Contacts of the helix formed by residues 112 - 133 (chain P) in PDB entry 5KHR
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 112 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P SER* 3.8 29.4 - - - +
113P LYS* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P LYS* 3.8 26.5 - - - +
114P ALA* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P LYS* 3.8 26.7 - - - +
115P TYR* 3.7 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 115 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P ALA* 3.7 30.1 - - - +
116P PHE* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P TYR* 3.8 26.2 - - - +
117P LEU* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P PHE* 3.8 29.2 - - - +
118P TYR* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P LEU* 3.8 26.5 - - - +
119P MET* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P TYR* 3.8 29.2 - - - +
120P TYR* 3.8 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 120 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119P MET* 3.8 28.5 - - - +
121P SER* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 121 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P TYR* 3.8 26.7 - - - +
122P ARG* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P SER* 3.8 28.9 - - - +
123P TYR* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 123 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG* 3.8 26.5 - - - +
124P LEU* 3.8 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P TYR* 3.8 28.3 - - - +
125P SER* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 125 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P LEU* 3.8 28.7 - - - +
126P GLY* 3.8 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P SER* 3.8 25.8 - - - +
127P GLU* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P GLY* 3.8 28.0 - - - +
128P LYS* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127P GLU* 3.8 25.4 - - - +
129P LYS* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P LYS* 3.8 29.2 - - - +
130P LYS* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P LYS* 3.8 24.7 - - - +
131P ASP* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P LYS* 3.8 29.2 - - - +
132P ASP* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131P ASP* 3.8 28.9 - - - +
133P GLU* 3.8 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P ASP* 3.8 29.2 - - - +
134P THR* 3.9 24.9 - - - +
----------------------------------------------------------
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