Contacts of the helix formed by residues 53 - 63 (chain R) in PDB entry 1KYO
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 ASN 53 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50R ALA 3.4 13.5 - - - +
51R GLU 2.9 4.8 + - - +
52R GLU* 1.3 75.0 - - - +
54R PRO* 1.3 74.3 - - + +
55R ILE* 3.4 30.7 - - - +
56R MET* 3.3 23.7 - - - +
57R GLN* 3.2 22.6 + - - +
9S TYR* 3.6 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 54 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R ASN* 1.3 86.0 - - + +
55R ILE* 1.3 60.3 + - + +
57R GLN* 3.0 8.8 + - + +
58R THR* 2.7 41.6 + - - +
9S TYR* 3.9 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R ASN* 3.4 14.2 - - - +
54R PRO* 1.3 81.2 - - + +
56R MET* 1.3 59.4 + - + +
58R THR* 3.3 7.1 + - - -
59R ALA* 3.0 26.2 + - - +
107R ILE* 4.1 13.9 - - + -
110R ALA* 3.7 34.9 - - + +
111R GLU* 3.8 31.2 - - + +
114R ALA* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 56 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R PHE* 5.6 2.5 - - + -
46R ASP 5.2 0.4 - - - +
49R ILE* 3.8 36.3 - - + +
50R ALA 3.4 13.2 - - - +
51R GLU* 3.7 30.3 - - + -
53R ASN* 3.3 21.6 + - - +
54R PRO 3.3 0.4 - - - -
55R ILE* 1.3 78.2 - - + +
57R GLN* 1.3 60.6 + - - +
59R ALA* 3.4 3.1 + - - +
60R LEU* 2.9 45.6 + - + +
71R ARG* 4.7 3.8 - - - +
103R LEU* 3.6 32.3 - - + -
107R ILE* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 57 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R GLU* 2.9 40.0 + - - +
53R ASN 3.2 16.1 + - - +
54R PRO* 3.0 11.1 + - + +
56R MET* 1.3 76.0 - - - +
58R THR* 1.3 65.0 + - - +
60R LEU* 3.4 7.6 + - - +
61R ARG* 2.9 33.6 + - - +
9S TYR* 4.1 23.7 - - + -
17S GLY 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 58 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R PRO* 2.7 21.1 + - - +
55R ILE* 3.4 9.1 - - - -
57R GLN* 1.3 78.1 - - - +
59R ALA* 1.3 56.5 + - - +
61R ARG* 3.5 29.3 + - - +
62R ARG* 3.1 60.5 + - - +
110R ALA* 3.9 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ILE 3.0 16.1 + - - +
56R MET* 3.7 6.3 - - - +
57R GLN 3.2 0.2 - - - -
58R THR* 1.3 73.6 - - - +
60R LEU* 1.3 60.2 + - - +
61R ARG 3.1 1.8 - - - -
62R ARG* 3.0 6.2 + - - +
63R LEU* 2.9 28.2 + - - +
103R LEU* 4.2 10.9 - - + +
106R TYR* 3.8 30.2 - - + +
107R ILE* 4.1 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R GLU* 3.6 39.3 - - + +
56R MET* 2.9 26.7 + - + +
57R GLN* 4.0 9.9 - - - +
59R ALA* 1.3 76.7 - - - +
61R ARG* 1.3 60.9 + - - +
63R LEU* 3.5 23.2 + - + +
68R SER* 4.7 8.3 + - - +
71R ARG* 3.2 44.4 - - - +
103R LEU* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 61 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLU* 3.1 29.9 + - - +
57R GLN* 2.9 23.4 + - - +
58R THR* 3.5 43.5 + - - +
60R LEU* 1.3 77.5 - - - +
62R ARG* 1.3 64.3 + - - +
63R LEU 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B HIS* 3.5 52.9 + - + +
121B GLU* 2.7 48.0 + - - +
58R THR* 3.1 42.4 + - - +
59R ALA* 3.0 7.9 + - - +
61R ARG* 1.3 80.2 - - - +
63R LEU* 1.3 59.3 + - - +
64R PRO* 3.3 9.5 - - - +
106R TYR* 3.7 26.3 + - + +
109R GLU* 4.9 10.7 + - - +
110R ALA* 4.7 12.9 - - - +
113R ALA* 5.4 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59R ALA 2.9 15.0 + - - +
60R LEU* 3.6 23.9 - - + +
61R ARG 3.3 4.1 - - - +
62R ARG* 1.3 74.9 - - - +
64R PRO* 1.3 73.1 - - + +
65R GLU 3.6 0.9 + - - -
67R GLU* 3.8 20.6 - - + +
68R SER* 4.1 30.0 - - - +
71R ARG* 4.5 4.3 - - - -
102R TYR* 3.7 35.4 - - + +
103R LEU* 3.7 19.5 - - + -
106R TYR* 3.7 23.3 - - + -
----------------------------------------------------------
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