Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324F SER* 3.7 23.3 + - - -
366F LEU* 3.4 27.1 - - - +
367F ALA* 4.7 9.9 - - - +
369F ASP* 3.5 13.8 + - + +
370F MET 3.0 1.0 - - - -
371F SER* 1.3 87.6 + - - +
373F HIS* 1.3 64.2 + - - +
374F MET 3.4 2.2 - - - -
375F ASN* 3.4 16.4 + - + +
376F LEU* 3.0 27.9 + - + +
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Residues in contact with HIS 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369F ASP 4.0 0.8 + - - -
370F MET* 3.1 31.5 + - + +
371F SER 3.4 0.6 - - - -
372F LYS* 1.3 77.9 - - - +
374F MET* 1.3 76.5 + - + +
376F LEU* 3.2 4.8 + - - +
377F LEU* 2.9 48.2 + - + +
412F HIS* 2.8 35.9 + + + +
472F TYR 4.5 1.8 + - - -
473F ILE* 3.6 43.1 + - + +
477F LEU* 3.9 26.0 - - + -
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Residues in contact with MET 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F SER 5.0 2.6 + - - +
372F LYS 3.4 0.6 - - - -
373F HIS* 1.3 98.8 - - + +
375F ASN* 1.3 62.6 + - - +
377F LEU* 3.4 10.9 + - - +
378F ALA* 2.9 28.8 + - - +
472F TYR* 4.7 7.4 - - + +
473F ILE* 4.5 13.0 - - + -
387L LYS* 4.7 15.7 - - + +
389L VAL* 5.4 16.8 - - + +
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Residues in contact with ASN 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371F SER 4.6 4.8 + - - -
372F LYS* 3.4 21.1 + - + +
373F HIS 3.3 0.4 - - - -
374F MET* 1.3 76.3 - - - +
376F LEU* 1.3 68.0 + - - +
378F ALA* 3.1 8.3 + - - +
379F ASP* 2.9 31.9 + - - +
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Residues in contact with LEU 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367F ALA* 3.6 36.8 - - + +
372F LYS* 3.0 20.8 + - + +
373F HIS* 3.5 4.9 - - - +
375F ASN* 1.3 78.6 - - - +
377F LEU* 1.3 56.8 + - - +
379F ASP* 3.3 7.2 + - - +
380F LEU* 3.0 21.7 + - - +
405F GLN* 5.2 3.1 - - + -
408F GLN* 4.1 25.1 - - + +
409F ASN* 3.2 44.1 + - - +
412F HIS* 4.0 28.5 - - + +
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Residues in contact with LEU 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373F HIS* 2.9 42.2 + - + +
374F MET* 3.7 12.6 - - - +
376F LEU* 1.3 73.3 - - - +
378F ALA* 1.3 60.9 + - - +
380F LEU* 3.2 6.6 + - + +
381F LYS* 2.9 45.4 + - - +
409F ASN* 4.5 2.5 - - - -
412F HIS* 6.2 0.2 - - - -
472F TYR 5.9 0.2 - - - +
476F PRO* 3.8 26.7 - - + +
477F LEU* 3.9 16.1 - - + +
480F THR* 3.4 33.7 - - + +
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Residues in contact with ALA 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374F MET 2.9 18.2 + - - +
375F ASN* 3.3 9.2 - - - +
377F LEU* 1.3 77.5 - - - +
379F ASP* 1.3 64.9 + - - +
381F LYS* 3.2 11.4 + - - +
382F THR* 3.1 26.2 + - - -
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Residues in contact with ASP 379 (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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375F ASN* 2.9 23.1 + - - +
376F LEU* 3.8 10.1 - - + +
378F ALA* 1.3 79.0 - - - +
380F LEU* 1.3 61.3 + - - +
382F THR* 3.4 9.5 + - - -
383F MET* 3.1 22.5 + - - +
405F GLN* 3.7 35.3 + - + +
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Residues in contact with LEU 380 (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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376F LEU 3.0 15.2 + - - +
377F LEU* 3.4 10.1 - - + +
378F ALA 3.1 0.2 - - - -
379F ASP* 1.3 77.7 - - - +
381F LYS* 1.3 57.2 + - - +
383F MET* 3.1 13.6 + - - +
384F VAL* 2.9 32.6 + - + +
405F GLN* 5.1 2.0 - - - +
406F VAL* 5.4 2.7 - - - -
409F ASN* 3.7 39.0 - - + +
477F LEU* 4.5 12.8 - - + -
480F THR* 3.4 28.7 - - + -
481F TRP* 4.1 17.9 - - + +
484F LEU* 4.2 26.9 - - + -
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Residues in contact with LYS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F LEU* 2.9 36.2 + - + +
378F ALA* 3.2 10.5 + - - +
380F LEU* 1.3 74.5 - - - +
382F THR* 1.3 66.4 + - - +
384F VAL* 3.0 16.3 + - - +
385F GLU* 3.2 19.5 + - - +
476F PRO* 5.1 4.3 - - - +
480F THR* 3.8 30.3 - - + +
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Residues in contact with THR 382 (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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378F ALA 3.1 15.9 + - - -
379F ASP* 3.6 13.3 + - - -
381F LYS* 1.3 76.6 - - - +
383F MET* 1.3 56.9 + - - +
385F GLU* 3.0 30.3 + - - +
386F THR* 3.4 13.9 + - + +
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Residues in contact with MET 383 (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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379F ASP 3.1 13.2 + - - +
380F LEU* 3.4 15.0 - - - +
381F LYS 3.0 0.8 - - - -
382F THR* 1.3 74.9 - - - +
384F VAL* 1.3 56.3 + - - +
385F GLU 2.6 17.9 - - - +
386F THR* 4.0 5.2 + - - +
387F LYS* 3.7 14.5 - - + +
397F LEU* 4.4 8.5 - - + -
402F ASP* 3.2 48.2 - - + +
405F GLN* 3.1 25.8 - - - +
406F VAL* 3.7 25.8 - - - -
484F LEU* 4.2 15.6 - - + +
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Residues in contact with VAL 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F LEU* 2.9 21.5 + - + +
381F LYS* 3.0 8.2 + - - +
383F MET* 1.3 73.5 - - - +
385F GLU* 1.3 62.9 - - + +
387F LYS* 3.0 29.7 - - - +
480F THR* 3.7 31.6 - - + +
483F ASP* 3.5 34.5 - - + +
484F LEU* 4.1 21.5 - - + +
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Residues in contact with GLU 385 (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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381C LYS* 5.2 14.8 + - - +
381F LYS* 3.2 15.0 + - - +
382F THR* 3.0 20.3 - - - +
383F MET 2.6 16.3 - - - +
384F VAL* 1.3 72.9 - - + +
386F THR* 1.3 81.0 + - + +
387F LYS 2.9 6.1 - - - -
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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