Contacts of the helix formed by residues 24 - 30 (chain A) in PDB entry 2BU6
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 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 1.3 75.4 - - - +
25A MET* 1.3 64.2 + - - +
26A LYS* 3.0 16.4 + - - +
27A GLN* 2.8 44.2 + - - +
28A PHE* 3.1 14.5 + - - -
356A SER 4.4 5.2 - - - -
357A THR* 4.6 4.8 - - - -
359A SER 3.3 6.3 - - - -
360A VAL* 3.9 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER* 1.3 73.1 - - - +
26A LYS* 1.3 60.0 + - - +
28A PHE* 3.6 11.5 - - - +
29A LEU* 3.2 20.8 + - - +
183A ILE* 3.3 28.2 - - + +
231A VAL* 3.8 33.7 - - + +
232A TYR* 3.7 22.0 - - - -
233A VAL* 3.3 33.0 - - + -
332A PHE* 4.1 19.5 - - + -
356A SER* 3.7 8.7 + - - +
359A SER* 2.6 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER* 3.0 8.5 + - - +
25A MET* 1.3 77.6 - - - +
27A GLN* 1.3 67.2 + - - +
28A PHE 3.1 1.6 - - - -
29A LEU* 2.9 20.8 + - + +
30A ASP* 2.9 37.0 + - - +
356A SER* 3.7 31.1 + - - +
357A THR* 4.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO 4.0 4.5 - - - +
23A LEU* 3.6 20.5 - - + -
24A SER* 2.8 49.7 + - - +
26A LYS* 1.3 72.6 - - - +
28A PHE* 1.3 60.6 + - - +
29A LEU 3.3 0.5 + - - -
30A ASP* 3.3 26.4 + - - +
31A PHE* 4.2 0.2 - - - -
360A VAL* 5.7 0.5 - - - +
1386A TF2 3.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.7 31.9 - - + -
24A SER 3.1 23.9 + - - -
25A MET* 3.6 7.9 - - - +
26A LYS 3.1 0.6 - - - -
27A GLN* 1.3 78.4 - - - +
29A LEU* 1.3 62.5 + - - +
31A PHE* 3.6 15.1 - - - +
159A MET* 3.8 26.9 - - + -
160A LEU* 3.7 17.9 - - + -
163A GLN* 4.1 15.4 + - + +
180A ILE* 3.6 10.9 - - - +
183A ILE* 3.3 23.3 - - + -
332A PHE* 4.3 4.0 - + - -
361A GLU* 3.9 20.6 - - + -
1386A TF2 2.9 43.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A MET 3.2 9.0 + - - +
26A LYS* 2.9 17.4 + - + +
28A PHE* 1.3 79.0 - - - +
30A ASP* 1.3 60.2 + - - +
31A PHE 2.8 13.0 + - - +
180A ILE* 2.9 55.2 - - + +
183A ILE* 3.8 19.7 - - + -
185A PRO* 3.8 24.0 - - + -
231A VAL* 3.7 29.6 - - + -
356A SER* 5.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 2.9 40.9 + - - +
27A GLN* 3.3 11.1 + - - +
29A LEU* 1.3 77.1 - - - +
31A PHE* 1.3 74.5 + - - +
36A ALA* 5.5 0.3 - - - +
1386A TF2 5.2 0.5 - - - -
----------------------------------------------------------
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