A TRP* 3.5 26.0 - - + +
439A SER 3.1 12.5 + - - +
440A ASP* 3.6 10.3 - - - +
442A TRP* 1.3 77.5 - - - +
444A PHE* 1.3 57.6 + - - +
446A VAL* 3.0 8.6 + - - +
447A LEU* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 3.9 10.5 - - + -
366A ILE* 3.6 34.3 - - + -
367A SER* 4.0 12.8 - - - -
370A MET* 4.9 0.7 - - + -
383A LEU* 3.9 12.1 - - + +
440A ASP 2.8 14.1 + - - +
441A VAL 3.1 8.3 + - - +
443A ALA* 1.3 76.7 - - - +
445A GLY* 1.3 59.9 + - - +
447A LEU* 3.4 10.1 - - + +
448A LEU* 2.8 45.4 + - + +
451A ILE* 6.0 0.7 - - + -
490A LEU* 5.2 0.4 - - + -
494A CYS* 4.2 14.4 - - - -
505A PHE* 3.6 22.0 - + + -
508A ILE* 3.8 22.7 - - + -
512A PHE* 3.7 26.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A VAL 3.1 6.3 + - - -
442A TRP 3.0 10.1 + - - -
444A PHE* 1.3 79.5 - - - +
446A VAL* 1.3 59.9 + - - +
448A LEU* 3.3 9.5 + - - +
449A TRP 3.1 17.0 + - - -
491A MET* 3.9 6.2 - - - +
494A CYS* 3.8 19.3 - - - -
495A TRP* 3.4 23.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LYS 3.5 24.0 - - - +
424A TRP* 3.5 30.1 - - + +
442A TRP* 3.3 20.6 + - + +
443A ALA 3.0 7.2 + - - +
445A GLY* 1.3 73.2 - - - +
447A LEU* 1.3 66.9 + - - +
449A TRP* 3.1 5.3 + - - +
450A GLU* 2.9 21.1 + - - +
458A PRO* 3.8 23.1 - - + -
459A TYR* 4.9 2.9 - - - +
477A MET* 4.3 7.2 - - + -
495A TRP* 3.6 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.4 4.7 - - + -
366A ILE* 3.9 19.3 - - + -
383A LEU* 3.7 33.4 - - + -
384A ALA* 4.2 8.7 - - - -
385A ALA* 3.5 33.9 - - + +
388A CYS* 3.9 9.9 - - - -
424A TRP* 4.5 0.6 - - - -
443A ALA 2.8 12.4 + - - +
444A PHE* 3.4 13.7 - - + +
446A VAL* 1.3 78.6 - - - +
448A LEU* 1.3 55.4 + - - +
450A GLU* 3.0 12.2 + - - +
451A ILE* 2.9 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 4.2 8.5 - - + -
444A PHE* 2.8 36.0 + - + +
445A GLY* 3.4 10.5 - - - +
446A VAL 3.2 0.2 - - - -
447A LEU* 1.3 75.1 - - - +
449A TRP* 1.3 56.2 + - - +
451A ILE* 3.2 7.8 + - + +
452A ALA* 2.9 30.1 + - - +
487A VAL* 3.9 23.6 - - + +
490A LEU* 4.4 7.9 - - + -
491A MET* 3.6 30.1 - - + +
494A CYS* 5.8 0.9 - - - -
512A PHE* 4.1 17.9 - - + -
538A MYR 4.1 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLY 3.1 12.4 + - - +
446A VAL 3.1 8.2 + - - +
448A LEU* 1.3 73.4 - - - +
450A GLU* 1.3 72.3 + - - +
452A ALA* 3.3 0.9 + - - -
453A THR* 3.0 47.1 + - + +
456A MET* 3.5 43.7 - - + -
457A SER 3.5 19.7 - - - -
458A PRO* 3.6 15.3 - - + -
459A TYR 4.5 1.3 - - - -
460A PRO* 4.8 9.6 - - + -
477A MET* 3.5 43.4 - - + +
478A GLU 3.3 21.6 + - - -
480A PRO* 3.5 24.5 - - + +
488A TYR* 5.5 0.2 - + - -
491A MET* 3.9 19.9 - - - +
495A TRP* 4.2 2.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 3.8 17.2 - - - +
346A LEU* 4.0 2.1 - - - +
385A ALA* 2.9 42.6 + - + +
386A ARG* 4.9 0.5 + - - -
424A TRP* 2.8 40.2 + - - +
446A VAL 2.9 16.6 + - - +
447A LEU* 3.0 13.0 + - - +
449A TRP* 1.3 78.3 - - - +
451A ILE* 1.3 62.0 + - - +
453A THR* 3.2 9.2 + - - -
455A GLY* 2.7 34.2 + - - -
456A MET 4.3 9.8 - - - +
458A PRO* 4.3 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.1 14.6 - - + -
346A LEU* 3.8 10.9 - - + +
359A LEU* 3.8 50.2 - - + +
362A MET* 4.8 3.6 - - + -
363A ALA* 4.0 21.8 - - + +
366A ILE* 3.9 28.3 - - + -
444A PHE* 6.0 1.1 - - + -
447A LEU* 2.9 30.8 + - + +
448A LEU* 3.5 10.1 - - - +
449A TRP 3.2 0.2 - - - -
450A GLU* 1.3 76.0 - - + +
452A ALA* 1.3 58.4 + - - +
454A TYR* 3.1 18.7 + - - -
538A MYR 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LEU* 4.7 1.6 - - - -
448A LEU 2.9 16.4 + - - +
449A TRP 3.3 4.0 + - - +
451A ILE* 1.3 77.7 - - - +
453A THR* 1.3 58.4 + - - +
454A TYR* 3.4 6.7 + - - -
480A PRO* 4.0 25.6 - - + +
481A GLU 4.8 2.6 - - - +
483A CYS* 4.3 4.2 - - - +
487A VAL* 5.3 0.4 - - + -
491A MET* 4.1 11.2 - - + -
538A MYR 4.2 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG* 4.7 4.9 + - - -
449A TRP* 3.0 40.1 + - + +
450A GLU* 3.2 6.1 + - - -
451A ILE 3.1 0.2 - - - -
452A ALA* 1.3 76.5 - - - +
454A TYR* 1.3 71.3 + - - +
455A GLY 3.4 0.2 + - - -
456A MET* 3.0 50.2 + - - +
480A PRO* 3.6 29.4 - - + -
----------------------------------------------------------
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