Contacts of the helix formed by residues 53 - 70 (chain O) in PDB entry 5KHU
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 53 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52O VAL* 3.8 28.7 - - - +
54O LEU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53O SER* 3.8 29.6 - - - +
55O MET* 3.8 25.4 - - - +
57O ARG* 4.2 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 55 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O LEU* 3.8 24.5 - - - +
56O GLU* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55O MET* 3.8 29.2 - - - +
57O ARG* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54O LEU* 4.2 18.6 - - - +
56O GLU* 3.8 28.5 - - - +
58O ARG* 3.8 27.1 - - - +
60O LEU* 4.5 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O ARG* 3.8 26.2 - - - +
59O ARG* 3.8 28.3 - - - +
61O ASN* 4.7 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 59 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O ARG* 3.8 28.7 - - - +
60O LEU* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O ARG* 4.5 14.6 - - - +
59O ARG* 3.8 29.4 - - - +
61O ASN* 3.8 24.9 - - - +
63O LEU* 4.4 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58O ARG* 4.7 16.4 - - - +
60O LEU* 3.8 24.7 - - - +
62O GLN* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61O ASN* 3.8 29.2 - - - +
63O LEU* 3.8 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O LEU* 4.4 16.6 - - - +
62O GLN* 3.8 26.9 - - - +
64O LEU* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O LEU* 3.8 27.1 - - - +
65O LEU* 3.8 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O LEU* 3.8 29.2 - - - +
66O PRO* 3.8 28.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 66 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65O LEU* 3.8 25.1 - - - -
67O LEU* 3.8 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O PRO* 3.8 29.6 - - - -
68O LEU* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67O LEU* 3.8 25.4 - - - +
69O GLN* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O LEU* 3.8 28.7 - - - +
70O GLY* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 70 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O GLN* 3.8 29.2 - - - +
71O PRO* 3.8 29.6 - - - -
----------------------------------------------------------
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