Contacts of the helix formed by residues 472 - 481 (chain B) in PDB entry 3IKM
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 472 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLU* 6.0 7.4 - - + +
406B LEU* 4.4 13.6 - - + +
409B ASN* 3.9 26.0 - - - +
411B ILE* 5.7 1.4 - - - +
469B SER 2.9 10.5 + - - +
470B LYS* 2.7 2.7 + - - +
471B LEU* 1.3 76.4 - - - +
473B ASP* 1.3 115.9 + - - +
474B PHE 2.8 20.3 - - - +
475B LEU* 5.3 0.2 - - - +
476B ILE* 3.3 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LYS* 3.1 13.7 + - + +
472B LYS* 1.3 119.0 + - - +
474B PHE* 1.3 60.5 + - - +
476B ILE* 3.6 7.4 - - - +
477B LYS* 3.0 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B PHE* 5.1 12.8 - + - -
455B LEU* 4.3 16.4 - - + -
466B MET* 4.1 20.2 - - - -
470B LYS 3.1 6.4 + - - +
471B LEU* 3.2 45.2 - - + +
472B LYS 2.8 14.0 - - - +
473B ASP* 1.3 76.5 - - - +
475B LEU* 1.3 92.5 + - + +
476B ILE* 2.6 19.3 + - - +
477B LYS* 4.4 9.6 - - + -
478B TYR* 5.2 10.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LYS* 5.8 3.1 - - + +
383B VAL* 5.2 15.9 - - + -
406B LEU* 4.6 13.2 - - + -
411B ILE* 4.6 19.3 - - + -
439B PHE* 3.7 36.6 - - + -
471B LEU* 3.8 26.5 - - + +
472B LYS 5.3 0.4 - - - +
474B PHE* 1.3 101.3 - - + +
476B ILE* 1.3 57.8 + - + +
477B LYS 2.8 2.7 - - - +
478B TYR* 2.6 10.0 + - - +
479B ILE* 2.2 54.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ASN* 6.3 1.6 - - + -
411B ILE* 4.4 27.1 - - + -
472B LYS* 3.3 25.1 - - - +
473B ASP* 3.6 15.3 - - - +
474B PHE 2.6 19.5 + - - +
475B LEU* 1.3 71.4 - - + +
477B LYS* 1.3 62.9 + - - +
479B ILE* 3.6 13.2 - - + +
480B SER* 2.4 49.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASP* 3.0 37.0 + - - +
474B PHE* 4.4 13.0 - - + -
475B LEU 2.6 5.1 + - - +
476B ILE* 1.3 78.1 - - - +
478B TYR* 1.3 58.3 + - - +
479B ILE 2.8 2.9 - - - -
480B SER* 4.9 1.6 - - - -
481B SER* 2.7 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PRO* 4.3 25.8 - - + +
438B LEU* 5.9 6.5 - - + +
439B PHE* 3.5 39.9 - + + -
457B SER* 4.2 3.3 + - - -
459B ASP* 3.6 20.1 + - - -
474B PHE* 5.2 10.7 - + + -
475B LEU* 2.6 19.0 + - - +
477B LYS* 1.3 77.1 - - - +
479B ILE* 1.3 53.4 + - + +
481B SER* 5.0 1.6 - - - -
482B ALA* 2.7 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B PRO* 5.7 3.6 - - + -
377B CYS* 5.3 12.7 - - + +
382B LYS* 4.9 26.7 - - + -
411B ILE* 5.5 5.2 - - + -
438B LEU* 6.5 0.9 - - + -
439B PHE* 5.4 1.3 - - + -
475B LEU* 2.2 70.4 + - + +
476B ILE* 3.4 15.0 - - + +
477B LYS 2.8 0.4 + - - -
478B TYR* 1.3 76.9 - - + +
480B SER* 1.3 65.6 + - - +
481B SER 3.0 0.9 - - - -
482B ALA* 2.7 30.3 + - - +
483B LYS* 3.5 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ILE* 2.4 41.8 + - - -
477B LYS* 4.4 0.9 - - - -
479B ILE* 1.3 77.2 - - - +
481B SER* 1.3 57.2 + - - -
482B ALA 3.4 0.2 + - - -
483B LYS* 3.5 21.1 + - - +
484B ASN* 2.8 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LYS* 2.7 27.9 + - - -
478B TYR* 4.2 1.6 - - - -
480B SER* 1.3 70.7 - - - +
482B ALA* 1.3 55.2 + - - +
483B LYS 3.1 0.2 - - - -
484B ASN* 2.8 49.6 + - - +
485B VAL* 4.3 3.8 + - - +
----------------------------------------------------------
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