Contacts of the helix formed by residues 473 - 485 (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 ILE 473 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370G MET* 3.8 25.8 - - + -
373G HIS* 3.7 34.7 + - + +
374G MET* 4.6 9.2 - - + -
416G LEU* 3.9 15.0 - - + -
469G PHE* 3.0 34.2 + - + +
471G ASP 3.7 0.2 - - - -
472G TYR* 1.3 98.4 - - + +
474G VAL* 1.3 66.7 + - - +
476G PRO* 3.3 4.9 - - - +
477G LEU* 3.1 24.4 + - - +
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Residues in contact with VAL 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416G LEU* 3.7 19.3 - - + +
419G PRO* 4.1 11.0 - - + -
420G THR* 4.4 0.9 - - + -
469G PHE* 3.1 49.9 + - + +
470G ILE* 3.9 9.2 - - - -
473G ILE* 1.3 74.0 - - + +
475G HIS* 1.3 59.7 + - - +
477G LEU* 3.3 6.0 + - - +
478G TRP* 2.9 51.1 + - + -
496G LEU* 3.8 21.8 - - + -
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Residues in contact with HIS 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470G ILE* 2.7 35.4 + - + +
471G ASP* 4.7 4.0 - - - +
474G VAL* 1.3 74.3 - - - +
476G PRO* 1.3 59.1 - - + +
479G GLU* 2.8 74.1 + - + +
493G LEU* 3.6 13.3 - - + +
496G LEU* 3.7 14.5 - - + +
497G GLU* 3.1 40.5 + - + +
500G ARG* 6.2 2.7 - - - -
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Residues in contact with PRO 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377G LEU* 3.7 20.0 - - + +
381G LYS* 5.0 5.6 - - - +
470G ILE 3.4 2.9 - - - +
471G ASP 3.2 27.4 - - - +
472G TYR* 3.6 13.9 - - - +
473G ILE 3.3 12.8 - - - +
475G HIS* 1.3 94.3 - - + +
477G LEU* 1.3 55.8 + - - +
479G GLU* 3.9 12.1 - - - +
480G THR* 2.8 27.5 + - - -
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Residues in contact with LEU 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373G HIS* 3.9 9.0 - - + -
377G LEU* 3.8 19.4 - - + +
380G LEU* 4.4 4.7 - - + -
409G ASN* 4.3 14.6 - - - +
412G HIS* 3.4 35.0 - - + +
413G CYS* 3.7 34.1 - - - -
416G LEU* 3.8 21.8 - - + -
473G ILE 3.1 15.2 + - - +
474G VAL* 3.6 2.9 - - - +
476G PRO* 1.3 77.7 - - - +
478G TRP* 1.3 66.7 + - + +
480G THR* 3.1 6.9 + - - -
481G TRP* 2.9 23.7 + - - +
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Residues in contact with TRP 478 (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 25.4 - + - -
272G LEU* 4.0 9.2 - - + -
413G CYS* 3.3 41.1 + - + +
416G LEU 3.2 18.5 + - - -
417G SER* 4.0 11.9 - - - -
420G THR* 3.7 15.6 - - + +
474G VAL* 2.9 44.7 + - + +
477G LEU* 1.3 76.5 - - + +
479G GLU* 1.3 56.1 + - - +
481G TRP* 3.7 31.3 - + + +
482G ALA* 2.7 35.7 + - - +
489G ALA* 5.0 3.8 - - + -
492G ILE* 3.9 28.5 - - + -
493G LEU* 4.4 8.6 - - + +
496G LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 479 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475G HIS* 2.8 48.3 + - + +
476G PRO* 3.9 9.4 - - - +
478G TRP* 1.3 76.1 - - - +
480G THR* 1.3 63.9 + - - +
482G ALA* 3.3 4.0 + - - +
483G ASP* 3.1 31.8 + - - +
493G LEU* 4.3 18.4 - - + +
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Residues in contact with THR 480 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377G LEU* 3.4 12.8 - - + +
380G LEU* 3.5 26.9 - - + -
381G LYS* 3.8 31.2 - - + +
384G VAL* 3.7 16.9 - - + +
476G PRO 2.8 18.5 + - - -
477G LEU 3.1 8.2 + - - -
479G GLU* 1.3 77.7 + - - +
481G TRP* 1.3 63.9 + - - +
483G ASP* 3.1 17.9 + - - +
484G LEU* 3.1 11.1 + - - +
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Residues in contact with TRP 481 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G LEU* 4.0 24.8 - - + +
275G THR* 4.9 2.5 - - + +
278G LEU* 4.2 5.6 - - + -
380G LEU* 4.1 8.7 - - + +
406G VAL* 3.8 31.0 - - + -
409G ASN* 4.4 9.6 - - + -
410G MET* 3.7 46.9 - - + -
413G CYS* 3.8 26.0 - - - -
477G LEU 2.9 13.9 + - - +
478G TRP* 3.7 28.3 - + - +
480G THR* 1.3 76.1 - - - +
482G ALA* 1.3 65.1 + - - +
483G ASP 3.1 0.2 + - - -
484G LEU* 3.1 20.0 + - + +
485G VAL* 3.1 50.5 + - + +
489G ALA* 4.1 5.3 - - + +
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Residues in contact with ALA 482 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478G TRP* 2.7 21.9 + - + +
479G GLU 3.5 6.1 - - - +
481G TRP* 1.3 73.2 - - - +
483G ASP* 1.3 57.7 + - - +
485G VAL* 3.6 0.7 - - - +
486G HIS* 2.9 34.3 + - + +
487G PRO* 4.6 2.1 - - + +
489G ALA* 3.7 28.7 - - + +
490G GLN* 5.1 2.9 - - - +
493G LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 483 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384G VAL* 3.5 24.0 - - + +
387G LYS* 3.1 16.4 + - - -
479G GLU* 3.1 23.9 + - - +
480G THR* 3.1 14.8 + - - +
481G TRP 3.0 0.4 - - - -
482G ALA* 1.3 76.8 - - - +
484G LEU* 1.3 66.3 + - - +
486G HIS* 3.1 20.9 + - - +
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Residues in contact with LEU 484 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277G ALA* 4.8 0.5 - - - +
278G LEU* 5.6 0.2 - - + -
380G LEU* 4.2 13.5 - - + -
383G MET* 4.3 28.7 - - + +
384G VAL* 4.1 18.1 - - + +
387G LYS* 3.6 19.9 + - + +
395G LEU* 3.8 43.3 - - + +
397G LEU* 6.2 0.9 - - + -
406G VAL* 4.3 16.8 - - + -
480G THR 3.1 8.0 + - - +
481G TRP* 3.1 37.0 + - + +
483G ASP* 1.3 82.2 - - - +
485G VAL* 1.3 61.1 + - + +
486G HIS 3.6 0.2 + - - -
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Residues in contact with VAL 485 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G THR* 4.1 14.4 - - + +
277G ALA* 3.7 24.0 - - + -
278G LEU* 4.5 7.4 - - + -
395G LEU* 4.8 1.3 - - + -
481G TRP* 3.2 51.8 - - + +
482G ALA 4.1 0.7 - - - +
484G LEU* 1.3 85.4 - - + +
486G HIS* 1.3 65.2 + - - +
488G ASP* 2.9 28.7 + - + +
489G ALA* 3.8 21.8 - - + +
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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