Contacts of the helix formed by residues 372 - 385 (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 LYS 372 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324C SER* 3.7 23.4 + - - -
366C LEU* 3.4 28.0 - - - +
367C ALA* 4.7 8.7 - - - +
369C ASP* 3.0 13.9 + - + +
370C MET 3.0 1.2 - - - -
371C SER* 1.3 87.9 + - - +
373C HIS* 1.3 63.7 + - - +
374C MET 3.4 2.5 - - - -
375C ASN* 3.4 16.2 + - + +
376C LEU* 3.0 28.0 + - + +
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Residues in contact with HIS 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C ASP 4.0 1.2 + - - -
370C MET* 3.0 31.7 + - + +
371C SER 3.4 0.8 - - - -
372C LYS* 1.3 76.8 - - - +
374C MET* 1.3 75.8 + - + +
376C LEU* 3.2 4.4 + - - +
377C LEU* 2.8 48.4 + - + +
412C HIS* 2.8 37.0 + + + +
472C TYR 4.6 2.0 + - - -
473C ILE* 3.7 44.4 + - + +
477C LEU* 3.9 26.5 - - + -
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Residues in contact with MET 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C MET 4.9 0.2 + - - -
371C SER 5.1 2.6 + - - +
372C LYS 3.4 0.6 - - - -
373C HIS* 1.3 99.9 - - + +
375C ASN* 1.3 62.4 + - - +
377C LEU* 3.4 10.5 + - - +
378C ALA* 2.9 28.8 + - - +
472C TYR* 4.7 7.6 - - + +
473C ILE* 4.5 13.2 - - + -
386F THR* 5.8 7.4 - - - -
387F LYS 4.5 16.8 - - - +
388F LYS* 5.8 7.9 - - + -
389F VAL 6.1 0.7 - - - +
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Residues in contact with ASN 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C SER 4.6 5.1 + - - -
372C LYS* 3.4 21.2 + - + +
373C HIS 3.3 0.4 - - - -
374C MET* 1.3 76.0 - - - +
376C LEU* 1.3 67.4 + - - +
378C ALA* 3.1 8.3 + - - +
379C ASP* 2.9 34.1 + - - +
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ALA* 3.5 36.3 - - + +
372C LYS* 3.0 20.5 + - + +
373C HIS 3.5 4.7 - - - +
375C ASN* 1.3 77.0 - - - +
377C LEU* 1.3 57.9 + - - +
379C ASP* 3.4 7.4 + - - +
380C LEU 3.0 22.2 + - - -
405C GLN* 5.2 3.1 - - + -
408C GLN* 4.1 25.4 - - + +
409C ASN* 3.2 44.3 + - - +
412C HIS* 4.0 29.6 - - + +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C HIS* 2.8 41.9 + - + +
374C MET* 3.7 11.9 - - - +
376C LEU* 1.3 73.5 - - - +
378C ALA* 1.3 60.6 + - - +
380C LEU* 3.2 6.5 + - + +
381C LYS* 2.9 47.2 + - + +
409C ASN* 4.5 2.7 - - - -
472C TYR 5.9 0.2 - - - +
476C PRO* 3.8 28.5 - - + +
477C LEU* 3.8 17.9 - - + +
480C THR* 3.4 31.6 - - + +
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Residues in contact with ALA 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C MET 2.9 14.4 + - - +
375C ASN* 3.3 12.3 - - - +
377C LEU* 1.3 77.3 - - - +
379C ASP* 1.3 64.5 + - - +
381C LYS* 3.2 11.1 + - - +
382C THR* 3.1 25.7 + - - -
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Residues in contact with ASP 379 (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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375C ASN* 2.9 22.2 + - - +
376C LEU* 3.8 9.9 - - + +
378C ALA* 1.3 78.8 - - - +
380C LEU* 1.3 61.9 + - - +
382C THR* 3.4 9.8 + - - -
383C MET* 3.0 22.5 + - - +
405C GLN* 3.7 35.4 + - + +
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C LEU 3.0 14.7 + - - +
377C LEU* 3.2 10.5 + - + +
379C ASP* 1.3 77.2 - - - +
381C LYS* 1.3 56.3 + - - +
383C MET* 3.1 15.2 + - + +
384C VAL* 2.9 31.8 + - + +
405C GLN* 5.1 2.2 - - + +
406C VAL* 5.4 2.2 - - - -
409C ASN* 3.7 39.0 - - + +
477C LEU* 4.4 13.0 - - + -
480C THR* 3.5 27.6 - - + +
481C TRP* 4.1 17.5 - - + +
484C LEU* 4.2 26.5 - - + -
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Residues in contact with LYS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 2.9 37.3 + - + +
378C ALA* 3.6 10.3 - - - +
380C LEU* 1.3 75.1 - - - +
382C THR* 1.3 66.8 + - - +
384C VAL* 3.0 15.2 + - - +
385C GLU* 3.2 19.7 + - - +
476C PRO* 5.1 4.4 - - - +
480C THR* 3.8 31.2 - - + +
385F GLU* 5.2 16.7 + - - +
386F THR 6.0 0.4 - - - +
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Residues in contact with THR 382 (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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378C ALA 3.1 15.1 + - - -
379C ASP* 3.5 13.6 + - - -
380C LEU 3.3 0.2 - - - -
381C LYS* 1.3 76.2 - - - +
383C MET* 1.3 57.6 + - - +
385C GLU* 3.0 30.9 + - - +
386C THR* 3.4 13.4 + - + +
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Residues in contact with MET 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ASP 3.0 13.8 + - - +
380C LEU* 3.4 15.5 - - - +
381C LYS 3.0 0.2 - - - -
382C THR* 1.3 75.5 - - - +
384C VAL* 1.3 55.8 + - - +
385C GLU 2.6 18.5 - - - +
386C THR* 4.0 4.8 + - - +
387C LYS* 3.7 14.0 - - - +
397C LEU* 4.3 8.7 - - + -
402C ASP* 3.2 49.1 - - + +
405C GLN* 3.1 26.5 - - - +
406C VAL* 3.7 25.4 - - - -
484C LEU* 4.3 14.4 - - + -
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Residues in contact with VAL 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU* 2.9 21.4 + - + +
381C LYS* 3.0 7.8 + - - +
383C MET* 1.3 72.4 - - - +
385C GLU* 1.3 63.3 + - + +
387C LYS* 3.0 29.0 - - - +
480C THR* 3.8 32.1 - - + +
483C ASP* 3.5 34.1 - - + +
484C LEU* 4.1 22.4 - - + +
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Residues in contact with GLU 385 (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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381C LYS* 3.4 13.0 - - - +
382C THR* 3.0 19.6 + - - +
383C MET 2.6 16.9 - - - +
384C VAL* 1.3 73.3 - - + +
386C THR* 1.3 79.6 + - + +
387C LYS 2.9 6.1 - - - -
381L LYS* 5.3 11.7 - - - +
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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