Contacts of the helix formed by residues 461 - 473 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459L ASN 4.1 4.9 + - - -
460L ALA* 1.3 75.0 + - - +
462L VAL* 1.3 66.0 + - - +
463L GLU* 3.1 8.3 - - - -
464L LYS* 2.8 50.9 + - - +
465L SER* 2.9 18.4 + - - -
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Residues in contact with VAL 462 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430L THR* 3.8 27.1 - - + -
431L ASP* 5.7 4.0 - - - +
434L MET* 3.9 34.8 - - + -
438L PHE* 4.8 4.7 - - + -
460L ALA* 3.6 8.2 - - + +
461L SER* 1.3 73.3 - - - +
463L GLU* 1.3 76.8 + - - +
465L SER* 3.4 8.1 + - - -
466L GLN* 3.1 23.9 + - - +
503L TYR* 4.7 5.2 - - + -
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Residues in contact with GLU 463 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461L SER* 2.9 7.2 + - - -
462L VAL* 1.3 87.5 + - - +
464L LYS* 1.3 63.5 + - - +
466L GLN* 3.2 5.0 + - - +
467L VAL* 3.1 24.6 + - - +
503L TYR* 3.6 22.0 - - + +
506L THR* 3.5 44.2 - - + +
507L ILE* 3.5 21.5 - - + -
508L PRO* 3.9 15.5 - - + +
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Residues in contact with LYS 464 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C SER 6.1 1.1 - - - +
461L SER* 2.8 35.9 + - - +
463L GLU* 1.3 75.6 - - - +
465L SER* 1.3 56.1 + - - +
467L VAL* 3.1 3.0 + - - +
468L GLY* 2.8 28.4 + - - -
507L ILE* 3.7 42.6 - - + -
508L PRO* 5.3 6.5 - - + -
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Residues in contact with SER 465 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C SER 5.6 5.0 - - - +
434L MET* 5.2 1.0 - - - +
454L MET* 3.5 46.4 - - - +
460L ALA* 6.0 0.3 - - - +
461L SER* 2.9 19.6 + - - -
462L VAL* 3.6 12.3 - - - -
464L LYS* 1.3 76.8 - - - +
466L GLN* 1.3 58.1 + - - +
468L GLY* 3.3 1.8 + - - -
469L PHE* 2.7 31.3 + - - +
3012L ZAR 4.1 2.3 - - - +
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Residues in contact with GLN 466 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426L TYR* 2.7 32.8 + - - +
430L THR* 3.4 35.2 - - + +
433L ILE* 4.6 3.8 - - - +
434L MET* 4.8 5.9 - - - -
462L VAL 3.1 15.1 + - - +
463L GLU 3.2 7.2 + - - +
465L SER* 1.3 77.3 - - - +
467L VAL* 1.3 57.7 + - - +
469L PHE* 3.2 7.7 + - - +
470L ILE* 2.9 37.4 + - + +
503L TYR* 3.9 22.2 - - + -
3012L ZAR 3.1 43.1 + - - +
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Residues in contact with VAL 467 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463L GLU 3.1 15.8 + - - +
464L LYS* 3.5 7.0 - - - +
466L GLN* 1.3 76.7 - - - +
468L GLY* 1.3 57.2 + - - +
470L ILE* 3.4 5.6 + - - +
471L ASP* 2.9 39.2 + - - +
500L ARG* 3.3 45.8 - - + +
503L TYR* 4.0 5.4 - - + -
504L GLN* 3.8 38.1 - - - +
507L ILE* 3.8 9.6 - - + -
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Residues in contact with GLY 468 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C SER 4.8 7.6 - - - -
392C SER 5.7 1.6 - - - -
464L LYS 2.8 13.3 + - - -
465L SER 3.7 2.7 - - - -
467L VAL* 1.3 74.9 - - - +
469L PHE* 1.3 57.2 + - - +
471L ASP* 3.1 3.3 + - - -
472L TYR* 2.8 63.8 + - - +
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Residues in contact with PHE 469 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C SER 5.5 0.2 + - - -
370L MET* 5.4 3.1 - - + -
416L LEU* 3.7 25.8 - - + -
419L PRO* 4.1 13.9 - - + -
465L SER 2.7 22.3 + - - +
466L GLN* 3.2 13.2 + - - +
468L GLY* 1.3 70.5 - - - +
470L ILE* 1.3 57.5 + - - +
472L TYR* 5.2 0.4 - - - -
473L ILE* 3.0 51.2 + - + +
474L VAL* 3.1 36.2 + - + -
3012L ZAR 3.6 69.3 - + - -
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Residues in contact with ILE 470 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419L PRO* 4.0 22.0 - - + -
426L TYR* 3.3 27.1 - - + +
466L GLN* 2.9 21.5 + - + +
467L VAL* 3.7 4.5 - - - +
469L PHE* 1.3 79.3 - - + +
471L ASP* 1.3 62.3 + - - +
474L VAL* 3.9 6.5 - - - -
475L HIS* 2.6 46.0 + - + +
476L PRO* 3.3 1.2 - - - +
496L LEU* 3.9 22.4 - - + +
497L GLU* 6.1 0.2 - - - -
499L ASN 4.7 0.4 - - - +
500L ARG* 3.9 45.1 - - + +
503L TYR* 5.5 0.9 - - + -
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Residues in contact with ASP 471 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486C HIS* 4.0 19.9 + - - +
487C PRO* 5.2 2.1 - - - +
467L VAL* 2.9 26.3 + - - +
468L GLY* 3.6 7.1 + - - +
470L ILE* 1.3 78.6 - - - +
472L TYR* 1.3 76.5 + - + +
475L HIS* 4.7 4.4 - - - +
476L PRO* 3.2 20.0 - - - +
500L ARG* 2.7 46.6 + - - -
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Residues in contact with TYR 472 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C LYS* 4.6 13.9 - - + -
389C VAL* 3.6 42.6 - - + +
390C THR 4.5 2.2 - - - -
391C SER* 4.2 11.4 - - - -
392C SER 4.9 0.9 - - - -
393C GLY* 3.2 32.9 + - - -
486C HIS* 4.2 17.2 + - + -
487C PRO* 5.8 0.2 - - - +
373L HIS* 4.5 3.1 + - - -
374L MET* 4.7 8.7 - - + +
468L GLY* 2.8 45.8 + - - +
469L PHE* 5.4 0.2 - - - -
471L ASP* 1.3 88.8 + - + +
473L ILE* 1.3 75.4 + - + +
476L PRO* 3.6 13.3 - - - +
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Residues in contact with ILE 473 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370L MET* 3.8 25.8 - - + -
373L HIS* 3.6 36.4 + - + +
374L MET* 4.5 9.4 - - + -
416L LEU* 3.8 15.0 - - + -
469L PHE* 3.0 34.1 + - + +
472L TYR* 1.3 96.1 - - + +
474L VAL* 1.3 66.9 + - - +
476L PRO* 3.2 4.9 - - - +
477L 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