Contacts of the helix formed by residues 489 - 507 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272G LEU* 6.4 0.2 - - + -
478G TRP* 5.0 3.1 - - + -
481G TRP* 4.1 11.9 - - + +
482G ALA* 3.7 32.3 - - + -
485G VAL* 3.8 13.2 - - + +
487G PRO 3.0 1.6 + - - -
488G ASP* 1.3 76.9 - - - +
490G GLN* 1.3 64.8 + - - +
491G ASP 3.3 2.5 - - - -
492G ILE* 3.2 21.1 + - + +
493G LEU* 3.0 22.2 + - - +
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Residues in contact with GLN 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482G ALA* 5.1 3.1 - - - +
486G HIS* 4.7 10.0 + - - -
487G PRO* 2.9 32.4 + - + +
488G ASP 3.4 0.4 - - - -
489G ALA* 1.3 75.8 - - - +
491G ASP* 1.3 65.4 + - - +
493G LEU* 3.4 21.2 + - - +
494G ASP* 3.0 44.9 + - - +
497G GLU* 5.5 0.4 + - - -
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Residues in contact with ASP 491 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488G ASP 4.8 3.9 + - - +
489G ALA 3.3 0.4 - - - -
490G GLN* 1.3 74.8 - - - +
492G ILE* 1.3 68.9 + - + +
494G ASP* 3.1 14.4 + - - +
495G THR* 2.9 28.5 + - - +
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Residues in contact with ILE 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TRP* 3.8 43.3 - - + +
271G VAL* 6.1 1.1 - - + -
272G LEU* 4.6 7.4 - - + -
420G THR* 3.3 32.0 - - + +
478G TRP* 3.9 30.3 - - + -
488G ASP 5.3 2.9 - - - +
489G ALA* 3.2 19.4 + - + +
491G ASP* 1.3 80.0 - - + +
493G LEU* 1.3 62.2 + - - +
495G THR* 3.3 8.2 + - - -
496G LEU* 3.0 22.3 + - - +
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Residues in contact with LEU 493 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475G HIS* 3.6 33.0 - - + +
478G TRP* 4.4 9.6 - - + +
479G GLU* 4.3 18.8 - - + +
482G ALA* 3.8 26.9 - - + -
489G ALA 3.0 11.4 + - - +
490G GLN* 3.6 24.5 - - - +
491G ASP 3.2 0.2 - - - -
492G ILE* 1.3 75.9 - - - +
494G ASP* 1.3 63.4 + - - +
496G LEU* 3.2 14.2 + - + +
497G GLU* 3.0 37.7 + - - +
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Residues in contact with ASP 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490G GLN* 3.0 43.1 + - - +
491G ASP* 3.1 15.9 + - - +
493G LEU* 1.3 76.3 - - - +
495G THR* 1.3 62.7 + - - +
497G GLU* 3.2 18.6 + - - +
498G ASP* 2.9 32.5 + - - +
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Residues in contact with THR 495 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G TRP* 6.1 0.3 - - - -
420G THR 3.4 22.1 + - - +
421G LYS 3.6 9.6 - - - +
422G PRO* 4.6 6.1 - - + -
491G ASP* 2.9 16.2 + - - +
492G ILE* 3.5 8.1 - - - -
494G ASP* 1.3 75.2 - - - +
496G LEU* 1.3 57.9 + - - +
498G ASP* 3.2 9.7 + - + +
499G ASN* 2.9 50.7 + - - +
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Residues in contact with LEU 496 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419G PRO* 3.5 42.8 - - + +
420G THR* 3.9 8.2 - - + +
470G ILE* 3.9 17.2 - - + +
474G VAL* 3.8 17.3 - - + -
475G HIS* 3.7 38.6 - - + -
478G TRP* 4.0 16.8 - - + -
492G ILE 3.0 13.2 + - - +
493G LEU* 3.3 13.0 - - + +
495G THR* 1.3 78.2 - - - +
497G GLU* 1.3 57.8 + - - +
499G ASN* 3.3 2.3 + - - +
500G ARG* 3.0 26.3 + - - +
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Residues in contact with GLU 497 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475G HIS* 3.1 36.2 + - + +
490G GLN* 5.5 0.5 + - - -
493G LEU* 3.0 26.5 + - - +
494G ASP* 3.6 21.8 - - - +
496G LEU* 1.3 73.0 - - - +
498G ASP* 1.3 66.9 + - - +
500G ARG* 3.5 10.1 + - - +
501G GLU* 3.3 26.5 + - - +
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Residues in contact with ASP 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494G ASP* 2.9 25.7 + - - +
495G THR* 3.5 11.0 - - + +
497G GLU* 1.3 75.7 - - - +
499G ASN* 1.3 68.1 + - - +
501G GLU* 3.0 9.6 + - - +
502G TRP* 3.0 20.8 + - - +
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Residues in contact with ASN 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419G PRO 2.8 22.8 + - - +
421G LYS 3.0 23.2 + - - -
423G LEU* 3.5 27.4 + - + +
426G TYR* 3.7 25.1 - - + -
470G ILE* 4.7 2.5 - - + -
495G THR* 2.9 25.5 + - - +
496G LEU 3.7 4.5 - - - +
498G ASP* 1.3 78.2 - - - +
500G ARG* 1.3 61.2 + - - +
502G TRP* 3.3 8.4 + - - +
503G TYR* 3.1 28.4 + - - +
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Residues in contact with ARG 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D HIS* 5.3 2.2 - - - -
487D PRO* 4.1 17.2 - - - +
467G VAL* 3.3 22.9 - - + +
470G ILE* 3.9 29.6 - - + +
471G ASP* 2.7 41.5 + - - +
475G HIS* 6.2 2.7 - - - -
496G LEU 3.0 13.1 + - - +
497G GLU* 3.6 13.2 - - - +
498G ASP 3.1 0.2 - - - -
499G ASN* 1.3 78.3 - - - +
501G GLU* 1.3 87.6 + - - +
503G TYR* 3.4 3.9 + - - +
504G GLN* 2.8 56.8 + - - +
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Residues in contact with GLU 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497G GLU 3.3 12.2 + - - +
498G ASP* 3.0 10.6 + - - +
500G ARG* 1.3 109.7 + - - +
502G TRP* 1.3 63.7 + - - +
504G GLN* 3.3 12.8 + - - +
505G SER* 2.9 31.4 + - - +
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Residues in contact with TRP 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G LEU* 3.6 29.4 - - + +
427G ARG* 3.1 50.5 - - - -
498G ASP 3.0 12.2 + - - +
499G ASN* 3.5 12.3 - - - +
500G ARG 3.2 0.2 - - - -
501G GLU* 1.3 78.0 - - - +
503G TYR* 1.3 104.7 + + - +
505G SER* 3.2 7.6 + - - -
506G THR* 2.9 44.5 + - + -
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Residues in contact with TYR 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G LEU* 4.6 0.7 - - + -
426G TYR* 3.5 46.0 - + - -
427G ARG* 3.7 18.9 + - + +
430G THR* 3.2 30.3 + - + +
431G ASP* 5.5 0.9 + - - -
462G VAL* 4.7 5.6 - - + -
463G GLU* 3.6 34.1 - - + +
466G GLN* 3.9 16.6 - - + -
467G VAL* 4.1 14.1 - - + +
470G ILE* 5.5 0.9 - - + -
499G ASN 3.1 14.6 + - - +
500G ARG* 3.9 3.8 - - - +
502G TRP* 1.3 108.0 - + - +
504G GLN* 1.3 64.7 + - - +
506G THR* 3.2 13.5 + - + -
507G ILE* 3.3 14.6 + - - +
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Residues in contact with GLN 504 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487D PRO* 6.0 0.6 - - - +
467G VAL* 3.8 11.0 - - + +
500G ARG* 2.8 52.2 + - - +
501G GLU* 3.3 17.5 - - - +
503G TYR* 1.3 77.3 - - - +
505G SER* 1.3 64.8 + - - +
507G ILE* 3.0 54.3 + - - +
509G GLN* 5.0 2.3 + - - -
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Residues in contact with SER 505 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G GLU* 2.9 16.2 + - - +
502G TRP* 3.5 10.0 - - - -
504G GLN* 1.3 78.3 - - - +
506G THR* 1.3 62.1 - - - +
507G ILE 3.1 7.6 + - - +
509G GLN* 5.3 1.9 + - - +
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Residues in contact with THR 506 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463G GLU* 3.5 25.8 - - + +
502G TRP* 2.9 41.6 + - + -
503G TYR* 3.2 10.9 + - - -
505G SER* 1.3 74.5 - - - +
507G ILE* 1.3 62.6 + - - +
508G PRO* 3.1 13.0 - - - +
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Residues in contact with ILE 507 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463G GLU* 3.5 13.7 - - + -
464G LYS* 3.8 52.0 - - + +
467G VAL* 3.8 11.0 - - + -
503G TYR 3.3 9.6 + - - +
504G GLN* 3.0 38.3 + - - +
505G SER 3.7 5.6 - - - +
506G THR* 1.3 75.8 - - - +
508G PRO* 1.3 67.4 - - + +
509G 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