Contacts of the helix formed by residues 473 - 485 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370C MET* 3.8 26.7 - - + -
373C HIS* 3.7 34.0 + - + +
374C MET* 4.5 10.5 - - + -
416C LEU* 3.8 15.9 - - + -
469C PHE* 3.0 33.5 + - + +
472C TYR* 1.3 98.5 - - + +
474C VAL* 1.3 67.1 + - - +
476C PRO* 3.2 5.8 - - - +
477C LEU* 3.1 23.4 + - - +
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Residues in contact with VAL 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C LEU* 3.7 17.7 - - + +
419C PRO* 4.1 9.9 - - + -
420C THR* 4.4 1.1 - - + -
469C PHE* 3.1 49.5 + - + +
470C ILE* 3.9 9.2 - - - -
473C ILE* 1.3 75.1 - - + +
475C HIS* 1.3 59.7 + - - +
477C LEU* 3.2 5.8 + - - +
478C TRP* 2.9 51.0 + - + +
496C LEU* 3.8 22.2 - - + -
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Residues in contact with HIS 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C ILE* 2.7 34.7 + - + +
471C ASP* 4.7 4.7 - - - +
474C VAL* 1.3 73.3 - - - +
476C PRO* 1.3 65.5 - - + +
479C GLU* 2.8 67.1 + - + +
493C LEU* 3.6 13.7 - - + +
496C LEU* 3.7 15.7 - - + +
497C GLU* 3.1 39.1 + - + +
500C ARG* 6.2 3.1 - - - -
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Residues in contact with PRO 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 3.8 19.9 - - + +
381C LYS* 5.1 4.8 - - - +
470C ILE 3.4 2.7 - - - +
471C ASP 3.2 27.8 - - - +
472C TYR* 3.6 13.9 - - - +
473C ILE 3.2 13.7 - - - +
475C HIS* 1.3 92.2 - - + +
477C LEU* 1.3 57.2 + - - +
479C GLU* 3.9 11.9 - - - +
480C THR* 2.8 28.1 + - - -
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Residues in contact with LEU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C HIS* 3.9 9.2 - - + -
377C LEU* 3.8 19.9 - - + +
380C LEU* 4.4 5.2 - - + -
409C ASN* 4.3 14.1 - - - +
412C HIS* 3.4 35.0 - - + +
413C CYS* 3.7 34.8 - - - -
416C LEU* 3.8 22.4 - - + -
473C ILE 3.1 14.9 + - - +
474C VAL* 3.6 2.9 - - - +
476C PRO* 1.3 78.9 - - - +
478C TRP* 1.3 62.5 + - + +
480C THR* 3.2 6.4 + - - -
481C TRP* 2.9 24.1 + - - +
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Residues in contact with TRP 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C TRP* 3.8 24.7 - + - -
272C LEU* 4.0 9.4 - - + -
413C CYS* 3.3 40.0 + - + +
416C LEU 3.2 18.6 + - - -
417C SER* 3.9 12.8 - - - -
420C THR* 3.7 15.6 - - + +
474C VAL* 2.9 44.4 + - + +
477C LEU* 1.3 77.1 - - + +
479C GLU* 1.3 57.2 + - - +
481C TRP* 3.7 30.9 - + - +
482C ALA* 2.7 35.2 + - - +
489C ALA* 5.0 4.0 - - + -
492C ILE* 3.8 27.6 - - + -
493C LEU* 4.4 9.3 - - + +
496C LEU* 4.0 13.7 - - + -
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Residues in contact with GLU 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475C HIS* 2.8 46.1 + - + +
476C PRO* 3.9 9.7 - - - +
478C TRP* 1.3 76.4 - - - +
480C THR* 1.3 64.5 + - - +
482C ALA* 3.4 2.9 + - - +
483C ASP* 3.1 34.3 + - - +
493C LEU* 4.3 18.4 - - + +
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Residues in contact with THR 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C LEU* 3.4 13.0 - - + +
380C LEU* 3.5 28.5 - - + -
381C LYS* 3.8 30.6 - - + +
384C VAL* 3.8 17.2 - - + +
476C PRO 2.8 17.9 + - - -
477C LEU 3.2 9.1 + - - -
479C GLU* 1.3 77.7 - - - +
481C TRP* 1.3 65.0 + - - +
483C ASP* 3.0 23.2 + - - +
484C LEU* 3.1 6.1 + - - +
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Residues in contact with TRP 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 4.1 25.1 - - + +
275C THR* 4.9 2.7 + - + +
278C LEU* 4.2 5.4 - - + -
380C LEU* 4.1 8.5 - - + +
406C VAL* 3.8 31.9 - - + -
409C ASN* 4.4 9.6 - - + -
410C MET* 3.7 46.0 - - + -
413C CYS* 3.8 25.6 - - - -
477C LEU 2.9 15.6 + - - +
478C TRP* 3.3 26.4 + + - +
480C THR* 1.3 76.4 - - - +
482C ALA* 1.3 64.6 + - - +
483C ASP 3.1 0.3 + - - -
484C LEU* 3.2 17.8 + - + +
485C VAL* 3.1 58.7 + - + +
489C ALA* 4.1 6.1 - - + +
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Residues in contact with ALA 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C TRP 2.7 21.7 + - - +
479C GLU 3.5 6.1 - - - +
481C TRP* 1.3 73.0 - - - +
483C ASP* 1.3 58.1 + - - +
485C VAL* 3.6 0.7 - - - +
486C HIS* 2.9 33.6 + - - +
487C PRO* 4.6 2.4 - - - +
489C ALA* 3.7 28.9 - - + +
490C GLN* 5.1 2.9 - - - +
493C LEU* 3.8 26.0 - - + -
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Residues in contact with ASP 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C VAL* 3.5 24.7 - - + +
387C LYS* 3.1 18.2 + - - -
479C GLU* 3.1 23.2 + - - +
480C THR* 3.0 14.5 + - + +
482C ALA* 1.3 77.0 - - - +
484C LEU* 1.3 66.6 + - - +
486C HIS* 3.1 18.9 + - - +
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Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ALA* 4.8 0.7 - - - +
380C LEU* 4.2 15.0 - - + -
383C MET* 4.3 29.2 - - + +
384C VAL* 4.1 18.5 - - + +
387C LYS* 3.7 19.4 + - + +
395C LEU* 3.7 44.9 - - + +
397C LEU* 6.2 0.4 - - + -
406C VAL* 4.3 16.4 - - + -
480C THR 3.1 8.0 + - - +
481C TRP* 3.5 35.4 - - + +
483C ASP* 1.3 81.1 - - - +
485C VAL* 1.3 59.5 + - + +
486C HIS 3.7 0.2 + - - -
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Residues in contact with VAL 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C THR* 4.2 14.6 - - + +
277C ALA* 3.7 24.2 - - + -
278C LEU* 4.4 6.7 - - + -
395C LEU* 4.8 1.3 - - + -
481C TRP* 3.2 53.8 - - + +
482C ALA 4.1 0.7 - - - +
484C LEU* 1.3 85.6 - - + +
486C HIS* 1.3 65.5 + - - +
488C ASP* 2.8 29.0 + - + +
489C ALA* 3.8 20.6 - - + +
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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