Contacts of the helix formed by residues 59 - 64 (chain F) in PDB entry 3NBN
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 59 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D PHE* 3.3 68.3 - - + -
97D GLU* 4.7 7.4 - - - +
98D MET* 4.6 10.8 - - + -
130D LYS* 3.9 24.2 - - + -
132D PHE* 4.0 9.6 - - + -
55F HIS* 3.2 41.0 + - + +
56F THR* 4.5 2.7 - - - -
57F PHE 2.6 5.5 + - - -
58F ALA* 1.3 76.4 - - - +
60F HIS* 1.3 60.9 + - - +
61F GLN 3.3 1.3 - - - -
62F ARG* 3.4 26.0 - - - +
63F CYS 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D PHE* 3.7 28.4 - + + -
134D GLY* 2.6 31.3 + - - -
135D ASN 5.3 0.4 - - - -
136D SER* 3.6 20.8 + - - +
56F THR 3.3 16.1 + - - +
57F PHE* 2.6 20.9 + - - +
59F LEU* 1.3 69.2 - - - +
61F GLN* 1.3 70.1 + - - -
62F ARG 2.7 17.4 + - - -
63F CYS* 2.9 14.9 + - + +
64F ILE* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F PHE* 3.3 46.1 + - - +
58F ALA* 4.6 11.5 - - - +
59F LEU 3.3 1.3 - - - -
60F HIS* 1.3 99.9 + - - +
62F ARG* 1.3 68.0 + - - +
64F ILE* 4.4 4.3 - - + +
65F GLN* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D PHE* 3.4 27.9 - - + -
97D GLU* 4.4 13.3 - - - +
98D MET 3.1 32.7 + - - +
99D GLN* 4.1 0.6 - - - +
100D GLN* 2.9 30.1 + - - +
58F ALA 4.6 11.9 + - - +
59F LEU* 3.4 27.0 - - - +
60F HIS 2.7 1.8 + - - -
61F GLN* 1.3 79.3 - - - +
63F CYS* 1.3 65.7 + - - +
64F ILE 3.1 1.5 + - - -
65F GLN* 2.8 10.9 + - - -
66F ALA* 3.5 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLN* 5.4 2.0 - - - -
86D CYS* 2.0 48.1 - - - -
88D PHE* 4.0 2.2 - - + -
100D GLN* 3.4 15.7 + - - +
132D PHE* 3.8 23.6 - - + -
134D GLY* 4.8 7.9 - - - -
59F LEU 3.5 3.7 + - - +
60F HIS* 2.9 16.4 + - + +
62F ARG* 1.3 80.8 - - - +
64F ILE* 1.3 61.9 + - - +
66F ALA 4.4 0.4 - - - -
67F LYS* 3.7 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D GLN* 5.2 17.5 - - + +
134D GLY* 5.0 5.8 - - - +
60F HIS* 3.0 37.3 + - + +
61F GLN* 4.4 5.6 - - + +
63F CYS* 1.3 87.3 - - - +
65F GLN* 1.3 83.1 + - + +
66F ALA 3.5 0.9 - - - -
67F LYS* 3.6 15.5 - - + +
68F ALA* 3.3 19.9 + - - +
----------------------------------------------------------
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