Contacts of the helix formed by residues 473 - 485 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370F MET* 3.8 25.8 - - + -
373F HIS* 3.6 35.3 + - + +
374F MET* 4.5 9.9 - - + -
416F LEU* 3.9 14.6 - - + -
469F PHE* 3.0 33.1 + - + +
471F ASP 3.7 0.2 - - - -
472F TYR* 1.3 96.2 - - + +
474F VAL* 1.3 65.1 + - - +
475F HIS 3.5 1.6 - - - -
476F PRO* 3.3 4.3 - - - +
477F LEU* 3.1 24.3 + - - +
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Residues in contact with VAL 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416F LEU* 3.7 17.5 - - + +
419F PRO* 4.1 11.0 - - + -
420F THR* 4.4 1.1 - - + -
469F PHE* 3.1 49.0 + - + +
470F ILE* 3.9 9.9 - - - -
473F ILE* 1.3 74.9 - - + +
475F HIS* 1.3 59.5 + - - +
477F LEU* 3.3 5.6 + - - +
478F TRP* 2.9 51.8 + - + -
496F LEU* 3.8 21.1 - - + -
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Residues in contact with HIS 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470F ILE* 2.7 35.8 + - + +
471F ASP* 4.7 4.5 - - - +
474F VAL* 1.3 74.0 - - - +
476F PRO* 1.3 65.8 - - + +
479F GLU* 2.8 67.2 + - + +
493F LEU* 3.6 12.9 - - + +
496F LEU* 3.7 15.4 - - + +
497F GLU* 3.1 40.9 + - + +
500F ARG* 6.2 3.1 - - - -
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Residues in contact with PRO 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F LEU* 3.8 19.4 - - + +
381F LYS* 5.1 5.3 - - - +
470F ILE 3.3 2.2 - - - +
471F ASP 3.2 28.3 - - - +
472F TYR 3.6 13.7 - - - +
473F ILE 3.3 12.3 - - - +
475F HIS* 1.3 93.5 - - + +
477F LEU* 1.3 59.4 + - - +
479F GLU* 3.9 12.3 - - - +
480F THR* 2.8 27.5 + - - -
486L HIS* 6.0 0.7 - - + -
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Residues in contact with LEU 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373F HIS* 3.9 9.0 - - + -
377F LEU* 3.9 19.5 - - + +
380F LEU* 4.5 4.3 - - + -
409F ASN* 4.3 14.4 - - - +
412F HIS* 3.4 35.4 - - + +
413F CYS* 3.7 34.5 - - - -
416F LEU* 3.8 22.7 - - + -
473F ILE 3.1 15.6 + - - +
474F VAL* 3.6 3.4 - - - +
476F PRO* 1.3 77.6 - - - +
478F TRP* 1.3 64.0 + - + +
480F THR* 3.1 6.8 + - - -
481F TRP* 2.9 23.9 + - - +
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Residues in contact with TRP 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F TRP* 3.8 25.4 - + - -
272F LEU* 4.0 9.0 - - + -
413F CYS* 3.4 39.4 + - + +
416F LEU 3.1 18.9 + - - -
417F SER* 3.9 12.8 - - - -
420F THR* 3.6 14.9 - - + +
474F VAL* 2.9 44.5 + - + +
477F LEU* 1.3 77.6 - - + +
479F GLU* 1.3 57.0 + - - +
481F TRP* 3.7 31.7 - + - +
482F ALA* 2.7 36.0 + - + +
489F ALA* 5.0 3.4 - - + -
492F ILE* 3.8 27.8 - - + -
493F LEU* 4.4 8.6 - - + +
496F LEU* 4.0 14.4 - - + -
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Residues in contact with GLU 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475F HIS* 2.8 51.2 + - + +
476F PRO* 3.9 10.2 - - - +
478F TRP* 1.3 73.0 - - - +
480F THR* 1.3 64.4 + - - +
482F ALA* 3.3 7.7 + - - +
483F ASP* 3.1 33.3 + - - +
493F LEU* 4.3 13.5 - - + +
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Residues in contact with THR 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377F LEU* 3.4 12.0 - - + +
380F LEU* 3.4 28.7 - - + -
381F LYS* 3.8 31.4 - - + +
384F VAL* 3.7 16.9 - - + +
476F PRO 2.8 17.9 + - - -
477F LEU 3.1 9.1 + - - -
479F GLU* 1.3 78.7 - - - +
481F TRP* 1.3 63.0 + - - +
483F ASP* 3.1 24.1 + - + +
484F LEU* 3.1 5.5 + - - +
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Residues in contact with TRP 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F LEU* 4.1 24.8 - - + +
275F THR* 5.0 2.3 + - + +
278F LEU* 4.2 5.6 - - + -
380F LEU* 4.1 8.9 - - + +
406F VAL* 3.8 32.3 - - + -
409F ASN* 4.4 9.9 - - + -
410F MET* 3.8 46.0 - - + -
413F CYS* 3.8 26.2 - - - -
477F LEU 2.9 15.1 + - - +
478F TRP* 3.3 26.0 + + - +
480F THR* 1.3 75.8 - - - +
482F ALA* 1.3 65.0 + - - +
484F LEU* 3.2 19.1 + - + +
485F VAL* 3.1 58.4 + - + +
489F ALA* 4.2 6.1 - - + +
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Residues in contact with ALA 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478F TRP 2.7 21.7 + - - +
479F GLU 3.5 6.1 - - - +
481F TRP* 1.3 74.9 - - - +
483F ASP* 1.3 58.6 + - - +
485F VAL* 3.6 0.9 - - - +
486F HIS* 2.9 33.7 + - - +
487F PRO* 4.6 2.3 - - - +
489F ALA* 3.7 28.6 - - + +
490F GLN* 5.2 3.4 - - - +
493F LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384F VAL* 3.5 25.0 - - + +
387F LYS* 3.2 16.4 + - - -
479F GLU* 3.1 24.2 + - - +
480F THR* 3.1 14.8 + - - +
482F ALA* 1.3 76.9 - - - +
484F LEU* 1.3 66.9 + - - +
486F HIS* 3.1 19.4 + - - +
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Residues in contact with LEU 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F ALA* 4.8 0.7 - - - +
380F LEU* 4.2 14.4 - - + -
383F MET* 4.2 30.1 - - + +
384F VAL* 4.1 18.1 - - + +
387F LYS* 3.6 20.1 + - + +
395F LEU* 3.7 43.4 - - + +
397F LEU* 6.2 0.9 - - + -
406F VAL* 4.3 15.9 - - + -
480F THR 3.1 8.0 + - - +
481F TRP* 3.2 35.2 + - + +
483F ASP* 1.3 80.6 - - - +
485F VAL* 1.3 59.9 + - + +
486F HIS 3.4 0.4 + - - -
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Residues in contact with VAL 485 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F THR* 4.1 14.8 - - + +
277F ALA* 3.7 24.9 - - + -
278F LEU* 4.4 7.4 - - + -
395F LEU* 4.8 1.1 - - + -
481F TRP* 3.1 55.4 + - + +
482F ALA 4.1 0.7 - - - +
484F LEU* 1.3 85.8 - - + +
486F HIS* 1.3 66.3 + - - +
488F ASP* 2.9 28.3 + - + +
489F ALA* 3.8 19.3 - - + +
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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