Contacts of the helix formed by residues 489 - 507 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E LEU* 6.4 0.2 - - + -
478E TRP* 5.0 3.4 - - + -
481E TRP* 4.2 11.7 - - + +
482E ALA* 3.7 31.4 - - + -
485E VAL* 3.8 13.2 - - + +
487E PRO* 3.0 1.8 - - - +
488E ASP* 1.3 77.7 - - - +
490E GLN* 1.3 62.8 + - - +
491E ASP 3.3 2.9 - - - -
492E ILE* 3.2 21.0 + - + +
493E LEU* 3.0 22.5 + - - +
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Residues in contact with GLN 490 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482E ALA* 5.1 3.8 - - - +
486E HIS* 4.7 10.0 + - - -
487E PRO* 2.9 32.9 + - + +
488E ASP 3.3 0.8 - - - -
489E ALA* 1.3 77.0 - - - +
491E ASP* 1.3 64.5 + - - +
493E LEU* 3.4 20.4 + - - +
494E ASP* 3.0 43.6 + - - +
497E GLU* 5.6 0.8 + - - -
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Residues in contact with ASP 491 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488E ASP 4.8 3.9 + - - +
489E ALA 3.3 0.6 - - - -
490E GLN* 1.3 75.6 - - - +
492E ILE* 1.3 69.4 + - + +
494E ASP* 3.1 13.6 + - - +
495E THR* 2.9 28.5 + - - +
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Residues in contact with ILE 492 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E TRP* 3.9 41.1 - - + +
271E VAL* 6.2 0.7 - - + -
272E LEU* 4.6 7.4 - - + -
420E THR* 3.4 31.9 - - + +
478E TRP* 3.8 34.3 - - + -
488E ASP 5.3 2.2 - - - +
489E ALA* 3.2 19.0 + - + +
491E ASP* 1.3 78.8 - - + +
493E LEU* 1.3 63.0 + - - +
495E THR* 3.2 8.7 + - - -
496E LEU* 2.9 21.3 + - - +
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Residues in contact with LEU 493 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E HIS* 3.6 34.5 - - + +
478E TRP* 4.4 9.1 - - + +
479E GLU* 4.3 19.1 - - + +
482E ALA* 3.8 26.7 - - + -
489E ALA 3.0 11.4 + - - +
490E GLN* 3.6 25.4 - - - +
491E ASP 3.2 0.2 - - - -
492E ILE* 1.3 77.0 - - - +
494E ASP* 1.3 64.4 + - - +
496E LEU* 3.2 14.3 + - + +
497E GLU* 3.0 37.0 + - - +
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Residues in contact with ASP 494 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490E GLN* 3.0 42.5 + - - +
491E ASP* 3.1 15.9 + - - +
493E LEU* 1.3 77.4 - - - +
495E THR* 1.3 61.7 + - - +
497E GLU* 3.2 18.1 + - - +
498E ASP* 2.9 32.1 + - - +
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Residues in contact with THR 495 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420E THR 3.4 21.3 + - - +
421E LYS 3.6 9.6 - - - +
422E PRO* 4.6 5.8 - - + -
491E ASP* 2.9 16.2 + - - +
492E ILE* 3.5 8.9 - - - -
494E ASP* 1.3 75.5 - - - +
496E LEU* 1.3 62.9 + - - +
498E ASP* 3.1 11.2 + - + +
499E ASN* 2.9 39.5 + - - +
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Residues in contact with LEU 496 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419E PRO* 3.5 43.5 - - + +
420E THR* 3.9 7.8 - - + +
470E ILE* 3.9 16.8 - - + +
474E VAL* 3.8 17.3 - - + -
475E HIS* 3.7 39.3 - - + -
478E TRP* 4.0 17.0 - - + -
492E ILE 2.9 13.6 + - - +
493E LEU* 3.3 12.3 - - + +
495E THR* 1.3 77.5 - - - +
497E GLU* 1.3 58.3 + - - +
499E ASN* 3.3 1.7 + - - +
500E ARG* 3.0 26.9 + - - +
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Residues in contact with GLU 497 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E ILE* 6.1 0.2 - - - -
475E HIS* 3.0 36.8 + - + +
490E GLN* 5.6 0.2 + - - -
493E LEU* 3.0 27.4 + - - +
494E ASP* 3.6 21.1 - - - +
496E LEU* 1.3 72.2 - - - +
498E ASP* 1.3 67.2 + - - +
500E ARG* 3.4 9.4 + - - +
501E GLU* 3.3 27.3 + - - +
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Residues in contact with ASP 498 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494E ASP* 2.9 25.3 + - - +
495E THR* 3.1 11.5 + - + +
497E GLU* 1.3 77.1 - - - +
499E ASN* 1.3 68.4 + - - +
501E GLU* 3.0 9.7 + - - +
502E TRP* 3.0 20.7 + - - +
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Residues in contact with ASN 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419E PRO 2.7 26.1 + - - +
421E LYS 3.0 22.6 + - - -
423E LEU* 3.5 27.2 + - + +
426E TYR* 3.7 25.1 - - + -
470E ILE* 4.7 1.8 - - + -
495E THR* 2.9 25.1 + - - +
496E LEU 3.7 1.6 - - - +
498E ASP* 1.3 78.2 - - - +
500E ARG* 1.3 62.4 + - - +
502E TRP* 3.3 8.1 + - - +
503E TYR* 3.1 28.1 + - - +
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Residues in contact with ARG 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467E VAL* 3.3 22.8 - - + +
470E ILE* 3.8 30.5 - - + +
471E ASP* 2.7 40.9 + - - +
475E HIS* 6.2 2.7 - - - -
496E LEU 3.0 13.5 + - - +
497E GLU* 3.6 11.9 - - - +
498E ASP 3.1 0.4 - - - -
499E ASN* 1.3 76.8 - - - +
501E GLU* 1.3 85.4 + - - +
503E TYR* 3.4 4.1 + - - +
504E GLN* 2.8 59.1 + - - +
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Residues in contact with GLU 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497E GLU 3.3 12.1 + - - +
498E ASP* 3.0 11.1 + - - +
500E ARG* 1.3 107.1 + - - +
502E TRP* 1.3 66.7 + - - +
504E GLN* 3.3 12.0 - - - +
505E SER* 2.9 30.3 + - - +
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Residues in contact with TRP 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E LEU* 3.6 28.7 - - + +
427E ARG* 3.2 48.7 - - - -
498E ASP 3.0 12.2 + - - +
499E ASN* 3.5 12.3 - - - +
500E ARG 3.2 0.2 - - - -
501E GLU* 1.3 78.9 - - - +
503E TYR* 1.3 107.1 + + - +
505E SER* 3.1 6.9 + - - -
506E THR* 2.9 36.8 + - + -
427L ARG* 5.7 1.1 - - - -
502L TRP* 3.2 45.2 + + - +
505L SER* 4.1 17.7 - - - -
506L THR* 3.2 20.6 + - + -
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Residues in contact with TYR 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423E LEU* 4.6 0.4 - - + -
426E TYR* 3.4 46.2 - + - -
427E ARG* 3.6 19.1 + - + +
430E THR* 3.2 30.6 + - + +
431E ASP* 5.5 0.9 + - - -
462E VAL* 4.7 5.8 - - + -
463E GLU* 3.6 34.4 - - + +
466E GLN* 3.9 15.3 - - + -
467E VAL* 4.0 13.7 - - + +
470E ILE* 5.5 0.7 - - + -
499E ASN 3.1 13.4 + - - +
500E ARG* 3.8 4.7 - - - +
502E TRP* 1.3 108.9 - + - +
504E GLN* 1.3 62.6 + - - +
506E THR* 3.2 13.6 + - + -
507E ILE* 3.3 15.4 + - - +
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Residues in contact with GLN 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E VAL* 3.8 9.4 - - + +
500E ARG* 2.8 55.9 + - - +
501E GLU* 3.3 16.4 - - - +
502E TRP 3.1 0.2 - - - -
503E TYR* 1.3 76.5 - - - +
505E SER* 1.3 63.6 + - - +
507E ILE* 3.0 54.0 + - - +
509E GLN* 4.9 2.3 + - - -
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Residues in contact with SER 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501E GLU* 2.9 16.7 + - - +
502E TRP* 3.5 8.0 - - - -
504E GLN* 1.3 77.6 - - - +
506E THR* 1.3 61.9 + - - +
507E ILE 3.1 7.7 + - - +
509E GLN* 5.3 1.9 + - - +
423L LEU* 3.9 18.3 - - - +
502L TRP* 3.7 22.0 - - - -
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Residues in contact with THR 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463E GLU* 3.5 26.1 - - + +
502E TRP* 2.9 30.9 + - + -
503E TYR* 3.2 10.7 + - + -
505E SER* 1.3 73.5 - - - +
507E ILE* 1.3 65.0 + - - +
508E PRO* 3.1 12.3 - - - +
423L LEU* 4.6 7.0 - - - -
424L GLN* 6.1 0.5 - - - +
427L ARG* 3.3 28.9 + - - +
502L TRP* 3.4 17.0 + - + -
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Residues in contact with ILE 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463E GLU* 3.5 13.9 - - + -
464E LYS* 3.7 52.7 - - + +
467E VAL* 3.8 11.7 - - + -
503E TYR 3.3 9.6 + - - +
504E GLN* 3.0 36.7 + - - +
505E SER 3.8 5.4 - - - +
506E THR* 1.3 75.8 - - - +
508E PRO* 1.3 68.0 - - + +
509E GLN* 2.7 37.1 + - - +
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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) + - + + + + + -
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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