Contacts of the helix formed by residues 372 - 385 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H SER* 3.7 23.1 + - - -
366H LEU* 3.4 27.6 - - - +
367H ALA* 4.6 9.6 - - - +
369H ASP* 3.0 13.9 + - + +
370H MET 3.0 1.0 - - - -
371H SER* 1.3 88.2 + - - +
373H HIS* 1.3 64.2 + - - +
374H MET 3.4 2.0 - - - -
375H ASN* 3.4 15.2 + - + +
376H LEU* 3.0 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 373 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369H ASP 3.9 1.2 + - - -
370H MET* 3.1 31.7 + - + +
371H SER 3.4 0.4 - - - -
372H LYS* 1.3 76.5 - - - +
374H MET* 1.3 76.8 + - + +
376H LEU* 3.2 4.7 + - - +
377H LEU* 2.9 47.7 + - + +
412H HIS* 2.8 36.1 + + + +
472H TYR 4.6 2.0 + - - -
473H ILE* 3.6 43.7 + - + +
477H LEU* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 374 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 5.0 12.8 - - - -
387A LYS 3.5 30.7 - - - +
388A LYS* 5.2 11.9 - - + -
389A VAL* 5.5 2.5 - - + +
371H SER 5.1 3.4 + - - +
372H LYS 3.4 0.6 - - - -
373H HIS* 1.3 97.8 - - + +
375H ASN* 1.3 63.5 + - - +
377H LEU* 3.7 11.1 - - - +
378H ALA* 2.9 28.6 + - - +
472H TYR* 4.7 7.2 - - + +
473H ILE* 4.5 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H SER 4.5 4.9 + - - -
372H LYS* 3.4 20.8 + - + +
373H HIS 3.3 0.6 - - - -
374H MET* 1.3 76.4 - - - +
376H LEU* 1.3 65.9 + - - +
378H ALA* 3.1 7.6 + - - +
379H ASP* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367H ALA* 3.6 37.2 - - + +
372H LYS* 3.0 20.0 + - + +
373H HIS* 3.5 4.5 - - - +
375H ASN* 1.3 77.0 - - - +
377H LEU* 1.3 59.0 + - - +
379H ASP* 3.4 7.0 + - - +
380H LEU 3.0 22.2 + - - -
405H GLN* 5.2 3.4 - - + -
408H GLN* 4.1 26.0 - - + +
409H ASN* 3.2 45.5 + - - +
412H HIS* 4.0 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373H HIS* 2.9 42.6 + - + +
374H MET* 3.7 12.6 - - - +
376H LEU* 1.3 73.9 - - - +
378H ALA* 1.3 60.6 + - - +
380H LEU* 3.1 6.6 + - + +
381H LYS* 2.9 48.0 + - + +
409H ASN* 4.3 2.9 + - - -
476H PRO* 3.8 27.6 - - + +
477H LEU* 3.9 16.4 - - + +
480H THR* 3.4 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 6.1 5.4 - - + -
374H MET 2.9 16.5 + - - +
375H ASN* 3.3 12.3 - - - +
377H LEU* 1.3 77.4 - - - +
379H ASP* 1.3 65.0 + - - +
381H LYS* 3.3 12.1 + - - +
382H THR* 3.0 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 379 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375H ASN* 2.9 25.9 + - - +
376H LEU* 3.8 7.8 - - + +
378H ALA* 1.3 78.3 - - - +
380H LEU* 1.3 62.0 + - - +
382H THR* 3.4 10.2 + - - -
383H MET* 3.1 22.3 + - - +
405H GLN* 3.7 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376H LEU 3.0 14.5 + - - +
377H LEU* 3.1 10.5 + - + +
379H ASP* 1.3 75.1 - - - +
381H LYS* 1.3 59.7 + - - +
383H MET* 3.1 14.5 + - - +
384H VAL* 2.9 31.9 + - + +
405H GLN* 5.1 2.2 - - + +
406H VAL* 5.4 2.2 - - - -
409H ASN* 3.7 40.1 - - + +
477H LEU* 4.4 12.8 - - + -
480H THR* 3.4 27.8 - - + -
481H TRP* 4.1 17.5 - - + +
484H LEU* 4.2 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 381 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 4.9 27.5 + - + +
377H LEU* 2.9 38.9 + - + +
378H ALA* 3.6 11.2 - - - +
380H LEU* 1.3 76.8 - - - +
382H THR* 1.3 62.1 + - - +
384H VAL* 2.9 15.9 + - - +
385H GLU* 3.2 19.9 + - - +
476H PRO* 5.1 5.0 - - - +
480H THR* 3.8 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 382 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378H ALA 3.0 15.1 + - - -
379H ASP* 3.6 14.1 + - - -
381H LYS* 1.3 77.3 - - - +
383H MET* 1.3 57.6 + - - +
385H GLU* 3.0 31.6 + - - +
386H THR* 3.4 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 383 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379H ASP 3.1 13.0 + - - +
380H LEU* 3.4 15.3 - - + +
381H LYS 3.0 0.6 - - - -
382H THR* 1.3 75.5 - - - +
384H VAL* 1.3 55.6 + - - +
385H GLU 2.6 19.4 - - - +
386H THR* 4.0 5.0 + - - +
387H LYS* 3.7 14.4 - - + +
397H LEU* 4.4 9.2 - - + -
402H ASP* 3.1 48.9 - - + +
405H GLN* 3.1 26.2 - - - +
406H VAL* 3.7 26.0 - - - -
484H LEU* 4.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380H LEU* 2.9 22.1 + - + +
381H LYS* 2.9 8.4 + - - +
383H MET* 1.3 73.1 - - - +
385H GLU* 1.3 62.5 + - + +
387H LYS* 3.0 29.8 - - - +
480H THR* 3.8 31.6 - - + +
483H ASP* 3.5 34.1 - - + +
484H LEU* 4.1 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 385 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H LYS* 3.2 13.9 + - - +
382H THR* 3.0 20.2 + - - +
383H MET 2.6 16.7 - - - +
384H VAL* 1.3 73.1 - - + +
386H THR* 1.3 80.5 + - + +
387H LYS 2.9 5.8 - - - -
381I LYS* 5.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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