Contacts of the helix formed by residues 472 - 490 (chain B) in PDB entry 1D0N
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 472 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLY 4.9 1.2 + - - -
470B GLN 4.9 4.3 - - - +
471B SER* 1.3 76.5 + - - +
473B GLN* 1.3 59.8 + - - +
474B ASP* 2.7 26.0 + - - -
475B GLU* 3.0 20.5 + - - +
476B VAL* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B SER 4.5 8.9 + - - -
472B THR* 1.3 71.5 - - - +
474B ASP* 1.3 58.5 + - - +
476B VAL* 3.7 15.3 - - - +
477B ALA* 2.7 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLY* 5.1 7.7 - - - +
472B THR* 2.7 28.3 + - - -
473B GLN* 1.3 74.3 + - - +
475B GLU* 1.3 70.8 + - - +
477B ALA* 3.6 5.1 - - - +
478B ALA* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 3.6 17.4 - - + +
426B GLU* 3.4 0.9 - - - -
427B GLY* 2.9 31.5 + - - +
444B GLY 4.4 6.4 - - - +
445B ASP* 5.1 0.9 - - - -
446B SER* 4.2 6.0 - - - -
471B SER* 4.0 8.3 + - - +
472B THR* 3.0 20.1 + - - +
474B ASP* 1.3 85.0 - - - +
476B VAL* 1.3 67.0 + - - +
478B ALA* 3.7 6.0 - - - +
479B SER* 2.9 25.1 + - - -
526B ARG* 2.8 45.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B SER* 3.9 7.0 - - - +
467B GLN* 3.7 33.0 + - + +
468B GLY 4.5 5.6 - - - +
471B SER* 3.6 30.5 - - - +
472B THR 2.9 20.4 + - - +
473B GLN* 3.7 19.3 - - - +
475B GLU* 1.3 75.1 - - - +
477B ALA* 1.3 64.6 + - - +
479B SER* 2.7 24.0 + - - -
480B ALA* 3.3 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B GLN* 2.7 24.8 + - - +
474B ASP* 3.6 5.6 - - - +
476B VAL* 1.3 74.5 - - - +
478B ALA* 1.3 61.4 + - - +
480B ALA* 3.1 16.4 + - - +
481B ILE* 3.2 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 4.1 6.5 - - + -
427B GLY 3.5 22.9 - - - +
428B SER* 4.7 7.2 - - - -
474B ASP 2.8 22.4 + - - +
475B GLU* 3.7 4.7 - - - +
477B ALA* 1.3 74.1 - - - +
479B SER* 1.3 57.6 - - - +
481B ILE* 4.0 9.5 - - - +
482B LEU* 3.0 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 3.9 19.7 - - - +
446B SER* 3.8 20.1 + - - -
448B ILE* 3.8 5.3 - - - +
465B ASN* 3.2 24.7 + - - -
467B GLN* 3.8 3.5 + - - +
475B GLU 2.9 13.8 + - - -
476B VAL* 2.7 20.4 + - - -
478B ALA* 1.3 74.4 - - - +
480B ALA* 1.3 55.6 + - - +
483B THR* 2.6 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ASN* 3.5 14.6 - - - +
467B GLN* 4.2 7.4 - - - +
476B VAL 3.3 6.0 + - - +
477B ALA* 3.1 10.8 + - - +
479B SER* 1.3 79.3 + - - +
481B ILE* 1.3 61.6 + - + +
483B THR* 3.1 5.2 + - - -
484B ALA* 2.9 29.3 + - - +
496B GLN* 5.0 1.9 + - - -
697B LEU* 5.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B ALA* 3.2 22.7 + - + +
478B ALA* 4.0 7.0 - - - +
480B ALA* 1.3 78.6 - - + +
482B LEU* 1.3 61.4 + - + +
484B ALA* 3.2 6.5 + - - +
485B GLN* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 4.2 14.8 - - + -
428B SER* 3.9 30.5 - - - +
429B ASN* 4.4 2.0 - - - -
430B LYS* 4.2 31.9 + - + +
448B ILE* 3.6 16.6 - - + +
478B ALA* 3.0 32.0 + - + +
481B ILE* 1.3 79.5 - - + +
483B THR* 1.3 58.6 + - - +
485B GLN* 3.7 21.6 - - + +
486B LEU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ILE* 3.9 12.4 - - - +
463B ILE* 3.9 21.9 - - + +
465B ASN* 3.4 28.6 + - + +
479B SER 2.6 24.0 + - - -
480B ALA* 3.2 8.5 - - - -
482B LEU* 1.3 76.7 - - - +
484B ALA* 1.3 63.2 + - - +
486B LEU* 3.3 6.5 + - - +
487B ASP* 3.1 21.1 + - - +
496B GLN* 3.6 31.4 - - + +
497B SER 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ALA 2.9 14.4 + - - +
481B ILE* 3.7 6.7 - - - +
483B THR* 1.3 76.4 - - - +
485B GLN* 1.3 61.7 + - - +
487B ASP* 3.4 4.5 + - - +
488B GLU* 3.1 22.7 + - - +
496B GLN* 4.2 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ILE* 2.8 29.4 + - - +
482B LEU* 3.7 24.4 - - - +
484B ALA* 1.3 76.2 - - - +
486B LEU* 1.3 63.0 + - - +
488B GLU* 3.4 16.3 + - - +
489B GLU* 3.1 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B TRP* 4.2 26.0 - - + -
430B LYS* 3.8 23.1 - - - +
448B ILE* 4.5 6.3 - - + -
450B LEU* 4.5 13.0 - - + -
463B ILE* 4.0 28.5 - - + -
482B LEU 2.9 17.0 + - - +
483B THR* 3.3 5.3 + - - +
485B GLN* 1.3 73.8 - - - +
487B ASP* 1.3 66.9 + - - +
489B GLU* 3.5 16.3 + - + +
490B LEU* 3.1 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ILE* 3.9 17.4 - - + +
483B THR 3.1 10.0 + - - +
484B ALA 3.4 10.4 - - - +
485B GLN 3.3 0.2 - - - -
486B LEU* 1.3 81.5 - - - +
488B GLU* 1.3 53.8 + - - +
490B LEU* 3.4 6.4 + - - +
491B GLY 3.4 0.3 + - - -
492B GLY* 2.7 46.9 + - - -
494B PRO* 3.6 11.9 - - - +
496B GLN* 2.9 25.4 - - - +
721B LYS* 3.3 20.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ALA 3.1 12.6 + - - +
485B GLN* 3.6 20.4 - - - +
486B LEU 3.2 0.2 - - - -
487B ASP* 1.3 73.3 - - - +
489B GLU* 1.3 60.3 + - - +
490B LEU 3.0 3.8 - - - -
491B GLY* 2.8 22.7 + - - -
492B GLY* 3.5 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LYS* 5.2 4.0 + - - -
485B GLN* 3.1 32.1 + - - +
486B LEU* 3.8 22.3 - - + +
488B GLU* 1.3 80.5 - - + +
490B LEU* 1.3 62.2 + - + +
491B GLY 3.3 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LEU* 4.0 35.2 - - + -
461B GLN* 4.2 18.0 - - - +
463B ILE* 4.8 0.7 - - + -
486B LEU* 3.1 35.1 + - + +
487B ASP 3.8 4.7 - - - +
488B GLU 2.9 1.2 + - - -
489B GLU* 1.3 84.0 - - + +
491B GLY* 1.3 58.4 + - - +
492B GLY 3.7 0.9 - - - -
493B THR* 4.3 11.1 + - - -
494B PRO* 4.1 17.6 - - + +
----------------------------------------------------------
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