Contacts of the helix formed by residues 473 - 485 (chain H) in PDB entry 1MKD
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 ILE 473 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370H MET* 3.8 26.0 - - + -
373H HIS* 3.6 35.1 + - + +
374H MET* 4.5 10.3 - - + -
416H LEU* 3.9 14.6 - - + -
469H PHE* 3.0 33.3 + - + +
472H TYR* 1.3 96.0 - - + +
474H VAL* 1.3 66.6 + - - +
475H HIS 3.5 0.9 - - - -
476H PRO* 3.3 3.9 - - - +
477H LEU* 3.2 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416H LEU* 3.7 19.1 - - + +
419H PRO* 4.1 10.5 - - + -
420H THR* 4.4 0.7 - - + -
469H PHE* 3.1 49.5 + - + +
470H ILE* 3.9 9.2 - - - -
473H ILE* 1.3 74.3 - - + +
475H HIS* 1.3 58.1 + - - +
477H LEU* 3.3 5.0 + - - +
478H TRP* 2.9 50.4 + - + +
496H LEU* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 475 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470H ILE* 2.7 34.2 + - + +
471H ASP* 4.7 4.5 - - - +
474H VAL* 1.3 74.1 - - - +
476H PRO* 1.3 67.0 - - + +
479H GLU* 2.8 67.0 + - + +
493H LEU* 3.5 14.2 - - + +
496H LEU* 3.7 14.5 - - + +
497H GLU* 3.1 39.8 + - + +
500H ARG* 6.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 476 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H LEU* 3.8 20.1 - - + +
381H LYS* 5.1 5.0 - - - +
470H ILE 3.4 2.2 - - - +
471H ASP 3.2 28.0 - - - +
472H TYR* 3.5 13.7 - - - +
473H ILE 3.3 12.6 - - - +
475H HIS* 1.3 93.3 - - + +
477H LEU* 1.3 58.2 + - - +
479H GLU* 3.9 11.7 - - - +
480H THR* 2.8 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373H HIS* 3.9 8.7 - - + -
377H LEU* 3.9 18.1 - - + +
380H LEU* 4.4 4.3 - - + -
409H ASN* 4.3 15.7 - - - +
412H HIS* 3.4 34.1 - - + +
413H CYS* 3.8 35.0 - - - -
416H LEU* 3.8 23.1 - - + -
473H ILE 3.2 15.4 + - - +
474H VAL* 3.6 2.5 - - - +
476H PRO* 1.3 77.3 - - - +
478H TRP* 1.3 66.2 + - + +
480H THR* 3.1 6.8 + - - -
481H TRP* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 478 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H TRP* 3.8 24.2 - + - -
272H LEU* 4.0 9.2 - - + -
413H CYS* 3.2 40.5 + - + +
416H LEU 3.2 18.7 + - - -
417H SER* 3.9 12.1 - - - -
420H THR* 3.7 15.1 - - + +
474H VAL* 2.9 44.4 + - + +
477H LEU* 1.3 77.5 - - + +
479H GLU* 1.3 57.4 + - - +
481H TRP* 3.7 31.4 - + - +
482H ALA* 2.7 35.7 + - - +
489H ALA* 5.0 3.6 - - + -
492H ILE* 3.8 28.3 - - + -
493H LEU* 4.4 8.1 - - + +
496H LEU* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 479 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475H HIS* 2.8 48.0 + - + +
476H PRO* 3.9 9.7 - - - +
478H TRP* 1.3 75.4 - - - +
480H THR* 1.3 63.9 + - - +
482H ALA* 3.3 3.8 + - - +
483H ASP* 3.1 33.9 + - - +
493H LEU* 4.3 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 480 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H LEU* 3.4 13.5 - - + +
380H LEU* 3.4 29.4 - - + -
381H LYS* 3.8 30.0 - - + +
384H VAL* 3.8 16.2 - - + +
476H PRO 2.8 17.9 + - - -
477H LEU 3.1 8.2 + - - -
479H GLU* 1.3 77.6 + - - +
481H TRP* 1.3 64.9 + - - +
483H ASP* 3.0 23.2 + - - +
484H LEU* 3.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 481 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 4.1 25.2 - - + +
275H THR* 4.9 2.0 + - + +
278H LEU* 4.2 5.6 - - + -
380H LEU* 4.1 8.2 - - + +
406H VAL* 3.8 33.0 - - + -
409H ASN* 4.4 11.2 - - + -
410H MET* 3.7 46.0 - - + -
413H CYS* 3.8 26.5 - - - -
477H LEU 2.9 15.3 + - - +
478H TRP* 3.7 26.0 - + - +
480H THR* 1.3 75.8 - - - +
482H ALA* 1.3 65.1 + - - +
484H LEU* 3.1 20.1 + - + +
485H VAL* 3.1 56.7 + - + +
489H ALA* 4.2 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478H TRP* 2.7 22.0 + - + +
479H GLU 3.5 6.1 - - - +
480H THR 3.2 0.2 - - - -
481H TRP* 1.3 73.7 - - - +
483H ASP* 1.3 57.3 + - - +
485H VAL* 3.6 0.7 - - - +
486H HIS* 2.9 34.4 + - + +
487H PRO* 4.6 1.7 - - - +
489H ALA* 3.7 28.0 - - + +
490H GLN* 5.2 3.1 - - - +
493H LEU* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 483 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H VAL* 3.5 23.6 - - + +
387H LYS* 3.1 18.3 + - - -
479H GLU* 3.1 24.2 + - - +
480H THR* 3.0 15.8 + - - +
482H ALA* 1.3 75.5 - - - +
484H LEU* 1.3 66.9 + - - +
486H HIS* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ALA* 4.8 0.5 - - - +
380H LEU* 4.2 14.8 - - + -
383H MET* 4.3 29.4 - - + +
384H VAL* 4.1 18.5 - - + +
387H LYS* 3.6 19.5 + - + +
395H LEU* 3.8 42.6 - - + +
397H LEU* 6.2 0.9 - - + -
406H VAL* 4.3 16.2 - - + -
480H THR 3.1 7.8 + - - +
481H TRP* 3.1 34.3 + - + +
483H ASP* 1.3 82.2 - - - +
485H VAL* 1.3 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 485 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H THR* 4.1 16.8 - - + +
277H ALA* 3.7 24.5 - - + -
278H LEU* 4.4 7.6 - - + -
395H LEU* 4.8 1.6 - - + -
481H TRP* 3.1 55.3 + - + +
482H ALA 4.1 0.4 - - - +
484H LEU* 1.3 84.1 - - + +
486H HIS* 1.3 67.0 + - - +
488H ASP* 2.9 25.1 + - + +
489H ALA* 3.9 19.1 - - + +
----------------------------------------------------------
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