Contacts of the helix formed by residues 489 - 507 (chain F) 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 ALA 489 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F LEU* 6.4 0.2 - - + -
478F TRP* 5.0 3.8 - - + -
481F TRP* 4.2 11.9 - - + +
482F ALA* 3.7 31.6 + - + -
485F VAL* 3.8 13.7 - - + +
487F PRO* 3.0 1.6 - - - +
488F ASP* 1.3 75.3 - - - +
490F GLN* 1.3 63.8 + - - +
491F ASP 3.3 2.7 - - - -
492F ILE* 3.2 22.0 + - + +
493F LEU* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 490 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482F ALA* 5.2 3.1 - - - +
486F HIS* 4.8 9.7 + - - -
487F PRO* 2.9 32.7 + - + +
488F ASP 3.3 0.6 - - - -
489F ALA* 1.3 78.4 - - - +
491F ASP* 1.3 64.3 + - - +
493F LEU* 3.4 20.9 + - - +
494F ASP* 3.0 43.3 + - - +
497F GLU* 5.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 491 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488F ASP 4.8 4.3 + - - +
489F ALA 3.3 0.6 - - - -
490F GLN* 1.3 75.6 - - - +
492F ILE* 1.3 68.5 + - + +
494F ASP* 3.1 13.9 + - - +
495F THR* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 492 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 3.8 43.7 - - + +
271F VAL* 6.2 0.4 - - + -
272F LEU* 4.6 7.4 - - + -
420F THR* 3.4 32.3 - - + +
478F TRP* 3.8 31.0 - - + -
488F ASP 5.3 2.2 - - - +
489F ALA* 3.2 19.3 + - + +
491F ASP* 1.3 77.8 - - + +
493F LEU* 1.3 64.1 + - - +
495F THR* 3.2 8.1 + - - -
496F LEU* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F HIS* 3.6 33.2 - - + +
478F TRP* 4.4 9.3 - - + +
479F GLU* 4.3 19.1 - - + +
482F ALA* 3.8 26.9 - - + -
489F ALA 3.0 11.9 + - - +
490F GLN* 3.6 25.4 - - - +
492F ILE* 1.3 77.5 - - - +
494F ASP* 1.3 62.6 + - - +
496F LEU* 3.1 14.5 + - + +
497F GLU* 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 494 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490F GLN* 3.0 42.4 + - - +
491F ASP* 3.1 15.7 + - - +
493F LEU* 1.3 76.8 - - - +
495F THR* 1.3 62.8 + - - +
497F GLU* 3.2 19.1 + - - +
498F ASP* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 495 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 6.1 0.3 - - - -
420F THR 3.4 21.7 + - - +
421F LYS 3.6 9.4 - - - +
422F PRO* 4.6 6.3 - - + -
423F LEU 5.4 0.2 - - - +
491F ASP* 2.9 16.6 + - - +
492F ILE* 3.6 9.0 - - - -
494F ASP* 1.3 75.5 - - - +
496F LEU* 1.3 64.7 + - - +
498F ASP* 3.2 9.5 + - + +
499F ASN* 2.9 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419F PRO* 3.5 44.0 - - + +
420F THR* 3.9 7.4 - - + +
470F ILE* 3.8 16.3 - - + +
474F VAL* 3.8 16.8 - - + -
475F HIS* 3.7 39.9 - - + -
478F TRP* 4.0 17.0 - - + -
492F ILE 2.9 12.6 + - - +
493F LEU* 3.3 12.6 - - + +
495F THR* 1.3 78.7 - - - +
497F GLU* 1.3 57.8 + - - +
499F ASN* 3.3 2.3 + - - +
500F ARG* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 497 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F HIS* 3.1 37.0 + - + +
490F GLN* 5.5 0.7 + - - -
493F LEU* 3.0 24.7 + - - +
494F ASP* 3.7 23.3 - - - +
496F LEU* 1.3 72.7 - - - +
498F ASP* 1.3 66.6 + - - +
500F ARG* 3.4 10.5 + - - +
501F GLU* 3.2 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 498 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494F ASP* 2.9 24.4 + - - +
495F THR* 3.2 11.7 + - + +
497F GLU* 1.3 73.9 - - - +
499F ASN* 1.3 69.9 + - - +
501F GLU* 3.0 10.3 + - - +
502F TRP* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 499 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419F PRO 2.8 26.8 + - - +
421F LYS 3.0 23.2 + - - -
423F LEU* 3.5 26.5 + - + +
426F TYR* 3.7 22.4 - - + -
470F ILE* 4.7 1.8 - - + -
495F THR* 2.9 25.5 + - - +
496F LEU 3.6 4.3 - - - +
498F ASP* 1.3 79.7 - - - +
500F ARG* 1.3 64.3 + - - +
502F TRP* 3.3 8.1 + - - +
503F TYR* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467F VAL* 3.2 24.0 - - + +
470F ILE* 3.9 29.1 - - + +
471F ASP* 2.7 41.1 + - - +
475F HIS* 6.2 2.9 - - - -
496F LEU 2.9 13.8 + - - +
497F GLU* 3.5 12.1 - - - +
498F ASP 3.1 0.4 - - - -
499F ASN* 1.3 78.1 - - - +
501F GLU* 1.3 86.0 + - - +
503F TYR* 3.4 3.7 + - - +
504F GLN* 2.8 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 501 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497F GLU 3.2 12.5 + - - +
498F ASP* 3.0 11.0 + - - +
500F ARG* 1.3 106.8 + - - +
502F TRP* 1.3 64.5 + - - +
504F GLN* 3.3 12.0 - - - +
505F SER* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 502 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F LEU* 3.6 28.5 - - + +
427F ARG* 3.1 49.1 - - - -
498F ASP 3.0 11.8 + - - +
499F ASN* 3.5 12.3 - - - +
500F ARG 3.2 0.2 - - - -
501F GLU* 1.3 79.5 - - - +
503F TYR* 1.3 108.6 + + - +
505F SER* 3.1 4.3 + - - -
506F THR* 2.9 37.8 + - + -
427J ARG* 5.2 3.6 - - - -
502J TRP* 3.2 53.3 + + - +
505J SER* 4.6 8.7 - - - -
506J THR* 3.1 24.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 503 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423F LEU* 4.6 0.7 - - + -
426F TYR* 3.5 46.2 - + - -
427F ARG* 3.6 18.9 + - + +
430F THR* 3.2 32.3 + - + +
431F ASP* 5.5 0.9 + - - -
462F VAL* 4.7 4.7 - - + -
463F GLU* 3.6 34.3 - - + +
466F GLN* 3.9 17.5 - - + -
467F VAL* 4.0 13.7 - - + +
470F ILE* 5.6 0.7 - - + -
499F ASN 3.1 13.6 + - - +
500F ARG* 3.9 4.7 - - - +
502F TRP* 1.3 107.9 - + - +
504F GLN* 1.3 63.0 + - - +
506F THR* 3.2 12.3 + - - -
507F ILE* 3.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 504 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467F VAL* 3.8 11.2 - - + +
500F ARG* 2.8 52.9 + - - +
501F GLU* 3.3 19.3 - - - +
502F TRP 3.1 0.2 - - - -
503F TYR* 1.3 78.0 - - - +
505F SER* 1.3 62.7 + - - +
507F ILE* 3.0 53.8 + - - +
509F GLN* 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 505 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501F GLU* 2.9 16.3 + - - +
502F TRP 3.4 8.1 - - - -
504F GLN* 1.3 77.9 - - - +
506F THR* 1.3 60.8 - - - +
507F ILE 3.1 7.3 + - - +
509F GLN* 5.3 1.9 + - - +
423J LEU* 4.0 18.4 - - - +
424J GLN 5.9 0.5 + - - -
502J TRP* 3.8 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 506 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463F GLU* 3.5 26.7 - - + +
502F TRP* 2.9 40.5 + - + -
503F TYR* 3.5 10.5 - - + -
504F GLN 3.2 0.4 - - - -
505F SER* 1.3 74.0 - - - +
507F ILE* 1.3 63.6 + - - +
508F PRO* 3.1 13.0 - - - +
423J LEU* 5.4 1.6 - - - -
427J ARG* 3.5 27.2 + - - +
502J TRP* 4.1 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 507 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463F GLU* 3.5 14.8 - - + -
464F LYS* 3.7 51.4 - - + +
467F VAL* 3.9 11.7 - - + -
503F TYR 3.3 9.6 + - - +
504F GLN* 3.0 36.9 + - - +
505F SER 3.1 5.4 - - - +
506F THR* 1.3 75.5 - - - +
508F PRO* 1.4 69.0 - - + +
509F GLN* 2.7 36.5 + - - +
----------------------------------------------------------
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