Contacts of the helix formed by residues 489 - 507 (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 ALA 489 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H LEU* 6.4 0.2 - - + -
478H TRP* 5.0 3.5 - - + -
481H TRP* 4.2 12.1 - - + +
482H ALA* 3.7 31.4 - - + -
485H VAL* 3.9 12.6 - - + +
487H PRO 3.0 1.2 - - - -
488H ASP* 1.3 76.9 - - - +
490H GLN* 1.3 64.6 + - - +
491H ASP 3.3 2.7 - - - -
492H ILE* 3.2 21.4 + - + +
493H LEU* 3.0 21.7 + - - +
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Residues in contact with GLN 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482H ALA* 5.2 2.6 - - - +
486H HIS* 4.8 9.4 + - - -
487H PRO* 2.9 31.4 + - + +
488H ASP 3.3 0.6 - - - -
489H ALA* 1.3 77.8 - - - +
491H ASP* 1.3 64.3 + - - +
493H LEU* 3.4 20.6 + - - +
494H ASP* 3.0 44.0 + - - +
497H GLU* 5.6 0.4 + - - -
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Residues in contact with ASP 491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488H ASP 4.8 3.9 + - - +
489H ALA 3.3 0.6 - - - -
490H GLN* 1.3 75.7 - - - +
492H ILE* 1.3 70.9 + - + +
494H ASP* 3.1 13.9 + - - +
495H THR* 2.9 27.5 + - - +
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Residues in contact with ILE 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H TRP* 3.8 43.5 - - + +
271H VAL* 6.2 0.9 - - + -
272H LEU* 4.6 7.2 - - + -
420H THR* 3.4 33.2 - - + +
478H TRP* 3.8 30.3 - - + -
488H ASP 5.3 2.9 - - - +
489H ALA* 3.2 19.8 + - + +
491H ASP* 1.3 78.7 - - + +
493H LEU* 1.3 64.6 + - - +
495H THR* 3.3 7.6 + - - -
496H LEU* 2.9 21.8 + - - +
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Residues in contact with LEU 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475H HIS* 3.5 35.0 - - + +
478H TRP* 4.4 8.7 - - + +
479H GLU* 4.3 19.1 - - + +
482H ALA* 3.8 27.4 - - + -
489H ALA 3.0 11.8 + - - +
490H GLN* 3.6 24.5 - - - +
492H ILE* 1.3 76.2 - - - +
494H ASP* 1.3 65.8 + - - +
496H LEU* 3.2 14.0 + - + +
497H GLU* 3.0 38.1 + - - +
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Residues in contact with ASP 494 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490H GLN* 3.0 42.9 + - - +
491H ASP* 3.1 16.2 + - - +
493H LEU* 1.3 77.4 - - - +
495H THR* 1.3 62.4 + - - +
497H GLU* 3.1 18.6 + - - +
498H ASP* 2.9 31.7 + - - +
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Residues in contact with THR 495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199H TRP* 6.1 0.2 - - - -
420H THR 3.4 21.1 - - - +
421H LYS 3.6 9.6 - - - +
422H PRO* 4.6 5.8 - - + -
491H ASP* 2.9 16.1 + - - +
492H ILE* 3.6 8.2 - - - -
494H ASP* 1.3 75.5 - - - +
496H LEU* 1.3 63.4 + - - +
498H ASP* 3.1 10.1 + - + +
499H ASN* 2.8 44.9 + - - +
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Residues in contact with LEU 496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419H PRO* 3.5 43.7 - - + +
420H THR* 3.9 8.9 - - + +
470H ILE* 3.9 16.1 - - + +
474H VAL* 3.8 16.6 - - + -
475H HIS* 3.7 39.0 - - + -
478H TRP* 4.0 17.0 - - + -
492H ILE 2.9 13.4 + - - +
493H LEU* 3.3 12.6 - - + +
495H THR* 1.3 78.0 - - - +
497H GLU* 1.3 57.4 + - - +
499H ASN* 3.2 2.1 + - - +
500H ARG* 3.0 26.3 + - - +
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Residues in contact with GLU 497 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475H HIS* 3.1 38.6 + - + +
490H GLN* 5.6 0.3 + - - -
493H LEU* 3.0 25.8 + - - +
494H ASP* 3.1 21.1 + - - +
496H LEU* 1.3 71.9 - - - +
498H ASP* 1.3 66.1 + - - +
500H ARG* 3.4 10.2 + - - +
501H GLU* 3.3 27.2 + - - +
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Residues in contact with ASP 498 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494H ASP* 2.9 24.3 + - - +
495H THR* 3.1 11.2 + - + +
497H GLU* 1.3 73.8 - - - +
499H ASN* 1.3 70.9 + - - +
501H GLU* 3.1 10.4 + - - +
502H TRP* 3.0 20.0 + - - +
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Residues in contact with ASN 499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419H PRO 2.8 27.0 + - - +
421H LYS 2.9 23.0 + - - -
423H LEU* 3.5 26.5 + - + +
426H TYR* 3.7 22.4 - - + -
470H ILE* 4.7 1.8 - - + -
495H THR* 2.8 24.7 + - - +
496H LEU 3.6 4.3 - - - +
498H ASP* 1.3 78.5 - - - +
500H ARG* 1.3 62.7 + - - +
502H TRP* 3.3 7.2 + - - +
503H TYR* 3.1 28.2 + - - +
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Residues in contact with ARG 500 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A HIS* 4.7 7.5 - - - -
487A PRO* 5.4 5.5 - - - +
467H VAL* 3.2 23.3 - - + +
470H ILE* 3.9 30.0 - - + +
471H ASP* 2.7 40.7 + - - +
475H HIS* 6.2 2.9 - - - -
496H LEU 3.0 12.7 + - - +
497H GLU* 3.6 12.8 - - - +
498H ASP 3.1 0.4 - - - -
499H ASN* 1.3 79.1 - - - +
501H GLU* 1.3 85.8 + - - +
503H TYR* 3.3 3.8 + - - +
504H GLN* 2.8 57.4 + - - +
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Residues in contact with GLU 501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497H GLU 3.3 12.5 + - - +
498H ASP* 3.1 11.5 + - - +
500H ARG* 1.3 107.2 + - - +
502H TRP* 1.3 65.3 + - - +
504H GLN* 3.2 12.9 + - - +
505H SER* 2.9 28.9 + - - +
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Residues in contact with TRP 502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H LEU* 3.6 30.2 - - + +
427H ARG* 3.2 49.1 - - - -
498H ASP 3.0 12.8 + - - +
499H ASN* 3.6 12.3 - - - +
500H ARG 3.2 0.2 - - - -
501H GLU* 1.3 78.6 - - - +
503H TYR* 1.3 106.2 + + - +
505H SER* 3.2 7.9 + - - -
506H THR* 2.9 45.3 + - + -
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Residues in contact with TYR 503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H LEU* 4.6 0.4 - - + -
426H TYR* 3.5 47.3 - + - -
427H ARG* 3.6 19.0 + - + +
430H THR* 3.2 30.9 + - + +
431H ASP* 5.5 0.3 + - - -
462H VAL* 4.7 5.6 - - + -
463H GLU* 3.6 34.6 - - + +
466H GLN* 3.9 16.6 - - + -
467H VAL* 4.0 13.2 - - + -
470H ILE* 5.6 0.7 - - + -
499H ASN 3.1 13.5 + - - +
500H ARG* 3.8 4.7 - - - +
502H TRP* 1.3 105.4 - + - +
504H GLN* 1.3 63.5 + - - +
506H THR* 3.2 13.7 + - + -
507H ILE* 3.3 14.6 + - - +
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Residues in contact with GLN 504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A PRO* 6.3 0.8 - - - +
467H VAL* 3.8 11.0 - - + +
500H ARG* 2.8 53.0 + - - +
501H GLU* 3.3 18.4 + - - +
502H TRP 3.1 0.2 - - - -
503H TYR* 1.3 76.5 - - - +
505H SER* 1.3 64.9 + - - +
507H ILE* 3.0 53.9 + - - +
509H GLN* 4.9 2.6 + - - -
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Residues in contact with SER 505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501H GLU* 2.9 15.2 + - - +
502H TRP* 3.2 10.7 + - - -
504H GLN* 1.3 78.9 - - - +
506H THR* 1.3 61.3 + - - +
507H ILE 3.1 7.6 + - - +
509H GLN* 5.3 1.9 + - - +
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Residues in contact with THR 506 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463H GLU* 3.4 26.9 - - + +
502H TRP* 2.9 42.1 + - + -
503H TYR* 3.5 10.3 - - + -
504H GLN 3.2 0.6 - - - -
505H SER* 1.3 74.5 - - - +
507H ILE* 1.3 64.5 + - - +
508H PRO* 3.1 12.6 - - - +
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Residues in contact with ILE 507 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463H GLU* 3.5 13.7 - - + -
464H LYS* 3.7 52.9 - - + +
467H VAL* 3.8 11.7 - - + -
503H TYR 3.3 10.1 + - - +
504H GLN* 3.0 37.7 + - - +
505H SER 3.8 5.0 - - - +
506H THR* 1.3 75.2 - - - +
508H PRO* 1.4 69.9 - - + +
509H GLN* 2.7 37.6 + - - +
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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