Contacts of the helix formed by residues 501 - 520 (chain A) in PDB entry 2B3O
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 THR 501 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY* 6.1 1.8 - - - -
56A ASN* 3.3 46.9 - - + +
57A SER 4.3 1.3 + - - -
58A GLY* 3.6 15.4 - - - +
248A PHE* 3.5 10.1 - - - -
421A GLY* 6.1 0.2 - - - -
499A VAL* 4.7 1.4 - - - +
500A GLN* 1.3 74.8 - - - +
502A GLU* 1.3 65.1 + - - +
503A ALA* 3.4 16.7 + - - +
504A GLN* 3.0 34.2 + - - +
505A TYR* 3.2 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 2.7 41.1 + - - +
244A PHE* 4.9 7.4 - - + +
245A TRP* 2.9 50.7 - - + +
248A PHE* 3.2 31.5 - - + -
501A THR* 1.3 73.4 - - - +
503A ALA* 1.3 63.3 + - - +
505A TYR* 3.2 7.7 + - + +
506A LYS* 3.0 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 5.9 5.4 - - + +
421A GLY* 4.9 9.4 - - - -
422A VAL* 3.3 30.6 - - + +
501A THR* 3.0 12.2 + - - +
502A GLU* 1.3 89.5 + - - +
504A GLN* 1.3 59.9 + - - +
506A LYS* 3.8 11.2 + - - +
507A PHE* 3.2 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLY* 3.4 26.8 + - - -
417A TRP* 4.9 4.8 - - + +
421A GLY 5.4 3.0 + - - +
422A VAL* 3.9 14.3 - - + +
458A GLY* 3.6 15.1 - - - -
459A ARG* 3.6 11.1 - - - +
462A THR* 3.2 26.2 + - + +
499A VAL* 3.8 4.2 - - + -
500A GLN 2.7 31.9 + - - -
501A THR* 3.0 22.0 + - - +
503A ALA* 1.3 74.8 - - - +
505A TYR* 1.3 61.5 + - - +
507A PHE* 3.0 7.8 + - - +
508A ILE* 2.8 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 3.7 30.7 - + + -
247A GLU* 3.3 30.0 + - + -
248A PHE* 3.9 23.1 - + + -
251A LEU* 4.6 8.1 - - + -
484A ILE* 4.6 1.6 - - + -
485A GLN* 3.0 34.8 + - + +
488A ILE* 3.8 27.6 - - + -
499A VAL* 4.6 2.8 - - + +
501A THR 3.2 8.8 + - - +
502A GLU* 3.2 18.1 + - - +
504A GLN* 1.3 79.2 - - - +
506A LYS* 1.3 61.5 + - - +
508A ILE* 3.4 15.4 + - - +
509A TYR* 3.3 44.9 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 3.8 37.0 - - + -
422A VAL* 6.1 3.6 - - - -
502A GLU* 3.0 22.5 + - - +
503A ALA* 4.1 9.4 - - - +
505A TYR* 1.3 84.5 - - - +
507A PHE* 1.3 58.5 + - - +
509A TYR* 3.0 9.5 + - - +
510A VAL* 2.9 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 4.0 20.6 - + - -
422A VAL* 3.9 18.2 - - + -
423A PRO* 3.8 42.0 - - + -
425A GLU 3.9 9.2 - - - -
426A PRO* 4.0 18.4 - - + -
429A VAL* 3.9 17.3 - - + -
462A THR* 3.9 18.2 - - + -
466A ILE* 4.0 16.4 - - + -
503A ALA 3.2 15.1 + - - +
504A GLN* 3.0 12.1 + - - +
506A LYS* 1.3 77.8 - - - +
508A ILE* 1.3 58.9 + - - +
510A VAL* 3.1 14.5 - - + +
511A ALA* 2.8 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A THR* 3.8 17.5 - - + -
465A VAL* 3.9 17.9 - - + -
466A ILE* 3.9 18.8 - - + -
469A LEU* 3.9 27.6 - - + -
484A ILE* 3.9 16.2 - - + -
488A ILE* 3.6 27.6 - - + -
499A VAL* 4.2 17.0 - - + -
504A GLN 2.8 21.0 + - - +
505A TYR* 3.6 7.9 - - - +
506A LYS 3.3 0.2 - - - -
507A PHE* 1.3 72.6 - - - +
509A TYR* 1.3 57.7 + - - +
511A ALA* 3.7 1.2 - - - +
512A ILE* 3.0 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 5.0 12.8 - - + -
224A GLU* 4.1 24.4 + - + -
225A ASN* 3.9 9.8 + - - +
244A PHE* 3.4 33.0 - + + -
247A GLU* 3.1 20.7 + - - -
484A ILE* 3.4 42.0 + - + +
485A GLN* 5.0 2.4 + - - +
505A TYR* 3.3 48.8 + + - -
506A LYS 3.0 8.9 + - - +
508A ILE* 1.3 75.3 - - - +
510A VAL* 1.3 67.1 + - + +
512A ILE* 3.3 2.5 + - - +
513A ALA* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASN* 3.6 17.5 - - + +
244A PHE* 5.8 1.1 - - + -
426A PRO* 3.9 17.3 - - + +
506A LYS* 2.9 37.5 + - + +
507A PHE* 3.1 33.2 - - + +
509A TYR* 1.3 73.4 - - + +
511A ALA* 1.3 66.9 + - - +
513A ALA* 3.6 1.7 + - - +
514A GLN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PRO* 3.4 24.2 - - + -
429A VAL* 6.2 1.3 - - + -
430A LEU* 3.5 14.5 - - + +
466A ILE* 4.0 28.0 - - + -
507A PHE* 2.8 25.0 + - + +
508A ILE 3.7 3.1 - - - +
510A VAL* 1.3 75.4 - - - +
512A ILE* 1.3 64.6 + - - +
514A GLN* 3.1 6.2 + - - +
515A PHE* 3.0 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 5.9 4.9 - - + -
466A ILE* 3.9 19.7 - - + +
469A LEU* 3.5 46.0 - - + +
470A MET* 4.1 11.7 - - + +
473A ILE* 4.3 10.8 - - + -
482A ILE* 4.6 13.5 - - + -
484A ILE* 5.2 6.1 - - + -
508A ILE* 3.0 23.0 + - + +
509A TYR* 3.8 4.7 - - - +
511A ALA* 1.3 76.9 - - - +
513A ALA* 1.3 51.9 + - - +
515A PHE* 2.7 10.8 + - + +
516A ILE* 2.7 50.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 6.0 1.8 - - + -
222A ASP* 3.8 16.1 - - - +
225A ASN* 2.9 37.5 - - - +
509A TYR 2.9 13.9 + - - +
510A VAL 3.8 4.0 - - - +
512A ILE* 1.3 76.9 - - - +
514A GLN* 1.3 62.4 + - - +
516A ILE* 3.2 12.0 + - - +
517A GLU* 3.1 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLU* 5.6 0.2 - - - +
426A PRO* 2.8 36.8 - - - +
427A GLY* 3.6 19.9 + - - -
430A LEU* 3.9 10.4 - - + +
510A VAL 3.2 7.5 + - - +
511A ALA 3.1 10.2 + - - +
513A ALA* 1.3 78.7 - - - +
515A PHE* 1.3 63.1 + - - +
517A GLU* 3.4 6.9 + - - +
518A THR* 2.9 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.2 14.6 - - + +
434A ASP* 6.2 0.4 - - + -
470A MET* 3.4 68.4 - - + -
473A ILE* 3.9 27.8 - - + -
474A SER* 3.8 13.9 - - - -
511A ALA 3.0 11.3 + - - +
512A ILE* 2.7 16.6 + - + +
514A GLN* 1.3 78.6 - - - +
516A ILE* 1.3 59.4 + - - -
518A THR* 3.5 10.1 + - + -
519A THR* 2.8 53.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASN 3.6 23.8 - - - +
220A ALA* 4.9 5.2 - - + -
221A ALA* 4.6 10.1 - - + +
222A ASP* 3.5 19.1 - - + +
473A ILE* 3.8 18.4 - - + -
478A LEU* 4.6 11.4 - - + -
482A ILE* 4.0 13.7 - - + -
512A ILE* 2.7 26.6 + - + +
513A ALA* 3.2 12.3 + - - +
515A PHE* 1.3 70.3 - - - +
517A GLU* 1.3 58.1 + - - +
519A THR* 2.8 8.2 + - - -
520A LYS* 2.7 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ASP* 3.2 32.8 - - - +
513A ALA 3.1 8.8 + - - +
514A GLN* 3.8 9.1 - - - +
516A ILE* 1.3 78.4 - - - +
518A THR* 1.3 69.6 + - - +
520A LYS* 3.0 22.4 + - + +
521A LYS* 3.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A GLN* 2.9 25.5 + - - +
515A PHE* 3.5 13.9 - - + +
517A GLU* 1.3 73.9 - - - +
519A THR* 1.3 62.6 + - + +
521A LYS* 2.8 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ILE* 4.9 3.4 - - + -
474A SER* 5.7 0.9 - - - +
478A LEU* 3.2 25.0 - - - +
515A PHE* 2.8 49.2 + - + +
516A ILE* 2.8 9.7 + - - -
518A THR* 1.3 79.3 - - + +
520A LYS* 1.3 62.7 + - - +
521A LYS* 2.7 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ASP* 5.4 2.7 - - - +
478A LEU* 3.6 25.6 - - + -
516A ILE* 2.7 27.9 + - + +
517A GLU* 3.0 15.5 + - + +
519A THR* 1.3 73.9 + - - +
521A LYS* 1.3 69.4 + - - +
522A LYS* 3.5 4.2 + - - +
----------------------------------------------------------
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