Contacts of the helix formed by residues 367 - 371 (chain K) 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 ALA 367 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363K ASP 3.5 12.2 + - - +
364K ILE 2.9 13.4 + - - +
366K LEU* 1.3 77.1 - - - +
368K THR* 1.3 58.6 + - - +
369K ASP 3.1 12.7 + - - +
372K LYS* 4.6 8.7 - - - +
376K LEU* 3.6 28.5 - - + +
408K GLN* 3.7 30.3 - - + +
412K HIS* 3.9 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 368 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297K HIS* 4.3 15.2 + - + -
327K GLU* 3.6 7.8 - - - +
364K ILE 3.7 10.1 - - - +
365K VAL* 2.6 30.5 + - - +
367K ALA* 1.3 77.2 - - - +
369K ASP* 1.3 64.4 + - - +
370K MET* 3.2 9.9 + - - +
408K GLN 6.0 0.7 - - - +
411K VAL* 4.3 26.9 - - + +
412K HIS* 4.5 12.5 + - - +
415K ASP* 4.1 21.2 - - + +
2022K MG 3.4 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 369 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306K ASN* 4.0 11.3 + - - -
324K SER* 2.7 31.0 + - - +
327K GLU* 3.6 27.2 - - + +
366K LEU 3.5 15.8 + - - +
367K ALA 3.1 4.1 - - - +
368K THR* 1.3 79.8 + - - +
370K MET* 1.3 67.9 + - - +
371K SER* 3.0 28.9 + - - -
372K LYS* 3.0 24.5 + - + +
373K HIS* 3.9 2.3 + - - -
412K HIS* 5.2 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 370 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327K GLU* 4.7 1.2 + - - -
368K THR 3.2 9.4 + - - +
369K ASP* 1.3 73.6 + - - +
371K SER* 1.3 57.5 + - - +
372K LYS 3.0 4.6 + - - -
373K HIS* 3.1 29.6 + - + +
412K HIS* 3.9 24.0 - - - -
416K LEU* 4.1 18.6 - - + -
469K PHE* 5.4 3.6 - - + -
473K ILE* 3.8 34.8 - - + -
3011K ZAR 3.4 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369K ASP* 3.0 27.2 + - - -
370K MET* 1.3 76.8 - - - +
372K LYS* 1.3 64.0 + - - +
373K HIS 3.4 1.7 + - - -
374K MET* 5.0 3.2 + - - +
375K ASN* 4.6 6.4 + - - -
----------------------------------------------------------
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