Contacts of the helix formed by residues 443 - 450 (chain B) in PDB entry 2PKG
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 LEU 443 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU* 4.4 21.1 - - + -
408B ILE* 6.5 0.7 - - + -
409B VAL* 4.6 2.5 - - + -
427B MET* 4.0 24.0 - - + -
430B LEU* 4.3 0.9 - - + -
431B ALA* 4.9 0.4 - - - -
434B LEU* 3.9 28.9 - - + -
438B PHE* 4.5 9.3 + - + +
439B PHE* 3.0 49.4 + - + +
442B LYS* 1.3 86.5 - - + +
444B ASN* 1.3 69.5 + - - +
445B SER 3.5 0.2 - - - -
446B LEU* 3.2 20.5 + - + +
447B CYS* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B PHE* 3.1 25.6 + - + +
440B ASP* 4.1 20.9 - - - +
441B GLU 4.6 0.6 + - - +
442B LYS 3.8 0.2 - - - -
443B LEU* 1.3 74.1 - - - +
445B SER* 1.3 71.4 + - - +
447B CYS* 2.8 16.2 + - - +
448B MET* 3.0 19.7 + - - +
481B THR* 3.3 30.1 - - + +
482B ILE* 3.4 13.0 - - - +
485B LYS* 2.8 41.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLU 4.4 5.5 + - - -
442B LYS* 4.0 23.8 + - - +
444B ASN* 1.3 83.6 - - - +
446B LEU* 1.3 59.8 + - - +
448B MET* 2.8 23.6 + - - +
449B ALA* 3.0 14.8 + - - +
485B LYS* 4.2 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 6.1 1.6 - - + -
409B VAL* 3.4 45.3 - - + -
412B ALA* 3.9 26.7 - - + -
413B GLU* 3.8 19.7 - - + +
423B ILE* 5.9 1.1 - - + -
427B MET* 5.5 4.9 - - - -
442B LYS 4.0 8.7 - - - +
443B LEU* 3.2 23.3 + - + +
444B ASN 3.2 0.4 - - - -
445B SER* 1.3 81.3 + - - +
447B CYS* 1.3 61.8 + - - +
448B MET 3.3 0.7 + - - -
449B ALA* 3.6 15.6 + - + +
450B TRP* 3.7 21.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B MET* 3.5 31.9 - - - -
439B PHE* 3.4 25.8 - - + -
443B LEU 3.0 17.9 + - - -
444B ASN 2.8 11.9 + - - +
446B LEU* 1.3 72.5 - - - +
448B MET* 1.3 68.5 + - + +
450B TRP* 3.7 25.2 - - - +
451B LEU* 4.6 4.2 + - - +
462B ALA* 5.1 5.5 - - - +
465B ASN* 4.2 7.9 - - - +
466B LEU* 5.0 6.4 - - + +
469B LEU* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ASN* 3.3 33.4 - - - +
445B SER* 2.8 11.3 + - - +
447B CYS* 1.3 78.2 - - + +
449B ALA* 1.3 66.2 + - - +
450B TRP 3.2 1.8 - - - -
451B LEU* 2.9 60.7 + - + +
452B VAL* 5.2 0.5 - - - +
466B LEU* 3.7 24.5 - - + -
482B ILE* 4.6 15.5 - - + +
485B LYS* 4.0 33.4 - - + -
486B VAL* 4.6 6.3 - - + -
489B MET* 4.5 9.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B SER 3.0 10.5 + - - +
446B LEU* 3.8 12.8 - - + +
447B CYS 3.6 0.2 - - - -
448B MET* 1.3 70.9 - - - +
450B TRP* 1.3 55.4 + - + +
451B LEU 2.8 4.3 - - - -
452B VAL* 2.6 39.6 + - - +
453B ASP 3.8 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ALA* 2.8 49.4 + - + +
420B ARG* 4.7 12.1 - - - +
423B ILE* 3.8 14.1 - - + -
424B ILE* 3.5 59.9 - - + +
427B MET* 4.5 13.2 - - + -
446B LEU* 3.7 15.1 + - + +
447B CYS* 3.7 37.2 - - + +
449B ALA* 1.3 81.0 - - + +
451B LEU* 1.3 57.5 + - - +
452B VAL 2.8 6.1 + - - -
453B ASP* 3.0 19.9 + - + +
458B ILE* 4.5 3.1 - - + -
459B ARG* 3.6 14.6 - - - -
462B ALA* 3.8 17.3 - - + -
465B ASN* 4.2 9.0 - - + -
----------------------------------------------------------
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