Contacts of the helix formed by residues 372 - 385 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B SER* 3.7 23.5 + - - -
366B LEU* 3.4 27.4 - - - +
367B ALA* 4.7 9.9 - - - +
369B ASP* 3.0 14.9 + - + +
371B SER* 1.3 87.1 + - - +
373B HIS* 1.3 65.1 + - - +
374B MET 3.4 2.2 - - - -
375B ASN* 3.4 15.9 + - + +
376B LEU* 3.0 29.5 + - + +
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Residues in contact with HIS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ASP 3.9 1.2 + - - -
370B MET* 3.1 30.4 + - + +
371B SER 3.4 0.4 - - - -
372B LYS* 1.3 77.4 - - - +
374B MET* 1.3 76.0 + - + +
376B LEU* 3.2 4.7 + - - +
377B LEU* 2.9 47.7 + - + +
412B HIS* 2.9 35.3 + + + +
472B TYR 4.6 1.6 + - - -
473B ILE* 3.7 45.2 + - + +
477B LEU* 3.9 25.4 - - + -
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Residues in contact with MET 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B SER 5.1 3.4 + - - +
372B LYS 3.4 0.4 - - - -
373B HIS* 1.3 98.0 - - + +
375B ASN* 1.3 62.9 + - - +
377B LEU* 3.4 11.7 + - - +
378B ALA* 2.9 28.5 + - - +
472B TYR* 4.7 7.4 - - + +
473B ILE* 4.5 13.5 - - + -
386E THR* 5.3 10.5 - - - -
387E LYS 3.4 30.7 - - - +
388E LYS* 5.0 15.5 - - + -
389E VAL* 5.1 5.4 - - + +
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Residues in contact with ASN 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B SER 4.6 5.1 + - - -
372B LYS* 3.4 21.3 + - + +
373B HIS 3.3 0.4 - - - -
374B MET* 1.3 75.7 - - - +
376B LEU* 1.3 67.7 + - - +
378B ALA* 3.1 8.3 + - - +
379B ASP* 2.9 32.5 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA* 3.6 37.0 - - + +
372B LYS* 3.0 20.8 + - + +
373B HIS* 3.5 4.5 - - - +
375B ASN* 1.3 77.3 - - - +
377B LEU* 1.3 57.4 + - - +
379B ASP* 3.4 7.7 + - - +
380B LEU 3.0 22.0 + - - -
405B GLN* 5.2 3.1 - - + -
408B GLN* 4.1 25.4 - - + +
409B ASN* 3.2 44.0 + - - +
412B HIS* 4.0 28.7 - - + +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B HIS* 2.9 41.3 + - + +
374B MET* 3.7 11.9 - - - +
376B LEU* 1.3 73.8 - - - +
378B ALA* 1.3 62.1 + - - +
380B LEU* 3.2 5.1 + - + +
381B LYS* 2.9 46.9 + - + +
409B ASN* 4.3 2.7 + - - -
476B PRO* 3.8 27.4 - - + +
477B LEU* 3.8 18.6 - - + +
480B THR* 3.4 30.5 - - + +
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Residues in contact with ALA 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B MET 2.9 14.9 + - - +
375B ASN* 3.1 13.0 + - - +
377B LEU* 1.3 77.2 - - - +
379B ASP* 1.3 64.5 + - - +
381B LYS* 3.2 11.6 + - - +
382B THR* 3.0 26.5 + - - -
386E THR* 6.3 3.8 - - + -
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Residues in contact with ASP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B ASN* 2.9 25.5 + - - +
376B LEU* 3.8 7.8 - - + +
378B ALA* 1.3 78.3 - - - +
380B LEU* 1.3 62.7 + - - +
382B THR* 3.4 10.2 + - - -
383B MET* 3.1 22.5 + - - +
405B GLN* 3.7 35.7 + - + +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU 3.0 14.5 + - - +
377B LEU* 3.5 9.6 - - + +
378B ALA 3.2 0.2 - - - -
379B ASP* 1.3 75.1 - - - +
381B LYS* 1.3 59.5 + - - +
383B MET* 3.1 14.3 + - + +
384B VAL* 2.9 32.1 + - + +
405B GLN* 5.1 2.5 - - + +
406B VAL* 5.5 2.5 - - - -
409B ASN* 3.8 38.6 - - + +
477B LEU* 4.5 12.6 - - + -
480B THR* 3.4 28.0 - - + -
481B TRP* 4.2 17.7 - - + +
484B LEU* 4.2 27.6 - - + -
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 2.9 38.2 + - + +
378B ALA* 3.6 10.8 - - - +
380B LEU* 1.3 71.7 - - - +
382B THR* 1.3 67.3 + - - +
384B VAL* 3.0 14.9 + - - +
385B GLU* 3.2 20.1 + - - +
476B PRO* 5.0 4.8 - - - +
480B THR* 3.8 31.2 - - + +
385E GLU* 5.1 20.9 - - + +
386E THR 5.9 0.4 - - - +
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Residues in contact with THR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B ALA 3.0 15.4 + - - -
379B ASP* 3.6 13.7 + - - -
381B LYS* 1.3 77.2 - - - +
383B MET* 1.3 57.4 + - - +
385B GLU* 3.0 31.3 + - - +
386B THR* 3.5 13.4 + - + +
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Residues in contact with MET 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ASP 3.1 12.1 + - - +
380B LEU* 3.4 15.9 - - - +
381B LYS 3.0 0.8 - - - -
382B THR* 1.3 75.5 - - - +
384B VAL* 1.3 55.4 + - - +
385B GLU 2.7 18.8 - - - +
386B THR* 4.0 4.9 + - - +
387B LYS* 3.7 14.8 + - + +
397B LEU* 4.4 7.6 - - + -
402B ASP* 3.2 47.8 - - + +
405B GLN* 3.0 27.6 - - - +
406B VAL* 3.8 25.8 - - - -
484B LEU* 4.3 14.3 - - + +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 2.9 21.1 + - + +
381B LYS* 3.0 8.7 + - - +
383B MET* 1.3 73.3 - - - +
385B GLU* 1.3 62.7 + - + +
387B LYS* 3.0 28.6 - - - +
480B THR* 3.7 31.6 - - + +
483B ASP* 3.5 34.1 - - + +
484B LEU* 4.1 21.5 - - + +
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B LYS* 3.4 13.5 - - - +
382B THR* 3.0 20.4 + - - +
383B MET 2.7 16.5 - - - +
384B VAL* 1.3 73.3 - - + +
386B THR* 1.3 78.7 + - + +
387B LYS 2.9 6.1 - - - -
381J LYS* 4.1 32.8 + - + +
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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
------------------------------------------------------------
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