Contacts of the helix formed by residues 471 - 490 (chain A) in PDB entry 2O2C
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 ASP 471 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LYS* 5.8 0.7 - - - +
469A ILE 3.3 0.2 + - - -
470A GLY* 1.3 75.8 - - - +
472A HIS* 1.3 65.5 + - - +
473A HIS 3.4 2.5 - - - -
474A LYS* 3.3 34.6 - - + +
475A ILE* 3.2 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ASN 5.9 1.3 - - - +
469A ILE* 3.0 47.9 + - + +
470A GLY* 3.4 1.2 - - - -
471A ASP* 1.3 78.7 + - - +
473A HIS* 1.3 57.5 + - - +
475A ILE* 3.4 10.0 + - + +
476A PHE* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR 5.7 0.4 + - - -
462A ALA* 3.0 30.2 + - - +
463A ILE 3.1 22.9 + - - -
464A GLN* 4.4 0.6 - - - -
465A SER* 3.6 33.2 + - - -
467A ASN 5.7 0.4 - - - +
468A LYS* 3.1 31.4 + - - +
469A ILE 4.7 0.2 + - - -
471A ASP 3.4 1.0 - - - -
472A HIS* 1.3 78.7 - - - +
474A LYS* 1.3 55.9 + - - +
476A PHE* 3.4 23.6 - + - +
477A MET* 2.8 49.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LYS* 5.0 1.4 - - - +
471A ASP* 3.3 41.9 - - + +
473A HIS* 1.3 74.4 - - - +
475A ILE* 1.3 62.5 + - + +
477A MET* 3.8 4.5 - - - +
478A SER* 3.0 30.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ASP* 3.2 34.1 + - + +
472A HIS* 3.7 8.5 - - + +
474A LYS* 1.3 78.2 - - + +
476A PHE* 1.3 59.1 + - - +
478A SER* 2.7 25.7 + - - +
479A ASN* 2.9 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.2 48.3 - + + -
395A ASP* 3.7 7.4 - - - -
396A GLN 4.9 2.9 - - - -
437A GLY 3.2 30.3 - - - -
438A THR* 3.7 13.5 - - + -
472A HIS 2.9 19.0 + - - +
473A HIS* 3.4 31.2 - + - +
475A ILE* 1.3 77.1 - - - +
477A MET* 1.3 65.1 + - - +
479A ASN* 3.2 24.3 + - - +
480A PHE* 3.5 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 4.8 2.9 - - - +
462A ALA 3.2 36.6 - - - +
463A ILE* 4.7 2.9 - - - +
473A HIS* 2.8 45.4 + - + +
474A LYS* 4.2 4.3 - - - +
476A PHE* 1.3 82.6 - - - +
478A SER* 1.3 63.7 + - - +
479A ASN 3.1 1.8 - - - -
480A PHE* 3.2 47.6 + - + +
481A PHE* 3.1 38.9 + - + -
530A LEU* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LYS 3.0 15.9 + - - -
475A ILE* 2.7 23.1 + - - +
476A PHE 3.2 0.2 - - - -
477A MET* 1.3 76.6 - - - +
479A ASN* 1.3 61.0 + - - +
481A PHE* 3.8 5.6 + - - +
482A ALA* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 4.2 2.5 - - + -
438A THR* 3.9 15.2 - - + +
441A GLN* 2.9 38.0 + - - +
475A ILE* 2.9 32.1 + - - +
476A PHE* 3.2 9.2 + - - +
477A MET 3.1 0.4 - - - -
478A SER* 1.3 83.9 + - - +
480A PHE* 1.3 58.5 + - - +
482A ALA* 4.3 4.5 - - - -
483A GLN* 3.0 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.5 38.5 - + + -
459A PHE* 3.6 24.8 - + + -
460A ILE 3.5 22.9 - - - -
461A GLY* 3.5 16.6 - - - -
476A PHE 3.5 2.0 + - - -
477A MET* 3.2 38.3 + - + +
479A ASN* 1.3 80.7 - - - +
481A PHE* 1.3 87.8 + + - +
483A GLN 4.0 2.8 + - - -
484A THR* 3.8 18.0 + - - +
528A THR* 3.7 32.3 - - + -
529A LEU 3.9 2.0 - - - -
530A LEU* 4.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 5.4 0.2 + - - -
463A ILE* 6.2 1.3 - - + -
477A MET* 3.1 44.4 + - + +
478A SER* 4.4 4.9 - - - +
480A PHE* 1.3 100.4 - + - +
482A ALA* 1.3 62.3 + - - +
484A THR* 3.1 20.2 + - - -
485A GLU* 3.3 13.2 + - - +
528A THR* 5.5 4.0 - - + -
530A LEU* 4.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A SER 3.1 21.7 + - - +
479A ASN* 3.4 5.8 + - - +
481A PHE* 1.3 76.2 - - - +
483A GLN* 1.3 63.1 + - + +
485A GLU* 3.4 13.5 + - - +
486A ALA* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.7 6.1 - - - +
441A GLN* 3.6 35.9 - - - +
445A TYR* 3.3 17.5 - - + +
449A HIS* 2.8 31.4 + - - -
459A PHE* 3.6 22.7 - - + -
479A ASN* 3.0 23.3 + - - +
480A PHE 4.4 0.2 - - - +
482A ALA* 1.3 78.7 - - - +
484A THR* 1.3 57.1 + - - +
486A ALA* 3.4 5.5 + - - +
487A LEU* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 3.3 31.7 + - - +
459A PHE* 3.6 36.3 - - + -
480A PHE 3.8 7.7 + - - +
481A PHE* 3.1 16.8 + - - -
483A GLN* 1.3 72.9 - - - +
485A GLU* 1.3 64.4 + - - +
487A LEU* 3.5 6.8 + - - +
488A MET 3.1 16.8 + - - -
524A ARG 5.1 0.2 - - - +
526A SER* 3.4 24.7 + - - +
528A THR* 3.6 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 4.3 11.2 - - - +
481A PHE 3.3 14.3 + - - +
482A ALA* 3.6 12.9 - - - +
483A GLN 3.3 0.2 - - - -
484A THR* 1.3 80.8 + - - +
486A ALA* 1.3 56.0 + - - +
488A MET* 3.2 4.3 + - + +
489A ILE* 2.9 60.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A HIS* 3.7 20.4 + - + +
482A ALA 2.8 18.8 + - - +
483A GLN* 3.5 9.4 - - - +
485A GLU* 1.3 76.7 - - - +
487A LEU* 1.3 60.6 - - - +
489A ILE* 4.5 5.8 - - - -
490A GLY* 3.0 25.2 + - - -
520A PHE* 5.4 3.1 - - + +
522A GLY* 4.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A TYR* 6.2 0.9 - - + -
448A ILE* 3.7 24.9 - - + +
449A HIS* 3.6 28.3 - - + +
457A CYS* 4.5 11.0 - - - -
459A PHE* 3.8 31.0 - - + -
483A GLN* 2.9 22.2 + - + +
484A THR* 3.7 5.2 - - - +
485A GLU 3.3 0.2 - - - -
486A ALA* 1.3 75.8 - - - +
488A MET* 1.3 57.4 + - - +
522A GLY* 3.4 6.2 - - - -
523A GLY 3.2 6.4 + - - -
524A ARG* 2.9 53.2 + - + +
525A PRO 4.5 3.8 - - - +
526A SER* 4.4 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.7 22.7 - - + -
72A LYS* 3.8 35.4 + - + +
75A PHE* 3.7 30.7 - - + -
105A LYS* 3.9 25.6 - - + -
484A THR 3.1 17.0 + - - +
485A GLU* 3.2 4.7 + - + +
487A LEU* 1.3 78.0 - - - +
489A ILE* 1.3 79.4 + - + +
523A GLY* 3.0 23.3 + - - +
524A ARG 3.8 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 2.7 40.3 + - + +
485A GLU* 2.9 50.3 + - + +
486A ALA* 4.5 4.0 - - - -
488A MET* 1.3 97.7 - - + +
490A GLY* 1.3 75.6 + - - +
491A LYS 3.8 0.3 + - - -
492A SER 5.5 0.2 + - - -
495A GLU* 5.0 2.6 - - - +
521A ILE 4.9 1.9 - - - +
522A GLY* 4.3 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA* 3.0 20.5 + - - -
488A MET 3.6 1.4 + - - -
489A ILE* 1.3 93.4 - - - +
491A LYS* 1.3 63.3 + - - +
495A GLU* 4.5 4.9 - - - +
520A PHE* 3.5 21.5 - - - -
522A GLY* 3.8 8.5 - - - -
----------------------------------------------------------
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