Contacts of the helix formed by residues 441 - 448 (chain A) in PDB entry 2P6U
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 THR 441 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 2.8 29.8 - - + +
161A ILE* 4.9 5.4 - - - +
164A THR* 4.3 8.4 + - - -
191A TRP* 3.4 7.3 - - - +
409A LEU* 3.2 27.5 - - + +
437A PHE* 3.9 2.3 + - - -
438A PHE* 2.7 34.2 + - - -
439A ALA 3.0 1.9 - - - +
440A ASP* 1.3 81.7 - - - +
442A PHE* 1.3 76.1 + - - +
443A PHE* 2.9 9.0 - - + +
444A PHE* 3.2 3.9 + - - +
445A LYS* 3.2 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 3.9 19.7 - - + -
160A GLU* 3.3 11.9 - - + +
184A ASN* 4.7 0.4 - - - -
187A GLU* 4.2 11.0 - - + -
188A ILE* 3.7 40.4 - - + -
191A TRP* 3.3 54.2 - + + +
405A ILE* 4.2 10.1 - - + -
407A SER* 3.5 20.6 - - - -
441A THR* 1.3 74.2 - - - +
443A PHE* 1.3 65.6 + - - +
445A LYS* 4.0 4.7 - - + -
446A GLN* 3.0 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLU* 2.8 5.0 + - - +
407A SER* 3.2 34.1 - - - +
408A LYS* 5.8 0.2 - - - -
409A LEU* 4.0 8.7 - - + -
410A GLY* 3.9 30.5 - - - -
438A PHE 5.4 2.5 - - - -
441A THR* 2.9 13.7 - - + +
442A PHE* 1.3 77.2 - - - +
444A PHE* 1.3 70.0 + - - +
446A GLN* 3.4 0.9 + - - +
447A ASN* 2.5 51.1 + - - +
448A GLU 4.2 0.2 + - - -
449A ILE* 4.1 31.9 - - + -
451A LEU* 3.7 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE 3.7 6.3 - - - +
439A ALA* 2.8 52.3 - - + +
441A THR* 3.2 4.1 + - - +
443A PHE* 1.3 79.8 - - + +
445A LYS* 1.3 67.6 + - - +
446A GLN 2.7 2.5 + - - -
447A ASN 2.8 0.5 + - - -
448A GLU* 2.6 74.5 + - + +
449A ILE 3.6 18.4 - - - -
450A SER* 4.8 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 4.3 12.1 - - + +
190A GLU* 3.4 49.1 + - - +
191A TRP* 3.9 30.3 - - + +
439A ALA 4.5 0.2 + - - -
441A THR 3.2 13.7 + - - +
442A PHE* 3.9 7.4 - - + +
444A PHE* 1.3 82.6 - - - +
446A GLN* 1.3 61.7 + - - +
448A GLU* 4.7 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASN* 3.3 0.4 - - - +
187A GLU* 3.2 34.4 + - - +
404A ARG* 3.9 13.0 + - - +
405A ILE 2.7 24.5 + - - -
406A THR* 3.3 6.7 - - - +
407A SER* 2.6 32.7 + - - -
442A PHE* 3.0 37.5 + - + +
443A PHE* 3.7 4.0 - - - +
444A PHE 2.7 5.7 + - - -
445A LYS* 1.3 77.2 - - - +
447A ASN* 1.3 71.7 + - - +
448A GLU* 3.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A THR* 6.2 1.2 - - - -
407A SER 5.5 2.4 + - - -
443A PHE* 2.5 50.8 - - - +
444A PHE 2.8 7.5 + - - -
446A GLN* 1.3 92.7 + - - +
448A GLU* 1.3 66.9 + - - +
449A ILE* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A PHE* 2.6 56.2 + - + +
445A LYS* 4.7 10.2 - - - +
446A GLN 5.5 1.0 - - - +
447A ASN* 1.3 71.2 - - - +
449A ILE* 1.3 58.9 + - - +
450A SER 4.1 0.7 + - - -
----------------------------------------------------------
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