Contacts of the helix formed by residues 461 - 473 (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 SER 461 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459F ASN 4.1 4.5 + - - -
460F ALA* 1.3 74.8 + - - +
462F VAL* 1.3 66.6 + - - +
463F GLU* 3.1 7.6 - - - -
464F LYS* 2.8 51.4 + - - +
465F SER* 2.9 18.2 + - - -
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Residues in contact with VAL 462 (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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430F THR* 3.8 26.9 - - + -
431F ASP* 5.7 3.8 - - - +
434F MET* 3.9 34.3 - - + -
438F PHE* 4.8 4.7 - - + -
460F ALA* 3.6 8.2 - - + +
461F SER* 1.3 73.5 - - - +
463F GLU* 1.3 76.6 + - - +
465F SER* 3.5 8.3 + - - -
466F GLN* 3.1 23.7 + - - +
503F TYR* 4.7 6.1 - - + -
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Residues in contact with GLU 463 (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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461F SER* 2.9 5.4 + - - -
462F VAL* 1.3 86.2 + - - +
464F LYS* 1.3 67.7 + - - +
466F GLN* 3.2 4.7 + - - +
467F VAL* 3.1 24.8 + - - +
503F TYR* 3.6 23.0 - - + +
506F THR* 3.5 44.7 - - + +
507F ILE* 3.5 22.4 - - + -
508F PRO* 3.9 15.5 - - + +
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Residues in contact with LYS 464 (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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461F SER* 2.8 35.2 + - - +
463F GLU* 1.3 74.8 - - + +
465F SER* 1.3 58.6 + - - +
467F VAL* 3.1 4.5 + - - +
468F GLY* 2.8 28.1 + - - -
507F ILE* 3.7 41.3 - - + -
508F PRO* 5.3 6.9 + - + -
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Residues in contact with SER 465 (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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434F MET* 5.2 1.4 - - - +
454F MET* 3.5 46.8 - - - +
460F ALA* 5.9 0.2 - - - +
461F SER* 2.9 20.4 + - - -
462F VAL* 3.6 11.6 + - - -
464F LYS* 1.3 77.1 - - - +
466F GLN* 1.3 52.0 + - - +
468F GLY* 3.3 1.4 + - - +
469F PHE* 2.7 36.7 + - - +
3006F ZAR 4.1 3.5 - - - +
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Residues in contact with GLN 466 (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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426F TYR* 2.6 31.7 + - - +
430F THR* 3.4 32.0 - - + +
433F ILE* 4.6 4.0 - - - +
434F MET* 4.8 5.1 - - - -
462F VAL 3.1 15.7 + - - +
463F GLU 3.2 7.2 + - - +
465F SER* 1.3 74.0 - - - +
467F VAL* 1.3 62.1 + - - +
469F PHE* 3.3 7.0 + - - +
470F ILE* 2.9 37.1 + - - +
503F TYR* 3.9 22.7 - - + -
3006F ZAR 3.0 47.8 + - - +
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Residues in contact with VAL 467 (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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463F GLU 3.1 15.0 + - - +
464F LYS* 3.1 7.5 + - - +
466F GLN* 1.3 74.8 - - - +
468F GLY* 1.3 58.1 + - - +
470F ILE* 3.5 5.1 + - - +
471F ASP* 2.9 39.0 + - - +
500F ARG* 3.2 44.2 - - + +
503F TYR* 4.0 5.6 - - + -
504F GLN* 3.8 32.3 - - - +
507F ILE* 3.9 14.4 - - + -
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Residues in contact with GLY 468 (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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464F LYS 2.8 13.9 + - - -
465F SER* 3.7 2.9 - - - -
467F VAL* 1.3 76.7 - - - +
469F PHE* 1.3 64.6 + - - +
471F ASP* 3.1 2.9 + - - -
472F TYR* 2.8 54.1 + - - -
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Residues in contact with PHE 469 (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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370F MET* 5.4 3.4 - - + -
416F LEU* 3.6 30.1 - - + -
419F PRO* 4.1 14.4 - - + -
465F SER 2.7 22.1 + - - +
466F GLN* 3.3 11.6 + - - +
468F GLY* 1.3 71.2 - - - +
470F ILE* 1.3 58.1 + - - +
473F ILE* 3.0 50.5 + - + +
474F VAL* 3.1 31.0 + - + -
3006F ZAR 3.6 70.4 - + - -
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Residues in contact with ILE 470 (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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419F PRO* 4.0 22.0 - - + -
426F TYR* 3.4 27.6 - - + +
466F GLN* 2.9 21.7 + - + +
467F VAL* 3.8 4.3 - - - +
469F PHE* 1.3 77.8 - - + +
471F ASP* 1.3 62.6 + - - +
474F VAL* 3.9 6.1 - - + -
475F HIS* 2.7 45.7 + - + +
476F PRO* 3.3 1.2 - - - +
496F LEU* 3.8 23.8 - - + -
499F ASN 4.7 0.4 - - - +
500F ARG* 3.9 44.2 - - + +
503F TYR* 5.6 1.1 - - + -
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Residues in contact with ASP 471 (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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467F VAL* 2.9 26.9 + - - +
468F GLY* 3.7 5.4 - - - +
470F ILE* 1.3 78.5 - - - +
472F TYR* 1.3 67.3 + - + +
475F HIS* 4.7 4.4 - - - +
476F PRO* 3.2 19.7 - - - +
500F ARG* 2.7 46.6 + - - -
486L HIS* 3.7 25.9 - - + -
487L PRO* 4.7 9.7 - - + +
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Residues in contact with TYR 472 (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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373F HIS* 4.5 3.3 + - - -
374F MET* 4.7 7.6 - - - +
468F GLY* 2.8 43.2 + - - +
469F PHE* 5.1 0.4 - - - -
471F ASP* 1.3 76.5 + - + +
473F ILE* 1.3 76.9 + - + +
476F PRO* 3.6 12.9 - - - +
393L GLY* 6.0 8.7 - - - -
486L HIS* 3.0 26.7 - + + -
487L PRO* 2.4 46.0 - - + +
488L ASP* 4.6 4.5 + - - -
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Residues in contact with ILE 473 (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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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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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