Contacts of the helix formed by residues 489 - 507 (chain L) 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 L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272L LEU* 6.3 0.2 - - + -
478L TRP* 5.0 2.9 - - + -
481L TRP* 4.1 11.9 - - + +
482L ALA* 3.7 31.9 - - + -
485L VAL* 3.8 14.3 - - + +
487L PRO 3.0 1.2 - - - -
488L ASP* 1.3 78.1 - - - +
490L GLN* 1.3 63.8 + - - +
491L ASP 3.3 2.7 - - - -
492L ILE* 3.2 22.8 + - + +
493L LEU* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 490 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482L ALA* 5.1 3.3 - - - +
486L HIS* 4.7 9.5 + - - -
487L PRO* 2.9 32.4 + - + +
488L ASP 3.4 0.6 - - - -
489L ALA* 1.3 78.6 - - - +
491L ASP* 1.3 63.6 + - - +
493L LEU* 3.4 20.1 + - - +
494L ASP* 3.0 48.4 + - - +
497L GLU* 5.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 491 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488L ASP 4.8 4.5 + - - +
489L ALA 3.3 0.6 - - - -
490L GLN* 1.3 74.8 - - - +
492L ILE* 1.3 69.3 + - + +
494L ASP* 3.1 13.7 + - - +
495L THR* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 492 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L TRP* 3.8 43.3 - - + +
271L VAL* 6.2 0.9 - - + -
272L LEU* 4.6 7.9 - - + -
420L THR* 3.4 32.0 - - + +
478L TRP* 3.8 31.4 - - + -
488L ASP 5.3 2.7 - - - +
489L ALA* 3.2 19.9 + - + +
491L ASP* 1.3 77.0 - - + +
493L LEU* 1.3 64.6 + - - +
495L THR* 3.3 7.9 + - - -
496L LEU* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 493 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475L HIS* 3.6 33.7 - - + +
478L TRP* 4.5 6.4 - - + +
479L GLU* 4.3 20.9 - - + +
482L ALA* 3.7 28.5 - - + -
489L ALA 3.0 11.4 + - - +
490L GLN* 3.6 24.7 - - - +
491L ASP 3.2 0.2 - - - -
492L ILE* 1.3 77.6 - - - +
494L ASP* 1.3 62.8 + - - +
496L LEU* 3.2 15.3 + - + +
497L GLU* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 494 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490L GLN* 3.0 43.3 + - - +
491L ASP* 3.1 14.9 + - - +
493L LEU* 1.3 76.3 - - - +
495L THR* 1.3 63.4 + - - +
497L GLU* 3.1 19.1 + - - +
498L ASP* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 495 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L TRP* 6.0 0.5 - - - -
420L THR 3.4 22.2 + - - +
421L LYS 3.6 9.2 - - - +
422L PRO* 4.5 7.0 - - + -
423L LEU 5.4 0.2 - - - +
491L ASP* 2.9 16.2 + - - +
492L ILE* 3.6 7.6 - - - -
494L ASP* 1.3 75.9 - - - +
496L LEU* 1.3 58.8 + - - +
498L ASP* 3.1 10.9 + - + +
499L ASN* 2.8 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419L PRO* 3.5 44.2 - - + +
420L THR* 3.9 7.6 - - + +
470L ILE* 3.9 16.3 - - + +
474L VAL* 3.7 17.5 - - + -
475L HIS* 3.7 39.3 - - + -
478L TRP* 4.0 17.0 - - + -
492L ILE 3.0 13.6 + - - +
493L LEU* 3.3 12.3 - - + +
495L THR* 1.3 76.7 - - - +
497L GLU* 1.3 56.7 + - - +
499L ASN* 3.2 3.1 + - - +
500L ARG* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 497 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475L HIS* 3.0 36.8 + - + +
490L GLN* 5.5 0.7 + - - -
493L LEU* 3.0 28.6 + - - +
494L ASP* 3.6 20.7 - - - +
496L LEU* 1.3 73.2 - - - +
498L ASP* 1.3 66.4 + - - +
500L ARG* 3.5 10.1 + - - +
501L GLU* 3.3 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 498 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494L ASP* 2.9 25.3 + - - +
495L THR* 3.5 10.3 - - + +
497L GLU* 1.3 74.8 - - - +
499L ASN* 1.3 70.2 + - - +
501L GLU* 3.1 9.8 + - - +
502L TRP* 3.0 20.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 499 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419L PRO 2.8 26.8 + - - +
421L LYS 2.9 23.6 + - - -
423L LEU* 3.4 27.0 + - + +
426L TYR* 3.7 22.2 - - + -
470L ILE* 4.7 1.8 - - + -
495L THR* 2.8 26.1 + - - +
496L LEU 3.6 4.5 - - - +
498L ASP* 1.3 78.0 - - - +
500L ARG* 1.3 62.5 + - - +
502L TRP* 3.3 7.4 + - - +
503L TYR* 3.1 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C HIS* 3.9 16.9 - - - -
487C PRO* 4.7 6.3 - - - +
467L VAL* 3.3 23.3 - - + +
470L ILE* 3.9 29.6 - - + +
471L ASP* 2.7 40.7 + - - +
475L HIS* 6.2 2.7 - - - -
496L LEU 3.0 14.2 + - - +
497L GLU* 3.6 12.1 - - - +
498L ASP 3.1 0.4 - - - -
499L ASN* 1.3 77.2 - - - +
501L GLU* 1.3 86.4 + - - +
503L TYR* 3.8 3.1 - - - +
504L GLN* 2.8 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 501 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497L GLU 3.3 13.3 + - - +
498L ASP* 3.1 10.0 + - - +
500L ARG* 1.3 109.4 + - - +
502L TRP* 1.3 64.4 + - - +
504L GLN* 3.3 12.1 + - - +
505L SER* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 502 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502E TRP* 3.2 49.8 + + - +
505E SER* 3.7 25.1 - - - -
506E THR* 3.4 20.7 + - - -
423L LEU* 3.6 21.0 - - + +
427L ARG* 3.1 45.8 - - - -
498L ASP 3.0 12.0 + - - +
499L ASN* 3.5 11.9 - - - +
500L ARG 3.2 0.2 - - - -
501L GLU* 1.3 78.8 - - - +
503L TYR* 1.3 107.4 + + - +
505L SER* 3.2 6.5 + - - -
506L THR* 2.9 38.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 503 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423L LEU* 4.6 0.2 - - + -
426L TYR* 3.5 46.9 - + - -
427L ARG* 3.7 19.0 + - + +
430L THR* 3.2 30.9 + - + +
431L ASP* 5.5 0.7 + - - -
462L VAL* 4.7 5.8 - - + -
463L GLU* 3.6 35.1 - - + +
466L GLN* 3.9 16.2 - - + -
467L VAL* 4.0 14.4 - - + +
470L ILE* 5.5 0.7 - - + -
499L ASN 3.1 14.0 + - - +
500L ARG* 3.9 4.3 - - - +
502L TRP* 1.3 108.2 - + - +
504L GLN* 1.3 61.8 + - - +
506L THR* 3.2 12.7 + - - -
507L ILE* 3.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 504 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C PRO* 5.1 9.1 - - - +
467L VAL* 3.8 11.8 - - + +
500L ARG* 2.8 55.0 + - - +
501L GLU* 3.3 15.5 - - - +
503L TYR* 1.3 76.2 - - - +
505L SER* 1.3 62.6 + - - +
507L ILE* 3.0 50.3 + - - +
509L GLN* 4.9 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 505 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 4.3 13.2 - - - +
502E TRP* 4.1 17.0 - - - -
501L GLU* 2.9 15.8 + - - +
502L TRP* 3.4 9.4 - - - -
504L GLN* 1.3 77.0 - - - +
506L THR* 1.3 62.6 + - - +
507L ILE 3.1 7.5 + - - +
509L GLN* 5.3 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 506 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 4.7 4.5 - - + -
427E ARG* 3.9 23.1 - - - +
502E TRP* 3.2 21.1 + - + +
463L GLU* 3.5 25.9 - - + +
502L TRP* 2.9 31.1 + - + -
503L TYR* 3.2 11.2 + - + -
505L SER* 1.3 75.0 - - - +
507L ILE* 1.3 63.8 + - - +
508L PRO* 3.1 12.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 507 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463L GLU* 3.5 14.1 - - + -
464L LYS* 3.7 52.7 - - + +
467L VAL* 3.8 11.7 - - + -
503L TYR 3.3 10.1 + - - +
504L GLN* 3.0 36.8 - - - +
505L SER 3.1 7.2 - - - +
506L THR* 1.3 74.1 - - - +
508L PRO* 1.3 70.4 - - + +
509L GLN* 2.7 36.9 + - - +
----------------------------------------------------------
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