Contacts of the helix formed by residues 372 - 385 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324J SER* 3.7 23.3 + - - -
366J LEU* 3.4 28.7 - - - +
367J ALA* 4.6 9.2 - - - +
369J ASP* 3.0 15.3 + - + +
371J SER* 1.3 88.2 + - - +
373J HIS* 1.3 65.5 + - - +
374J MET 3.4 1.8 - - - -
375J ASN* 3.4 15.6 + - + +
376J LEU* 3.0 28.0 + - + +
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Residues in contact with HIS 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369J ASP 3.9 1.4 + - - -
370J MET* 3.1 31.8 + - + +
371J SER 3.4 0.4 - - - -
372J LYS* 1.3 77.6 - - - +
374J MET* 1.3 76.5 + - + +
376J LEU* 3.2 4.6 + - - +
377J LEU* 2.8 48.4 + - + +
412J HIS* 2.8 34.6 + + + +
472J TYR 4.5 2.4 + - - -
473J ILE* 3.6 45.7 + - + +
477J LEU* 3.9 26.0 - - + -
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Residues in contact with MET 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR* 5.3 13.5 - - - -
387B LYS 4.1 20.9 - - - +
388B LYS* 5.6 10.5 - - + -
389B VAL 6.0 1.1 - - - +
371J SER 5.1 2.4 + - - +
372J LYS 3.4 0.6 - - - -
373J HIS* 1.3 98.2 - - + +
375J ASN* 1.3 62.5 + - - +
377J LEU* 3.7 11.0 - - - +
378J ALA* 2.9 29.2 + - - +
472J TYR* 4.7 7.2 - - + +
473J ILE* 4.6 14.4 - - + -
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Residues in contact with ASN 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J SER 4.5 4.9 + - - -
372J LYS* 3.4 21.5 + - + +
373J HIS 3.3 0.4 - - - -
374J MET* 1.3 75.3 - - - +
376J LEU* 1.3 66.4 + - - +
378J ALA* 3.1 7.5 + - - +
379J ASP* 2.9 33.2 + - - +
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Residues in contact with LEU 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J ALA* 3.6 37.0 - - + +
372J LYS* 3.0 20.1 + - + +
373J HIS* 3.5 4.7 - - - +
375J ASN* 1.3 79.4 - - - +
377J LEU* 1.3 56.9 + - - +
379J ASP* 3.4 7.5 + - - +
380J LEU* 3.0 22.5 + - - +
405J GLN* 5.2 3.4 - - + -
408J GLN* 4.0 24.7 - - + +
409J ASN* 3.2 46.3 + - - +
412J HIS* 4.0 27.6 - - + +
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Residues in contact with LEU 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373J HIS* 2.8 43.0 + - + +
374J MET* 3.7 10.8 - - - +
376J LEU* 1.3 74.0 - - - +
378J ALA* 1.3 61.1 + - - +
380J LEU* 3.1 7.7 + - + +
381J LYS* 2.9 46.4 + - - +
409J ASN* 4.5 2.5 - - - -
472J TYR 5.9 0.2 - - - +
476J PRO* 3.7 28.3 - - + +
477J LEU* 3.9 16.1 - - + +
480J THR* 3.4 32.8 - - + +
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Residues in contact with ALA 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR* 6.0 6.1 - - + -
374J MET 2.9 18.2 + - - +
375J ASN* 3.1 9.8 + - - +
377J LEU* 1.3 78.1 - - - +
379J ASP* 1.3 65.0 + - - +
381J LYS* 3.3 11.3 + - - +
382J THR* 3.1 26.6 + - - -
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Residues in contact with ASP 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375J ASN* 2.9 25.4 + - - +
376J LEU* 3.8 8.5 - - + +
378J ALA* 1.3 77.3 - - - +
380J LEU* 1.3 62.7 + - - +
382J THR* 3.4 9.5 + - - -
383J MET* 3.0 22.0 + - - +
405J GLN* 3.6 36.9 + - + +
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Residues in contact with LEU 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376J LEU 3.0 14.3 + - - +
377J LEU* 3.1 10.1 + - + +
379J ASP* 1.3 74.3 - - - +
381J LYS* 1.3 59.5 + - - +
383J MET* 3.1 14.7 + - - +
384J VAL* 2.9 31.9 + - + +
405J GLN* 5.1 2.5 - - - +
406J VAL* 5.4 2.5 - - - -
409J ASN* 3.7 38.8 - - + +
477J LEU* 4.5 12.3 - - + -
480J THR* 3.4 28.9 - - + -
481J TRP* 4.1 18.2 - - + +
484J LEU* 4.2 26.7 - - + -
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Residues in contact with LYS 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B GLU* 4.1 38.4 - - + +
386B THR 5.3 1.4 - - - +
377J LEU* 2.9 38.0 + - + +
378J ALA* 3.6 10.5 - - - +
380J LEU* 1.3 74.2 - - - +
382J THR* 1.3 63.7 + - - +
384J VAL* 3.0 16.0 + - - +
385J GLU* 3.2 20.1 + - + +
476J PRO* 5.1 4.4 - - - +
480J THR* 3.8 30.5 - - + +
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Residues in contact with THR 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378J ALA 3.1 15.2 + - - -
379J ASP* 3.5 13.4 + - - -
381J LYS* 1.3 75.9 - - - +
383J MET* 1.3 57.7 + - - +
385J GLU* 3.0 31.2 + - - +
386J THR* 3.4 14.4 + - + +
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Residues in contact with MET 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379J ASP 3.0 12.9 + - - +
380J LEU* 3.4 15.0 - - - +
381J LYS 3.0 0.2 - - - -
382J THR* 1.3 75.7 - - - +
384J VAL* 1.3 55.7 + - - +
385J GLU 2.6 18.9 - - - +
386J THR* 4.0 4.9 + - - +
387J LYS* 3.7 14.1 - - - +
397J LEU* 4.4 8.7 - - + -
402J ASP* 3.2 48.9 - - + +
405J GLN* 3.1 26.2 - - - +
406J VAL* 3.8 24.9 - - - -
484J LEU* 4.3 15.7 - - + +
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Residues in contact with VAL 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380J LEU* 2.9 22.1 + - + +
381J LYS* 3.0 7.6 + - - +
383J MET* 1.3 72.9 - - - +
385J GLU* 1.3 63.3 + - + +
387J LYS* 3.0 30.0 + - - +
480J THR* 3.7 32.5 - - + +
483J ASP* 3.5 33.7 - - + +
484J LEU* 4.1 22.4 - - + +
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Residues in contact with GLU 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378E ALA* 5.8 3.4 - - + -
381J LYS* 3.4 14.1 - - + +
382J THR* 3.0 19.5 - - - +
383J MET 2.6 17.2 - - - +
384J VAL* 1.3 73.3 - - + +
386J THR* 1.3 78.8 + - + +
387J LYS 2.9 5.8 - - - -
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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
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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