Contacts of the helix formed by residues 417 - 421 (chain B) 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 SER 417 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.9 17.5 - - - -
264B ASP* 4.5 1.2 + - - -
268B SER* 3.7 3.8 + - - -
413B CYS 3.3 9.6 - - - -
414B ALA* 2.9 24.5 + - - -
415B ASP 3.4 1.4 + - - -
416B LEU* 1.3 75.6 - - - +
418B ASN* 1.3 71.2 + - - +
419B PRO* 3.3 3.4 - - - -
420B THR* 2.7 32.4 + - - -
421B LYS* 3.3 24.7 + - - +
478B TRP* 3.9 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 2.5 41.9 + - - -
261B HIS* 5.3 2.4 + - - -
264B ASP* 3.3 24.9 + - - -
415B ASP 5.2 2.7 + - - -
416B LEU* 5.6 0.4 - - - -
417B SER* 1.3 79.9 + - - +
419B PRO* 1.3 58.9 - - + +
420B THR 3.0 5.5 + - - -
421B LYS* 3.1 18.7 + - - +
426B TYR* 3.4 18.4 - - + +
429B TRP* 3.5 27.2 - - + +
3002B ZAR 3.1 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU 4.0 11.9 - - - +
417B SER 3.6 3.6 - - - -
418B ASN* 1.3 93.2 - - + +
420B THR* 1.3 54.7 + - - +
421B LYS 3.4 0.4 - - - -
426B TYR* 3.5 39.7 - - + +
469B PHE* 4.1 18.8 - - + -
470B ILE* 4.0 5.6 - - + -
474B VAL* 4.1 7.2 - - + -
496B LEU* 3.4 31.0 - - + +
499B ASN* 2.8 25.0 + - - +
3002B ZAR 3.7 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.3 33.3 + - - -
417B SER* 2.7 20.5 + - - +
419B PRO* 1.3 78.7 - - - +
421B LYS* 1.3 61.2 + - - +
422B PRO* 4.8 0.2 - - - +
474B VAL* 4.4 2.7 - - + -
478B TRP* 3.6 37.0 - - + +
492B ILE* 3.4 20.5 - - + +
495B THR* 3.4 20.2 - - - +
496B LEU* 3.9 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TRP* 3.4 58.9 + - + +
200B GLY* 4.6 1.3 - - - -
264B ASP* 3.0 31.1 + - - +
267B GLN* 5.0 1.0 + - - -
268B SER* 3.1 18.5 + - - -
417B SER* 3.3 22.8 + - - +
418B ASN* 3.1 14.8 + - - +
420B THR* 1.3 79.6 - - - +
422B PRO* 1.3 79.5 - - + +
425B LEU* 4.2 16.8 - - + +
426B TYR* 4.2 0.9 - - - +
429B TRP* 5.4 3.3 - - + +
495B THR* 3.6 3.2 - - - +
499B ASN* 2.9 21.1 + - - -
----------------------------------------------------------
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