Contacts of the helix formed by residues 72 - 87 (chain C) in PDB entry 1KYZ
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 ASP 72 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ASN* 3.0 18.8 + - - +
71C PRO* 1.3 83.7 - - - +
73C ALA* 1.3 65.6 + - - +
74C PRO* 3.3 1.9 - - - -
75C VAL* 3.3 9.9 + - + +
76C MET* 3.1 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA* 4.2 11.9 - - + -
66C LEU* 5.0 7.0 - - + -
68C THR* 4.7 15.5 - - + -
70C ASN* 3.1 33.2 + - + +
72C ASP* 1.3 77.1 - - - +
74C PRO* 1.3 62.0 - - + +
76C MET* 3.2 7.6 + - - +
77C LEU* 2.8 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PRO* 3.2 24.2 - - + +
60C ILE* 3.8 34.3 - - + +
63C ALA* 3.6 16.8 - - + -
70C ASN 4.0 2.2 - - - +
71C PRO 3.4 18.8 - - - +
72C ASP 3.5 1.1 - - - -
73C ALA* 1.3 93.4 - - + +
75C VAL* 1.3 59.3 + - + +
77C LEU* 3.2 1.5 + - + -
78C ASP* 2.8 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO 5.7 1.3 - - - +
72C ASP* 3.3 11.4 + - + +
74C PRO* 1.3 77.4 - - + +
76C MET* 1.3 65.2 + - + +
78C ASP* 3.2 9.4 + - + +
79C ARG* 3.1 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ASN* 3.9 20.6 - - - -
72C ASP* 3.1 25.3 + - + +
73C ALA* 3.5 7.4 - - - +
75C VAL* 1.3 78.0 - - + +
77C LEU* 1.3 64.2 + - + +
79C ARG* 3.3 12.8 + - - +
80C MET* 3.2 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.1 16.2 - - + -
44C LEU* 3.8 28.0 - - + -
59C PRO* 3.7 7.0 - - + +
62C ILE* 3.7 14.8 - - + -
63C ALA* 3.7 41.7 - - + +
66C LEU* 3.7 12.8 - - + -
73C ALA* 2.8 23.2 + - + +
74C PRO 3.5 4.0 - - - +
76C MET* 1.3 75.4 - - + +
78C ASP* 1.3 60.7 + - - +
80C MET* 3.0 10.3 + - - +
81C LEU* 2.7 46.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PRO* 3.6 20.6 - - + +
74C PRO 2.8 14.6 + - - +
75C VAL* 3.2 14.0 + - + +
77C LEU* 1.3 76.0 - - - +
79C ARG* 1.3 59.4 + - + +
81C LEU* 4.3 1.6 - - - -
82C ARG* 2.8 32.1 + - - +
104C ARG* 2.6 39.7 + - - +
106C TYR* 2.7 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C VAL* 3.1 30.6 + - + +
76C MET* 3.7 11.4 - - - +
77C LEU 3.2 0.4 - - - -
78C ASP* 1.3 78.9 - - + +
80C MET* 1.3 62.6 + - + +
82C ARG* 3.7 31.2 + - - +
83C LEU* 3.6 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 3.7 32.4 - - + +
38C SER* 3.8 29.4 - - - -
39C ALA* 3.9 16.8 - - + +
42C LEU* 4.0 17.3 - - + -
44C LEU* 4.5 3.6 - - + -
76C MET* 3.2 19.6 + - - +
77C LEU* 3.0 21.6 + - - +
79C ARG* 1.3 75.0 - - + +
81C LEU* 1.3 69.5 + - + +
83C LEU* 3.2 16.3 + - - +
84C LEU* 3.3 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.8 30.5 - - + -
45C LEU* 5.8 0.9 - - + -
48C ILE* 4.8 5.4 - - + -
59C PRO* 4.8 3.1 - - + -
62C ILE* 4.3 18.4 - - + -
77C LEU* 2.7 51.6 + - + +
78C ASP* 4.0 2.0 - - - +
80C MET* 1.3 70.5 - - - +
82C ARG* 1.3 66.9 + - - +
84C LEU* 3.0 14.8 + - + +
85C ALA* 2.9 19.1 + - - +
90C LEU* 3.6 21.9 - - + +
106C TYR* 3.5 36.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP* 2.8 19.2 + - - +
79C ARG* 3.8 36.3 + - - +
80C MET 3.2 0.2 - - - -
81C LEU* 1.3 77.4 - - - +
83C LEU* 1.3 62.5 + - - +
85C ALA* 3.2 4.4 + - - +
86C CYS* 3.1 32.9 + - - -
104C ARG* 3.9 36.7 - - - +
106C TYR* 3.4 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 3.4 38.4 - - + +
32C LEU* 4.0 8.7 - - + -
35C ILE* 3.5 31.9 - - + -
79C ARG 3.6 7.9 + - - +
80C MET 3.2 8.0 + - - +
81C LEU 3.2 0.4 - - - -
82C ARG* 1.3 79.3 - - - +
84C LEU* 1.3 66.9 + - + +
86C CYS* 3.2 16.8 + - + +
87C TYR* 3.3 41.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.4 8.5 - - + -
35C ILE* 4.0 18.2 - - + -
36C LEU* 4.2 19.5 - - + +
39C ALA* 4.0 27.1 - - + -
45C LEU* 4.8 9.4 - - + -
80C MET 3.3 12.1 + - - +
81C LEU* 3.0 17.8 + - + +
83C LEU* 1.3 79.6 - - + +
85C ALA* 1.3 59.1 + - - +
87C TYR* 3.3 7.4 + - - +
89C ILE* 3.0 51.2 + - + +
90C LEU* 3.7 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU 2.9 12.7 + - - +
82C ARG* 3.6 8.3 - - - +
83C LEU 3.2 0.2 - - - -
84C LEU* 1.3 73.2 - - - +
86C CYS* 1.3 61.1 + - - +
87C TYR 3.1 1.6 - - - -
88C ILE* 2.9 21.7 + - - +
90C LEU* 3.5 25.6 - - + +
92C CYS* 4.1 24.2 - - + -
106C TYR* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ARG* 3.1 32.0 + - - -
83C LEU* 3.2 12.5 + - + +
85C ALA* 1.3 77.6 - - - +
87C TYR* 1.3 66.9 + - + +
88C ILE* 3.2 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR 4.8 9.6 - - - -
25C GLN* 2.9 37.9 + - - +
29C ALA* 5.9 2.3 - - - -
31C VAL* 6.0 0.4 - - + -
32C LEU* 3.5 51.5 - - + +
83C LEU* 3.3 37.8 + - + +
84C LEU 3.3 6.5 + - - +
85C ALA 3.1 0.8 - - - -
86C CYS* 1.3 83.2 - - + +
88C ILE* 1.3 74.8 + - - +
89C ILE* 3.2 11.9 + - + +
----------------------------------------------------------
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