Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324L SER* 3.6 23.7 + - - -
366L LEU* 3.4 28.7 - - - +
367L ALA* 4.7 9.0 - - - +
369L ASP* 3.0 14.2 + - + +
370L MET 3.0 1.4 - - - -
371L SER* 1.3 89.0 + - - +
373L HIS* 1.3 64.1 + - - +
374L MET 3.4 2.0 - - - -
375L ASN* 3.4 16.3 + - + +
376L LEU* 3.0 28.7 + - + +
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Residues in contact with HIS 373 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369L ASP 3.9 1.0 + - - -
370L MET* 3.0 30.9 + - + +
371L SER 3.4 0.4 - - - -
372L LYS* 1.3 77.6 - - - +
374L MET* 1.3 76.4 + - + +
376L LEU* 3.3 4.3 + - - +
377L LEU* 2.9 50.3 + - + +
412L HIS* 2.9 35.1 + + + +
472L TYR 4.5 2.0 + - - -
473L ILE* 3.6 47.0 + - + +
477L LEU* 3.9 23.8 - - + -
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Residues in contact with MET 374 (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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386C THR* 6.3 4.0 - - - -
387C LYS 4.7 15.3 - - - +
388C LYS* 5.6 11.9 - - + -
389C VAL 5.9 1.6 - - - +
370L MET 4.9 0.2 + - - -
371L SER 5.1 3.2 + - - +
372L LYS 3.4 0.6 - - - -
373L HIS* 1.3 97.8 - - + +
375L ASN* 1.3 62.6 + - - +
377L LEU* 3.4 10.8 + - - +
378L ALA* 2.9 29.3 + - - +
472L TYR* 4.7 7.4 - - + +
473L ILE* 4.5 13.5 - - + -
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Residues in contact with ASN 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371L SER 4.6 4.9 + - - -
372L LYS* 3.4 21.1 + - + +
373L HIS 3.3 0.4 - - - -
374L MET* 1.3 75.6 - - - +
376L LEU* 1.3 67.8 + - - +
378L ALA* 3.1 8.2 + - - +
379L ASP* 2.9 32.6 + - - +
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Residues in contact with LEU 376 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367L ALA* 3.6 37.2 - - + +
372L LYS* 3.0 20.9 + - + +
373L HIS* 3.5 4.0 - - - +
375L ASN* 1.3 78.4 - - - +
377L LEU* 1.3 57.6 + - - +
379L ASP* 3.4 7.5 + - - +
380L LEU* 3.0 22.7 + - - +
405L GLN* 5.2 2.9 - - + -
408L GLN* 4.1 25.4 - - + +
409L ASN* 3.2 43.7 + - - +
412L HIS* 4.0 28.9 - - + +
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Residues in contact with LEU 377 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373L HIS* 2.9 42.4 + - + +
374L MET* 3.7 12.1 - - - +
376L LEU* 1.3 73.5 - - - +
378L ALA* 1.3 61.1 + - - +
380L LEU* 3.2 4.5 + - + +
381L LYS* 2.9 46.2 + - + +
409L ASN* 4.5 2.5 - - - -
472L TYR 5.9 0.4 - - - +
476L PRO* 3.8 27.4 - - + +
477L LEU* 3.9 16.8 - - + +
480L THR* 3.4 32.3 - - + +
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Residues in contact with ALA 378 (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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374L MET 2.9 15.4 + - - +
375L ASN* 3.3 12.3 - - - +
377L LEU* 1.3 77.0 - - - +
379L ASP* 1.3 66.8 + - - +
381L LYS* 3.2 11.9 + - - +
382L THR* 3.0 25.6 + - - -
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Residues in contact with ASP 379 (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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375L ASN* 2.9 24.6 + - - +
376L LEU* 3.8 8.1 - - + +
378L ALA* 1.3 77.9 - - - +
380L LEU* 1.3 63.3 + - - +
382L THR* 3.4 10.1 + - - -
383L MET* 3.0 22.9 + - - +
405L GLN* 3.7 35.0 + - + +
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Residues in contact with LEU 380 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L LEU 3.0 15.4 + - - +
377L LEU* 3.5 9.4 - - + +
378L ALA 3.2 0.2 - - - -
379L ASP* 1.3 77.9 - - - +
381L LYS* 1.3 56.5 + - - +
383L MET* 3.1 14.0 + - - +
384L VAL* 2.9 32.2 + - + +
405L GLN* 5.1 2.0 - - + +
406L VAL* 5.4 2.5 - - - -
409L ASN* 3.7 39.4 - - + +
477L LEU* 4.4 12.8 - - + -
480L THR* 3.4 27.8 - - + -
481L TRP* 4.1 17.7 - - + +
484L LEU* 4.2 26.9 - - + -
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Residues in contact with LYS 381 (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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385C GLU* 5.3 13.5 - - - +
386C THR 5.5 3.2 - - - +
377L LEU* 2.9 38.2 + - + +
378L ALA* 3.5 10.8 - - - +
380L LEU* 1.3 74.7 - - - +
382L THR* 1.3 65.0 + - - +
384L VAL* 3.0 15.2 + - - +
385L GLU* 3.2 20.0 + - - +
476L PRO* 5.1 4.8 - - - +
480L THR* 3.8 30.3 - - + +
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Residues in contact with THR 382 (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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378L ALA 3.0 15.0 + - - -
379L ASP* 3.5 13.9 + - - -
381L LYS* 1.3 76.5 - - - +
383L MET* 1.3 58.0 + - - +
385L GLU* 2.9 31.7 + - - +
386L THR* 3.4 13.4 + - + +
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Residues in contact with MET 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L ASP 3.0 13.7 + - - +
380L LEU* 3.4 15.0 - - + +
381L LYS 3.0 0.4 - - - -
382L THR* 1.3 74.5 - - - +
384L VAL* 1.3 55.1 + - - +
385L GLU 2.6 18.6 - - - +
386L THR* 4.0 5.3 + - - +
387L LYS* 3.7 14.6 + - - +
397L LEU* 4.4 8.3 - - + -
402L ASP* 3.2 48.9 - - + +
405L GLN* 3.1 26.7 - - - +
406L VAL* 3.7 26.2 - - - -
484L LEU* 4.3 15.2 - - + +
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Residues in contact with VAL 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380L LEU* 2.9 21.0 + - + +
381L LYS* 3.0 8.0 + - - +
383L MET* 1.3 73.3 - - - +
385L GLU* 1.3 62.5 + - + +
387L LYS* 3.0 29.7 - - - +
480L THR* 3.7 32.1 - - + +
483L ASP* 3.5 34.3 - - + +
484L LEU* 4.1 23.6 - - + +
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Residues in contact with GLU 385 (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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381L LYS* 3.4 14.6 - - - +
382L THR* 2.9 21.5 + - - +
383L MET 2.6 17.2 - - - +
384L VAL* 1.3 72.7 - - + +
386L THR* 1.3 79.6 + - + +
387L LYS 2.9 5.6 - - - -
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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