Contacts of the helix formed by residues 473 - 485 (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 ILE 473 (chain L).
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Specific contacts
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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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Residues in contact with VAL 474 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416L LEU* 3.7 17.7 - - + +
419L PRO* 4.1 11.2 - - + -
420L THR* 4.3 1.1 - - + -
469L PHE* 3.1 49.8 + - + +
470L ILE* 3.9 9.2 - - - -
473L ILE* 1.3 74.8 - - + +
475L HIS* 1.3 63.7 + - - +
477L LEU* 3.3 5.1 + - - +
478L TRP* 2.9 46.4 + - + +
496L LEU* 3.7 21.8 - - + -
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Residues in contact with HIS 475 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470L ILE* 2.6 35.4 + - + +
471L ASP* 4.7 4.9 - - - +
474L VAL* 1.3 74.9 - - - +
476L PRO* 1.3 67.2 - - + +
479L GLU* 2.8 68.7 + - + +
493L LEU* 3.6 13.1 - - + +
496L LEU* 3.7 15.2 - - + +
497L GLU* 3.0 40.7 + - + -
500L ARG* 6.2 2.5 - - - -
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Residues in contact with PRO 476 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377L LEU* 3.8 19.7 - - + +
381L LYS* 5.1 4.6 - - - +
470L ILE 3.3 3.1 - - - +
471L ASP 3.2 27.6 - - - +
472L TYR* 3.6 13.7 - - - +
473L ILE 3.2 12.8 - - - +
475L HIS* 1.3 94.8 - - + +
477L LEU* 1.3 58.9 + - - +
479L GLU* 3.9 11.3 - - - +
480L THR* 2.8 28.1 + - - -
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Residues in contact with LEU 477 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373L HIS* 3.9 9.0 - - + -
377L LEU* 3.9 18.5 - - + +
380L LEU* 4.4 4.4 - - + +
409L ASN* 4.2 15.7 - - - +
412L HIS* 3.4 35.7 - - + +
413L CYS* 3.7 33.9 - - - -
416L LEU* 3.8 22.7 - - + -
473L ILE 3.1 17.9 + - - +
474L VAL* 3.6 3.1 - - - +
476L PRO* 1.3 78.1 - - - +
478L TRP* 1.3 62.2 + - + +
480L THR* 3.1 6.9 + - - -
481L TRP* 2.9 23.9 + - - +
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Residues in contact with TRP 478 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L TRP* 3.8 24.9 - + - -
272L LEU* 4.0 8.7 - - + -
413L CYS* 3.3 40.9 + - + +
416L LEU 3.2 18.9 + - - -
417L SER* 3.9 12.6 - - - -
420L THR* 3.7 15.4 - - + +
474L VAL* 2.9 44.5 + - + +
477L LEU* 1.3 75.8 - - + +
479L GLU* 1.3 56.2 + - - +
481L TRP* 3.6 31.7 - + - +
482L ALA* 2.7 36.5 + - - +
489L ALA* 5.0 3.6 - - + -
492L ILE* 3.8 28.5 - - + -
493L LEU* 4.5 8.2 - - + +
496L LEU* 4.0 13.9 - - + -
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Residues in contact with GLU 479 (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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475L HIS* 2.8 51.3 + - + +
476L PRO* 3.9 10.0 - - - +
478L TRP* 1.3 71.4 - - - +
480L THR* 1.3 63.6 + - - +
482L ALA* 3.3 3.3 + - - +
483L ASP* 3.1 33.9 + - - +
493L LEU* 4.3 18.2 - - + +
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Residues in contact with THR 480 (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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377L LEU* 3.4 12.1 - - + +
380L LEU* 3.4 28.5 - - + -
381L LYS* 3.8 31.6 - - + +
384L VAL* 3.7 17.2 - - + +
476L PRO 2.8 17.9 + - - -
477L LEU 3.1 8.6 + - - -
479L GLU* 1.3 78.8 - - - +
481L TRP* 1.3 64.9 + - - +
483L ASP* 3.0 23.2 + - - +
484L LEU* 3.1 5.7 + - - +
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Residues in contact with TRP 481 (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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272L LEU* 4.0 25.0 - - + +
275L THR* 5.0 2.3 + - + +
278L LEU* 4.2 5.6 - - + -
380L LEU* 4.1 8.9 - - + +
406L VAL* 3.8 31.6 - - + -
409L ASN* 4.4 11.0 - - + -
410L MET* 3.7 46.2 - - + -
413L CYS* 3.8 27.1 - - - -
477L LEU 2.9 13.5 + - - +
478L TRP* 3.2 27.1 + + - +
480L THR* 1.3 75.9 - - - +
482L ALA* 1.3 64.9 + - - +
483L ASP 3.1 0.3 + - - -
484L LEU* 3.1 18.3 + - + +
485L VAL* 3.1 57.9 + - + +
489L ALA* 4.1 5.7 - - + +
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Residues in contact with ALA 482 (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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478L TRP* 2.7 20.8 + - + +
479L GLU 3.5 5.6 - - - +
480L THR 3.2 0.2 - - - -
481L TRP* 1.3 73.4 - - - +
483L ASP* 1.3 57.5 + - - +
485L VAL* 3.6 1.1 - - - +
486L HIS* 2.9 34.5 + - + +
487L PRO* 4.6 2.1 - - - +
489L ALA* 3.7 28.7 - - + +
490L GLN* 5.1 2.9 - - - +
493L LEU* 3.7 26.7 - - + -
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Residues in contact with ASP 483 (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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384L VAL* 3.5 24.1 - - + +
387L LYS* 3.1 18.6 + - - -
479L GLU* 3.1 23.8 + - - +
480L THR* 3.0 15.0 + - + +
482L ALA* 1.3 74.9 - - - +
484L LEU* 1.3 66.8 + - - +
486L HIS* 3.1 18.7 + - - +
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Residues in contact with LEU 484 (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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277L ALA* 4.8 0.7 - - - +
380L LEU* 4.2 14.6 - - + -
383L MET* 4.3 30.1 - - + +
384L VAL* 4.1 19.0 - - + +
387L LYS* 3.6 23.9 + - + +
395L LEU* 3.7 38.7 - - + +
397L LEU* 6.2 0.7 - - + -
406L VAL* 4.3 16.4 - - + -
480L THR 3.1 8.0 + - - +
481L TRP* 3.5 34.3 - - + +
483L ASP* 1.3 81.4 - - - +
485L VAL* 1.3 60.3 + - + +
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Residues in contact with VAL 485 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L THR* 4.1 17.3 - - + +
277L ALA* 3.7 24.5 - - + -
278L LEU* 4.4 7.6 - - + -
395L LEU* 4.7 1.3 - - + -
481L TRP* 3.1 55.6 + - + +
482L ALA 4.1 0.2 - - - +
484L LEU* 1.3 85.0 - - + +
486L HIS* 1.3 67.2 + - - +
488L ASP* 2.9 25.8 + - + +
489L 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