Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324A SER* 3.6 23.8 + - - -
366A LEU* 3.4 28.7 - - + +
367A ALA* 4.6 8.7 - - - +
369A ASP* 3.5 13.1 + - + +
370A MET 3.0 1.2 - - - -
371A SER* 1.3 88.4 + - - +
373A HIS* 1.3 64.9 - - - +
374A MET 3.4 1.8 - - - -
375A ASN* 3.4 16.2 + - + +
376A LEU* 3.0 27.8 + - + +
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Residues in contact with HIS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP 3.9 1.4 + - - -
370A MET* 3.0 31.5 + - + +
371A SER 3.4 0.2 - - - -
372A LYS* 1.3 78.3 - - - +
374A MET* 1.3 75.9 + - + +
376A LEU* 3.2 5.0 + - - +
377A LEU* 2.8 48.2 + - + +
412A HIS* 2.8 34.9 + + + +
472A TYR 4.5 1.6 + - - -
473A ILE* 3.6 45.7 + - + +
477A LEU* 3.9 25.8 - - + -
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Residues in contact with MET 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A SER 5.1 2.6 + - - +
372A LYS 3.4 0.4 - - - -
373A HIS* 1.3 97.6 - - + +
375A ASN* 1.3 63.0 + - - +
377A LEU* 3.4 11.3 + - - +
378A ALA* 2.9 29.5 + - - +
472A TYR* 4.7 7.9 - - + +
473A ILE* 4.5 13.0 - - + -
387I LYS 6.0 2.2 - - - +
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Residues in contact with ASN 375 (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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371A SER 4.5 4.8 + - - -
372A LYS* 3.4 20.6 + - + +
373A HIS 3.3 0.4 - - - -
374A MET* 1.3 77.2 - - - +
376A LEU* 1.3 67.1 + - - +
378A ALA* 3.1 8.1 + - - +
379A ASP* 2.9 32.9 + - - +
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA* 3.6 36.8 - - + +
372A LYS* 3.0 21.7 + - + +
373A HIS* 3.5 4.5 - - - +
375A ASN* 1.3 77.2 - - - +
377A LEU* 1.3 58.8 + - - +
379A ASP* 3.4 7.5 + - - +
380A LEU* 3.0 22.9 + - - +
405A GLN* 5.2 2.7 - - + -
408A GLN* 4.1 24.9 - - + +
409A ASN* 3.2 44.7 + - - +
412A HIS* 4.0 27.6 - - + +
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A HIS* 2.8 41.0 + - + +
374A MET* 3.7 12.3 - - - +
376A LEU* 1.3 73.7 - - - +
378A ALA* 1.3 61.5 + - - +
380A LEU* 3.2 6.9 + - + +
381A LYS* 2.9 47.7 + - - +
409A ASN* 4.5 2.7 - - - -
412A HIS* 6.2 0.2 - - - -
472A TYR 5.9 0.2 - - - +
476A PRO* 3.8 27.1 - - + +
477A LEU* 3.9 16.8 - - + +
480A THR* 3.4 33.0 - - + +
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Residues in contact with ALA 378 (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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374A MET 2.9 15.6 + - - +
375A ASN* 3.1 12.1 + - - +
377A LEU* 1.3 76.3 - - - +
379A ASP* 1.3 65.2 + - - +
381A LYS* 3.2 11.7 + - - +
382A THR* 3.1 25.9 + - - -
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Residues in contact with ASP 379 (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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375A ASN* 2.9 22.7 + - - +
376A LEU* 3.8 10.1 - - + +
378A ALA* 1.3 78.7 - - - +
380A LEU* 1.3 63.0 + - - +
382A THR* 3.4 9.7 + - - -
383A MET* 3.0 22.9 + - - +
405A GLN* 3.7 35.9 + - + +
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Residues in contact with LEU 380 (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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376A LEU 3.0 15.0 + - - +
377A LEU* 3.2 10.5 + - + +
379A ASP* 1.3 78.3 - - - +
381A LYS* 1.3 56.6 + - - +
383A MET* 3.1 14.1 + - - +
384A VAL* 2.9 31.8 + - + +
405A GLN* 5.1 2.5 - - + +
406A VAL* 5.4 2.7 - - - -
409A ASN* 3.7 39.0 - - + +
477A LEU* 4.5 13.9 - - + -
480A THR* 3.4 26.2 - - + -
481A TRP* 4.2 18.4 - - + +
484A LEU* 4.2 26.7 - - + -
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 2.9 37.9 + - + +
378A ALA* 3.6 10.5 - - - +
380A LEU* 1.3 74.0 - - - +
382A THR* 1.3 66.1 + - - +
384A VAL* 2.9 15.1 + - - +
385A GLU* 3.2 20.1 + - + +
476A PRO* 5.1 4.8 - - - +
480A THR* 3.8 30.7 - - + +
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Residues in contact with THR 382 (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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378A ALA 3.1 15.4 + - - -
379A ASP* 3.5 13.6 + - - -
381A LYS* 1.3 76.1 - - - +
383A MET* 1.3 57.3 + - - +
385A GLU* 3.0 31.3 + - - +
386A THR* 3.4 14.2 + - + +
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Residues in contact with MET 383 (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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379A ASP 3.0 12.7 + - - +
380A LEU* 3.4 16.2 - - + +
381A LYS 3.0 0.6 - - - -
382A THR* 1.3 75.5 - - - +
384A VAL* 1.3 54.8 + - - +
385A GLU 2.7 17.9 - - - +
386A THR* 4.0 5.0 + - - +
387A LYS* 3.7 14.6 - - - +
397A LEU* 4.4 8.5 - - + -
402A ASP* 3.2 49.4 - - + +
405A GLN* 3.1 26.0 - - - +
406A VAL* 3.7 26.0 - - - -
484A LEU* 4.3 15.4 - - + +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 2.9 22.3 + - + +
381A LYS* 2.9 8.2 + - - +
383A MET* 1.3 73.2 - - - +
385A GLU* 1.3 63.5 + - + +
387A LYS* 3.0 29.7 - - - +
480A THR* 3.7 31.4 - - + +
483A ASP* 3.5 34.1 - - + +
484A LEU* 4.1 21.8 - - + +
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Residues in contact with GLU 385 (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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381A LYS* 3.2 13.9 + - - +
382A THR* 3.0 19.7 + - - +
383A MET 2.7 15.8 - - - +
384A VAL* 1.3 72.5 - - + +
386A THR* 1.3 80.3 + - + +
387A LYS 2.9 6.1 - - - -
381H LYS* 4.9 25.4 + - + +
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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