Contacts of the helix formed by residues 68 - 78 (chain C) in PDB entry 2OZL
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 GLN 68 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C CYS* 2.9 23.7 + - + +
67C GLY* 1.3 77.5 - - - +
69C GLU* 1.3 56.9 + - - +
70C ALA* 3.2 3.4 - - - -
71C CYS* 3.0 28.6 + - + +
72C CYS* 3.7 5.9 + - - -
90C ARG* 3.9 19.2 - - - +
194C GLU* 3.5 26.5 - - - +
196C ASN* 3.1 32.4 + - - +
227C GLY 5.3 0.7 - - - -
257C THR* 3.3 31.2 - - + +
258C TYR 3.4 8.7 - - - +
259C ARG* 3.4 18.9 - - - +
1330C TPP 5.4 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C MET* 3.6 40.4 - - + +
42C VAL* 3.8 19.7 - - + +
43C ARG* 2.6 48.6 + - - -
65C CYS* 4.3 0.9 - - - +
66C ASP* 3.1 15.9 - - - -
67C GLY* 2.8 25.9 + - - -
68C GLN* 1.3 75.0 + - - +
70C ALA* 1.3 65.1 + - - +
72C CYS* 3.8 8.2 - - - -
73C VAL* 3.2 28.6 + - - +
287C PRO* 3.7 5.2 - - + +
288C ILE* 4.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C MET* 4.1 8.5 - - - -
68C GLN 3.2 1.0 - - - -
69C GLU* 1.3 77.9 - - - +
71C CYS* 1.3 57.4 + - - +
74C GLY* 2.9 27.4 + - - -
227C GLY 3.5 19.3 - - - +
228C MET 3.7 10.5 - - - +
229C ASP 4.1 1.3 - - - -
230C ILE* 3.7 22.2 - - + +
233C VAL* 3.7 8.4 - - + +
287C PRO* 3.7 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C GLN* 3.0 14.9 + - - +
70C ALA* 1.3 75.3 - - - +
72C CYS* 1.3 61.5 + - - +
75C LEU* 2.9 38.0 + - - +
94C PHE* 4.8 1.6 - - + -
194C GLU* 3.8 22.7 - - - +
227C GLY* 3.6 18.4 - - - -
233C VAL* 4.4 6.5 - - - -
255C LEU* 3.8 32.5 - - + -
257C THR* 4.0 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 4.4 8.7 - - - -
65C CYS* 5.3 3.1 - - - -
68C GLN 3.7 2.8 + - - +
69C GLU* 3.8 18.8 - - - -
71C CYS* 1.3 79.2 - - - +
73C VAL* 1.3 67.9 + - - +
75C LEU* 4.1 1.2 - - - +
76C GLU* 3.2 23.4 + - - +
93C GLY* 3.9 22.2 - - - -
94C PHE* 3.4 43.6 - - + +
97C THR* 3.8 19.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 4.1 14.6 - - + +
38C MET* 4.0 30.5 - - + +
39C MET* 3.5 31.6 - - + +
42C VAL* 4.9 1.1 - - + -
69C GLU 3.2 18.1 + - - +
72C CYS* 1.3 78.9 - - - +
74C GLY* 1.3 61.2 + - - +
76C GLU* 3.4 3.8 + - - +
77C ALA* 3.0 26.9 + - - +
97C THR* 4.1 15.9 - - + -
230C ILE* 3.4 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ALA 2.9 21.6 + - - -
73C VAL* 1.3 76.5 - - - +
75C LEU* 1.3 63.8 + - - +
77C ALA* 3.4 3.9 + - - +
78C GLY 3.3 15.1 + - - -
230C ILE* 3.7 19.2 - - - +
233C VAL* 3.6 14.4 - - - -
234C ARG* 3.5 13.9 - - - -
237C THR* 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C CYS 2.9 24.3 + - - +
72C CYS 4.1 2.7 - - - +
74C GLY* 1.3 76.1 - - - +
76C GLU* 1.3 63.5 + - - +
78C GLY* 3.0 10.7 + - - -
79C ILE* 3.3 21.8 + - - +
85C LEU* 4.9 3.1 - - + -
94C PHE* 3.5 32.8 - - + -
162C LEU* 4.1 14.8 - - + -
164C LEU* 3.8 17.3 - - + -
192C ILE* 4.0 14.1 - - + -
233C VAL* 3.7 7.2 - - + +
237C THR* 3.2 23.1 - - - +
253C MET* 3.5 22.7 - - + -
255C LEU* 4.3 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C MET* 4.6 9.4 - - + -
72C CYS 3.2 16.6 + - - +
73C VAL* 3.7 4.9 - - - +
75C LEU* 1.3 80.0 - - - +
77C ALA* 1.3 61.3 + - - +
78C GLY 3.2 0.7 + - - -
79C ILE* 3.2 29.5 + - - +
80C ASN 4.8 0.9 - - - +
81C PRO* 5.0 4.3 - - - +
85C LEU* 5.4 3.3 - - - +
94C PHE* 6.0 0.2 - - - -
97C THR* 3.3 37.9 + - - +
98C ARG* 3.0 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.5 40.2 + - + +
73C VAL 3.0 16.4 + - - +
74C GLY* 3.7 7.6 - - - +
76C GLU* 1.3 77.0 - - - +
78C GLY* 1.3 59.4 + - - +
79C ILE 3.5 1.8 - - - +
230C ILE* 5.7 0.9 - - + -
234C ARG* 3.7 19.1 - - + +
238C ARG* 4.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLY 3.3 7.1 + - - -
75C LEU 3.0 7.7 + - - -
77C ALA* 1.3 78.8 - - - +
79C ILE* 1.3 65.5 + - - +
234C ARG 4.2 2.7 - - - -
237C THR* 3.7 18.7 - - - +
238C ARG* 3.9 31.4 - - - +
241C ALA* 4.3 5.9 - - - +
245C ARG* 5.1 0.9 + - - -
----------------------------------------------------------
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