Contacts of the helix formed by residues 473 - 485 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390G THR 6.1 0.2 - - - +
391G SER* 5.5 12.3 - - - +
370K MET* 3.8 25.1 - - + -
373K HIS* 3.6 36.2 + - + +
374K MET* 4.5 9.9 - - + -
416K LEU* 3.9 15.3 - - + -
469K PHE* 3.0 33.7 + - + +
471K ASP 3.7 0.2 - - - -
472K TYR* 1.3 95.3 - - + +
474K VAL* 1.3 65.8 + - - +
475K HIS 3.5 0.9 - - - -
476K PRO* 3.3 4.6 - - - +
477K LEU* 3.1 23.2 + - - +
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Residues in contact with VAL 474 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416K LEU* 3.7 18.6 - - + +
419K PRO* 4.1 9.4 - - + -
420K THR* 4.4 1.3 - - + -
469K PHE* 3.1 49.5 + - + +
470K ILE* 3.9 10.1 - - - -
473K ILE* 1.3 74.0 - - + +
475K HIS* 1.3 60.7 + - - +
477K LEU* 3.3 5.2 + - - +
478K TRP* 2.9 50.5 + - + -
496K LEU* 3.8 22.4 - - + -
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Residues in contact with HIS 475 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470K ILE* 2.7 34.1 + - + +
471K ASP* 4.8 4.0 - - - +
474K VAL* 1.3 74.2 - - - +
476K PRO* 1.3 65.5 - - + +
479K GLU* 2.8 67.5 + - + +
493K LEU* 3.6 12.7 - - + +
496K LEU* 3.7 15.0 - - + +
497K GLU* 3.1 41.3 + - + +
500K ARG* 6.2 3.1 - - - -
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Residues in contact with PRO 476 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373K HIS* 5.4 0.2 - - - +
377K LEU* 3.8 18.8 - - + +
381K LYS* 5.0 4.6 - - - +
470K ILE 3.4 1.8 - - - +
471K ASP 3.2 28.3 - - - +
472K TYR* 3.6 14.1 - - - +
473K ILE 3.3 12.8 - - - +
475K HIS* 1.3 94.8 - - + +
477K LEU* 1.3 58.1 + - - +
479K GLU* 3.8 12.2 + - - +
480K THR* 2.8 27.4 + - - -
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Residues in contact with LEU 477 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373K HIS* 3.9 8.7 - - + -
377K LEU* 3.9 19.4 - - + +
380K LEU* 4.4 5.4 - - + -
409K ASN* 4.3 15.0 - - - +
412K HIS* 3.5 35.0 - - + +
413K CYS* 3.7 33.7 - - - -
416K LEU* 3.8 22.4 - - + -
473K ILE 3.1 14.7 + - - +
474K VAL* 3.6 2.5 - - - +
476K PRO* 1.3 79.7 - - - +
478K TRP* 1.3 64.6 + - + +
480K THR* 3.2 6.2 + - - -
481K TRP* 2.9 24.1 + - - +
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Residues in contact with TRP 478 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K TRP* 3.8 26.0 - + - -
272K LEU* 4.0 9.2 - - + -
413K CYS* 3.3 41.7 + - + +
416K LEU 3.2 18.6 + - - -
417K SER* 4.0 12.8 - - - -
420K THR* 3.7 14.7 - - + +
474K VAL* 2.9 45.1 + - + +
477K LEU* 1.3 77.4 - - + +
479K GLU* 1.3 56.8 + - - +
481K TRP* 3.6 30.7 - + - +
482K ALA* 2.7 36.1 + - - +
489K ALA* 5.0 3.8 - - + -
492K ILE* 3.8 29.8 - - + -
493K LEU* 4.4 9.1 - - + +
496K LEU* 4.0 14.1 - - + -
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Residues in contact with GLU 479 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475K HIS* 2.8 48.6 + - + +
476K PRO* 3.9 9.5 - - - +
478K TRP* 1.3 75.4 - - - +
480K THR* 1.3 64.5 + - - +
482K ALA* 3.3 3.8 + - - +
483K ASP* 3.1 32.2 + - - +
493K LEU* 4.3 18.6 - - + +
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Residues in contact with THR 480 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377K LEU* 3.3 13.5 - - + +
380K LEU* 3.4 28.5 - - + -
381K LYS* 3.8 30.3 - - + +
384K VAL* 3.7 17.0 - - + +
476K PRO 2.8 17.0 + - - -
477K LEU 3.2 8.4 + - - -
479K GLU* 1.3 77.3 - - - +
481K TRP* 1.3 66.3 + - - +
483K ASP* 3.0 23.0 + - - +
484K LEU* 3.1 5.5 + - - +
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Residues in contact with TRP 481 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K LEU* 4.1 24.6 - - + +
275K THR* 5.0 2.1 + - + +
278K LEU* 4.2 5.6 - - + -
380K LEU* 4.1 8.9 - - + +
406K VAL* 3.8 31.9 - - + -
409K ASN* 4.4 10.5 - - + -
410K MET* 3.7 46.7 - - + -
413K CYS* 3.8 25.8 - - - -
477K LEU 2.9 15.5 + - - +
478K TRP* 3.7 26.5 - + - +
480K THR* 1.3 76.7 - - - +
482K ALA* 1.3 64.2 + - - +
483K ASP 3.1 0.3 + - - -
484K LEU* 3.1 18.5 + - + +
485K VAL* 3.1 58.4 + - + +
489K ALA* 4.2 5.6 - - + +
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Residues in contact with ALA 482 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478K TRP* 2.7 21.5 + - + +
479K GLU 3.5 6.1 - - - +
481K TRP* 1.3 74.5 - - - +
483K ASP* 1.3 57.9 + - - +
485K VAL* 3.6 0.9 - - - +
486K HIS* 2.9 33.7 + - - +
487K PRO* 4.6 2.3 - - - +
489K ALA* 3.7 29.3 - - + +
490K GLN* 5.1 2.7 - - - +
493K LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 483 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384K VAL* 3.5 25.3 - - + +
387K LYS* 3.1 18.8 + - - -
479K GLU* 3.1 23.4 + - - +
480K THR* 3.0 15.6 + - - +
482K ALA* 1.3 76.4 - - - +
484K LEU* 1.3 65.5 + - - +
486K HIS* 3.2 18.6 + - - +
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Residues in contact with LEU 484 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277K ALA* 4.8 0.7 - - - +
278K LEU* 5.6 0.2 - - + -
380K LEU* 4.2 14.6 - - + -
383K MET* 4.2 29.6 - - + +
384K VAL* 4.1 18.1 - - + +
387K LYS* 3.6 23.9 + - + +
395K LEU* 3.7 39.8 - - + +
397K LEU* 6.2 0.4 - - + -
406K VAL* 4.3 15.7 - - + -
480K THR 3.1 7.6 + - - +
481K TRP* 3.5 36.1 - - + +
483K ASP* 1.3 82.0 - - - +
485K VAL* 1.3 59.2 + - + +
486K HIS 3.7 0.3 + - - -
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Residues in contact with VAL 485 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K THR* 4.1 17.0 - - + +
277K ALA* 3.7 24.0 - - + -
278K LEU* 4.4 7.4 - - + -
395K LEU* 4.8 1.1 - - + -
481K TRP* 3.1 56.5 - - + +
482K ALA 4.1 0.4 - - - +
484K LEU* 1.3 85.1 - - + +
486K HIS* 1.3 66.4 + - - +
488K ASP* 2.9 26.3 + - + +
489K ALA* 3.8 19.5 - - + +
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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