Contacts of the helix formed by residues 473 - 485 (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 ILE 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A MET* 3.8 25.1 - - + -
373A HIS* 3.6 36.2 + - + +
374A MET* 4.5 9.6 - - + -
416A LEU* 3.9 15.5 - - + -
469A PHE* 3.0 33.9 + - + +
471A ASP 3.7 0.2 - - - -
472A TYR* 1.3 98.4 - - + +
474A VAL* 1.3 67.5 + - - +
475A HIS 3.5 0.9 - - - -
476A PRO* 3.3 5.1 - - - +
477A LEU* 3.1 23.6 + - - +
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.7 18.2 - - + +
419A PRO* 4.1 10.5 - - + -
420A THR* 4.4 1.1 - - + -
469A PHE* 3.1 49.1 + - + +
470A ILE* 4.0 9.0 - - - -
473A ILE* 1.3 75.1 - - + +
475A HIS* 1.3 61.0 + - - +
477A LEU* 3.3 5.7 + - - +
478A TRP* 2.9 50.4 + - + -
496A LEU* 3.8 21.8 - - + -
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Residues in contact with HIS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 2.7 35.6 + - + +
471A ASP* 4.7 4.5 - - - +
474A VAL* 1.3 72.8 - - - +
476A PRO* 1.3 66.4 - - + +
479A GLU* 2.8 66.7 + - + +
493A LEU* 3.6 12.2 - - + +
496A LEU* 3.7 16.1 - - + +
497A GLU* 3.1 42.0 + - + +
500A ARG* 6.2 2.9 - - - -
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Residues in contact with PRO 476 (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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377A LEU* 3.8 19.7 - - + +
381A LYS* 5.1 4.4 - - - +
470A ILE 3.4 2.2 - - - +
471A ASP 3.2 28.7 - - - +
472A TYR* 3.6 13.2 - - - +
473A ILE 3.3 11.9 - - - +
475A HIS* 1.3 94.3 - - + +
477A LEU* 1.3 58.5 + - - +
479A GLU* 3.8 12.3 - - - +
480A THR* 2.8 27.5 + - - -
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Residues in contact with LEU 477 (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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373A HIS* 3.9 9.0 - - + -
377A LEU* 3.9 19.4 - - + +
380A LEU* 4.5 5.3 - - + +
409A ASN* 4.3 14.6 - - - +
412A HIS* 3.4 35.4 - - + +
413A CYS* 3.7 32.8 - - - -
416A LEU* 3.8 22.7 - - + -
473A ILE 3.1 15.2 + - - +
474A VAL* 3.6 2.7 - - - +
475A HIS 3.1 0.4 - - - -
476A PRO* 1.3 80.2 - - - +
478A TRP* 1.3 63.3 + - + +
480A THR* 3.2 6.2 + - - -
481A TRP* 2.9 24.3 + - - +
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Residues in contact with TRP 478 (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* 3.8 25.6 - + - -
272A LEU* 4.0 9.0 - - + -
413A CYS* 3.3 40.1 + - + +
416A LEU 3.2 18.2 + - - -
417A SER* 4.0 13.0 - - - -
420A THR* 3.6 15.1 - - + +
474A VAL* 2.9 44.9 + - + +
477A LEU* 1.3 78.5 - - + +
479A GLU* 1.3 56.6 + - - +
481A TRP* 3.7 32.0 - + - +
482A ALA* 2.7 35.3 + - - +
489A ALA* 5.0 3.8 - - + -
492A ILE* 3.8 27.6 - - + -
493A LEU* 4.4 9.0 - - + +
496A LEU* 4.0 12.8 - - + -
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Residues in contact with GLU 479 (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* 2.8 47.4 + - + +
476A PRO* 3.8 10.3 - - - +
478A TRP* 1.3 76.2 - - - +
480A THR* 1.3 64.0 + - - +
482A ALA* 3.3 3.5 + - - +
483A ASP* 3.1 33.2 + - - +
493A LEU* 4.3 17.3 - - + +
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Residues in contact with THR 480 (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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377A LEU* 3.4 13.3 - - + +
380A LEU* 3.4 27.4 - - + -
381A LYS* 3.8 30.2 - - + +
384A VAL* 3.7 16.6 - - + +
476A PRO 2.8 17.4 + - - -
477A LEU 3.2 9.1 + - - -
479A GLU* 1.3 76.6 + - - +
481A TRP* 1.3 64.2 + - - +
483A ASP* 3.1 23.1 + - - +
484A LEU* 3.1 6.4 + - - +
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Residues in contact with TRP 481 (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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272A LEU* 4.1 25.2 - - + +
275A THR* 5.0 2.5 - - + +
278A LEU* 4.2 5.8 - - + -
380A LEU* 4.2 9.2 - - + +
406A VAL* 3.8 32.1 - - + -
409A ASN* 4.4 10.3 - - + -
410A MET* 3.8 46.2 - - + -
413A CYS* 3.9 26.5 - - - -
477A LEU 2.9 15.8 + - - +
478A TRP* 3.7 26.0 - + - +
479A GLU 3.3 0.2 - - - -
480A THR* 1.3 75.8 - - - +
482A ALA* 1.3 63.6 + - - +
484A LEU* 3.1 19.9 + - + +
485A VAL* 3.1 55.9 + - + +
489A ALA* 4.2 6.1 - - + +
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Residues in contact with ALA 482 (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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478A TRP 2.7 17.9 + - - +
479A GLU 3.5 6.3 - - - +
481A TRP* 1.3 76.6 - - - +
483A ASP* 1.3 57.9 + - - +
485A VAL* 3.6 1.1 - - - +
486A HIS* 2.9 33.8 + - + +
487A PRO* 4.6 1.9 - - - +
489A ALA* 3.7 28.2 - - + +
490A GLN* 5.1 3.1 - - - +
493A LEU* 3.8 25.8 - - + -
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Residues in contact with ASP 483 (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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384A VAL* 3.5 24.8 - - + +
387A LYS* 3.1 19.3 + - - -
479A GLU* 3.1 23.2 + - - +
480A THR* 3.1 15.2 + - - +
482A ALA* 1.3 76.5 - - - +
484A LEU* 1.3 65.7 + - - +
486A HIS* 3.2 18.9 + - - +
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Residues in contact with LEU 484 (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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277A ALA* 4.8 0.5 - - - +
278A LEU* 5.7 0.2 - - + -
380A LEU* 4.2 14.6 - - + -
383A MET* 4.3 29.4 - - + +
384A VAL* 4.1 18.7 - - + +
387A LYS* 3.6 18.8 + - + +
395A LEU* 3.8 44.2 - - + +
397A LEU* 6.2 0.4 - - + -
406A VAL* 4.4 16.4 - - + -
480A THR 3.1 8.7 + - - +
481A TRP* 3.1 34.7 + - + +
483A ASP* 1.3 82.3 - - - +
485A VAL* 1.3 61.6 + - + +
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A THR* 4.1 17.7 - - + +
277A ALA* 3.7 23.5 - - + +
278A LEU* 4.4 7.2 - - + -
395A LEU* 4.8 1.3 - - + -
481A TRP* 3.2 54.7 - - + +
482A ALA 4.1 0.4 - - - +
484A LEU* 1.3 86.0 - - + +
486A HIS* 1.3 66.4 + - - +
488A ASP* 2.9 25.7 + - + +
489A ALA* 3.8 19.1 - - + +
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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
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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