Contacts of the helix formed by residues 489 - 507 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A TRP* 5.0 3.4 - - + -
481A TRP* 4.2 11.2 - - + +
482A ALA* 3.7 32.3 + - + -
485A VAL* 3.8 14.1 - - + +
487A PRO 3.0 1.0 - - - -
488A ASP* 1.3 76.5 - - - +
490A GLN* 1.3 64.1 + - - +
491A ASP 3.3 3.1 - - - -
492A ILE* 3.2 21.9 + - + +
493A LEU* 3.0 22.0 + - - +
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Residues in contact with GLN 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ALA* 5.1 3.3 - - - +
486A HIS* 4.7 9.9 + - - -
487A PRO* 2.9 32.7 + - + +
488A ASP 3.3 1.0 - - - -
489A ALA* 1.3 77.4 - - - +
491A ASP* 1.3 64.1 + - - +
493A LEU* 3.4 20.9 + - - +
494A ASP* 3.0 50.9 + - - +
497A GLU* 5.5 0.2 + - - -
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Residues in contact with ASP 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A PRO 4.9 0.2 + - - -
488A ASP 4.8 3.5 + - - +
489A ALA 3.3 0.6 - - - -
490A GLN* 1.3 75.6 - - - +
492A ILE* 1.3 69.6 + - + +
494A ASP* 3.1 14.5 + - - +
495A THR* 2.9 27.4 + - - +
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 3.9 43.7 - - + +
271A VAL* 6.2 0.4 - - + -
272A LEU* 4.6 6.7 - - + -
420A THR* 3.4 31.5 - - + +
478A TRP* 3.8 31.6 - - + -
488A ASP 5.3 3.1 - - - +
489A ALA* 3.2 20.5 + - + +
491A ASP* 1.3 77.4 - - + +
493A LEU* 1.3 64.2 + - - +
495A THR* 3.3 7.8 + - - -
496A LEU* 3.0 21.9 + - - +
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Residues in contact with LEU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A HIS* 3.6 34.3 - - + +
478A TRP* 4.4 9.8 - - + +
479A GLU* 4.3 19.3 - - + +
482A ALA* 3.8 26.5 - - + -
489A ALA 3.0 12.1 + - - +
490A GLN* 3.6 25.4 - - - +
492A ILE* 1.3 77.2 - - - +
494A ASP* 1.3 62.3 + - - +
496A LEU* 3.2 13.9 + - + +
497A GLU* 3.0 37.2 + - - +
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Residues in contact with ASP 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A GLN* 3.0 43.3 + - - +
491A ASP* 3.1 16.2 + - - +
493A LEU* 1.3 76.5 - - - +
495A THR* 1.3 56.7 + - - +
497A GLU* 3.2 18.6 + - - +
498A ASP* 2.9 37.8 + - - +
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Residues in contact with THR 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 6.1 0.3 - - - -
420A THR 3.4 21.0 + - - +
421A LYS 3.6 10.3 - - - +
422A PRO* 4.5 5.6 - - + -
491A ASP* 2.9 16.0 + - - +
492A ILE* 3.6 8.7 - - - -
494A ASP* 1.3 75.9 - - - +
496A LEU* 1.3 58.3 + - - +
498A ASP* 3.1 10.0 + - + +
499A ASN* 2.8 49.8 + - - +
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A PRO* 3.4 43.3 + - + +
420A THR* 3.9 8.0 - - + +
470A ILE* 3.9 16.2 - - + -
474A VAL* 3.8 17.5 - - + -
475A HIS* 3.7 37.9 - - + -
478A TRP* 4.0 17.0 - - + -
492A ILE 3.0 13.6 + - - +
493A LEU* 3.2 13.0 + - + +
495A THR* 1.3 77.5 - - - +
497A GLU* 1.3 57.1 + - - +
499A ASN* 3.3 2.4 + - - +
500A ARG* 3.0 25.5 + - - +
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Residues in contact with GLU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A ILE* 6.1 0.2 - - - -
475A HIS* 3.1 37.3 + - + +
490A GLN* 5.5 0.3 + - - -
493A LEU* 3.0 26.3 + - - +
494A ASP* 3.6 21.8 - - - +
496A LEU* 1.3 73.6 - - - +
498A ASP* 1.3 65.3 + - - +
500A ARG* 3.4 9.6 + - - +
501A GLU* 3.2 27.8 + - - +
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Residues in contact with ASP 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494A ASP* 2.9 24.9 + - - +
495A THR* 3.5 10.8 - - + +
497A GLU* 1.3 77.0 - - - +
499A ASN* 1.3 67.3 + - - +
501A GLU* 3.0 11.0 + - - +
502A TRP* 3.0 20.4 + - - +
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Residues in contact with ASN 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A PRO 2.8 24.3 + - - +
421A LYS 2.9 23.0 + - - -
423A LEU* 3.5 26.7 + - + +
426A TYR* 3.7 25.8 - - + -
470A ILE* 4.7 2.7 - - + -
495A THR* 2.8 25.8 + - - +
496A LEU 3.7 4.3 - - - +
498A ASP* 1.3 78.0 - - - +
500A ARG* 1.3 62.8 + - - +
502A TRP* 3.3 8.1 + - - +
503A TYR* 3.1 27.2 + - - +
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Residues in contact with ARG 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A VAL* 3.2 23.6 - - + +
470A ILE* 3.9 29.8 - - + +
471A ASP* 2.7 41.6 + - - +
475A HIS* 6.2 3.1 - - - -
496A LEU 3.0 13.8 + - - +
497A GLU* 3.5 12.3 - - - +
498A ASP 3.1 0.4 - - - -
499A ASN* 1.3 77.2 - - - +
501A GLU* 1.3 87.0 + - - +
503A TYR* 3.4 3.5 + - - +
504A GLN* 2.9 57.4 + - - +
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Residues in contact with GLU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497A GLU 3.2 13.1 + - - +
498A ASP* 3.0 10.4 + - - +
500A ARG* 1.3 110.4 + - - +
502A TRP* 1.3 64.7 + - - +
504A GLN* 3.2 12.2 + - - +
505A SER* 2.9 29.2 + - - +
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Residues in contact with TRP 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 3.6 29.8 - - + +
427A ARG* 3.1 48.9 - - - -
498A ASP 3.0 11.6 + - - +
499A ASN* 3.5 12.6 - - - +
500A ARG 3.3 0.2 - - - -
501A GLU* 1.3 78.2 - - - +
503A TYR* 1.3 106.9 + + - +
505A SER* 3.2 7.6 + - - -
506A THR* 2.9 46.1 + - + -
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Residues in contact with TYR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A LEU* 4.6 0.9 - - + -
426A TYR* 3.5 46.4 - + - -
427A ARG* 3.6 19.9 + - + +
430A THR* 3.2 30.3 + - + +
431A ASP* 5.5 1.0 + - - -
462A VAL* 4.7 4.9 - - + -
463A GLU* 3.6 35.4 - - + +
466A GLN* 3.9 16.2 - - + -
467A VAL* 4.0 13.2 - - + -
470A ILE* 5.8 0.2 - - + -
499A ASN 3.1 14.9 + - - +
500A ARG* 3.9 4.9 - - - +
502A TRP* 1.3 104.7 - + - +
504A GLN* 1.3 63.8 + - - +
506A THR* 3.2 13.4 + - + -
507A ILE* 3.3 14.6 + - - +
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Residues in contact with GLN 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A VAL* 3.8 10.5 - - + +
500A ARG* 2.9 55.2 + - - +
501A GLU* 3.3 16.1 + - - +
503A TYR* 1.3 76.7 - - - +
505A SER* 1.3 62.1 - - - +
507A ILE* 3.0 54.3 + - - +
509A GLN* 4.9 2.4 + - - -
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Residues in contact with SER 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501A GLU* 2.9 15.0 + - - +
502A TRP* 3.5 10.6 - - - -
504A GLN* 1.3 78.2 - - - +
506A THR* 1.3 61.5 - - - +
507A ILE 3.2 7.4 + - - +
509A GLN* 5.3 2.3 + - - +
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Residues in contact with THR 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A GLU* 3.5 25.9 - - + +
502A TRP* 2.9 41.8 + - + -
503A TYR* 3.2 11.2 + - - -
505A SER* 1.3 76.0 - - - +
507A ILE* 1.3 63.8 + - - +
508A PRO* 3.1 12.5 - - - +
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A GLU* 3.5 14.8 - - + -
464A LYS* 3.7 51.8 - - + +
467A VAL* 3.8 11.7 - - + -
503A TYR 3.3 10.0 + - - +
504A GLN* 3.0 38.0 + - - +
505A SER 3.8 5.5 - - - +
506A THR* 1.3 75.7 - - - +
508A PRO* 1.3 69.0 - - + +
509A GLN* 2.7 37.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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