Contacts of the helix formed by residues 473 - 485 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D MET* 3.8 25.6 - - + -
373D HIS* 3.6 36.3 + - + +
374D MET* 4.5 10.3 - - + -
416D LEU* 3.9 14.8 - - + -
469D PHE* 3.0 33.9 + - + +
471D ASP 3.7 0.2 - - - -
472D TYR* 1.3 97.1 - - + +
474D VAL* 1.3 67.0 + - - +
476D PRO* 3.3 5.1 - - - +
477D LEU* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 474 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D LEU* 3.7 18.4 - - + +
419D PRO* 4.2 10.1 - - + -
420D THR* 4.4 0.9 - - + -
469D PHE* 3.1 49.8 + - + +
470D ILE* 3.9 9.0 - - - -
473D ILE* 1.3 70.9 - - + +
475D HIS* 1.3 67.4 + - - +
477D LEU* 3.3 4.9 + - - +
478D TRP* 2.9 47.1 + - + +
496D LEU* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 475 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D ILE* 2.7 35.0 + - + +
471D ASP* 4.7 4.3 - - - +
474D VAL* 1.3 73.9 - - - +
476D PRO* 1.3 65.6 - - + +
479D GLU* 2.8 66.7 + - + +
493D LEU* 3.6 13.6 - - + +
496D LEU* 3.7 15.6 - - + +
497D GLU* 3.0 41.0 + - + +
500D ARG* 6.2 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 476 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D LEU* 3.8 18.8 - - + +
381D LYS* 5.1 5.2 - - - +
470D ILE 3.4 2.2 - - - +
471D ASP 3.2 28.0 - - - +
472D TYR* 3.6 13.5 - - - +
473D ILE 3.3 12.6 - - - +
475D HIS* 1.3 94.4 - - + +
477D LEU* 1.3 57.7 + - - +
479D GLU* 3.9 12.6 - - - +
480D THR* 2.9 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 477 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373D HIS* 3.9 9.0 - - + -
377D LEU* 3.8 19.0 - - + +
380D LEU* 4.5 4.9 - - + +
409D ASN* 4.3 14.8 - - - +
412D HIS* 3.5 35.4 - - + +
413D CYS* 3.7 33.7 - - - -
416D LEU* 3.8 22.7 - - + -
473D ILE 3.1 17.3 + - - +
474D VAL* 3.7 2.2 - - - +
476D PRO* 1.3 77.8 - - - +
478D TRP* 1.3 63.1 + - + +
480D THR* 3.2 6.4 + - - -
481D TRP* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 478 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D TRP* 3.8 24.7 - + - -
272D LEU* 4.0 9.6 - - + -
413D CYS* 3.3 40.6 + - + +
416D LEU 3.2 19.1 + - - -
417D SER* 3.9 13.0 - - - -
420D THR* 3.6 15.6 - - + +
474D VAL* 2.9 44.7 + - + +
477D LEU* 1.3 75.8 - - + +
479D GLU* 1.3 57.0 + - - +
481D TRP* 3.8 31.6 - + - +
482D ALA* 2.7 35.6 + - - +
489D ALA* 5.0 3.4 - - + -
492D ILE* 3.8 28.3 - - + -
493D LEU* 4.4 9.0 - - + +
496D LEU* 4.0 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 479 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475D HIS* 2.8 49.1 + - + +
476D PRO* 3.9 9.8 - - - +
478D TRP* 1.3 76.2 - - - +
480D THR* 1.3 63.7 + - - +
482D ALA* 3.3 3.8 + - - +
483D ASP* 3.1 33.9 + - - +
493D LEU* 4.3 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 480 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D LEU* 3.4 13.0 - - + +
380D LEU* 3.4 28.3 - - + -
381D LYS* 3.8 30.4 - - + +
384D VAL* 3.7 16.8 - - + +
476D PRO 2.9 17.8 + - - -
477D LEU 3.2 8.6 + - - -
479D GLU* 1.3 76.9 + - - +
481D TRP* 1.3 65.1 + - - +
483D ASP* 3.0 22.8 + - - +
484D LEU* 3.1 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 481 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LEU* 4.0 25.0 - - + +
275D THR* 5.0 2.1 - - + +
278D LEU* 4.2 5.8 - - + -
380D LEU* 4.1 9.1 - - + +
406D VAL* 3.8 32.1 - - + -
409D ASN* 4.4 9.4 - - + -
410D MET* 3.8 47.3 - - + -
413D CYS* 3.8 25.8 - - - -
477D LEU 2.9 15.8 + - - +
478D TRP* 3.3 26.2 + + - +
480D THR* 1.3 76.3 - - - +
482D ALA* 1.3 63.9 + - - +
484D LEU* 3.1 18.7 + - + +
485D VAL* 3.1 54.6 + - + +
489D ALA* 4.2 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478D TRP 2.7 22.3 + - - +
479D GLU 3.5 6.3 - - - +
480D THR 3.2 0.2 - - - -
481D TRP* 1.3 72.2 - - - +
483D ASP* 1.3 57.9 + - - +
485D VAL* 3.6 0.7 - - - +
486D HIS* 2.9 34.6 + - - +
487D PRO* 4.6 1.7 - - - +
489D ALA* 3.7 29.1 - - + +
490D GLN* 5.1 2.7 - - - +
493D LEU* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 483 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D VAL* 3.5 25.4 - - + +
387D LYS* 3.1 17.8 + - - -
479D GLU* 3.1 24.0 + - - +
480D THR* 3.0 15.0 + - - +
482D ALA* 1.3 76.8 - - - +
484D LEU* 1.3 65.6 + - - +
486D HIS* 3.2 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 484 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ALA* 4.8 0.5 - - - +
380D LEU* 4.2 13.2 - - + -
383D MET* 4.3 28.9 - - + +
384D VAL* 4.1 17.7 - - + +
387D LYS* 3.6 18.6 + - + +
395D LEU* 3.7 44.1 - - + +
397D LEU* 6.2 0.7 - - + -
406D VAL* 4.3 15.3 - - + -
480D THR 3.1 8.2 + - - +
481D TRP* 3.1 37.0 + - + +
483D ASP* 1.3 81.5 - - - +
485D VAL* 1.3 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 485 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D THR* 4.1 13.9 - - + +
277D ALA* 3.7 23.8 - - + -
278D LEU* 4.4 7.6 - - + -
395D LEU* 4.8 1.1 - - + -
481D TRP* 3.1 55.2 + - + +
482D ALA 4.1 0.2 - - - +
484D LEU* 1.3 85.6 - - + +
486D HIS* 1.3 66.4 + - - +
488D ASP* 2.9 28.7 + - + +
489D ALA* 3.8 19.3 - - + +
----------------------------------------------------------
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