Contacts of the helix formed by residues 66 - 73 (chain C) in PDB entry 3IOT
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 ARG 66 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 3.7 20.7 + - + +
45C GLU* 3.0 37.4 + - - -
48C PRO* 4.9 3.4 - - - +
62C TRP* 3.5 33.0 - - + +
63C ALA 3.3 1.9 + - - +
64C HIS 3.3 0.6 - - - -
65C ASP* 1.3 88.1 - - - +
67C PHE* 1.3 62.2 - - - +
68C GLY 3.2 1.1 + - - -
69C GLY* 3.3 12.5 + - - -
70C TYR* 3.5 47.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 3.4 30.1 - - + -
62C TRP* 3.8 26.9 - - + -
63C ALA 3.8 7.2 - - - -
64C HIS* 3.3 13.0 + - + +
65C ASP 3.2 0.8 - - - -
66C ARG* 1.3 75.5 - - - +
68C GLY* 1.3 54.7 + - - +
69C GLY 3.2 0.4 - - - -
70C TYR* 3.4 26.5 - + - +
71C ALA* 2.7 37.9 + - - +
76C LEU* 3.8 15.0 - - + -
97C VAL* 5.7 0.9 - - + -
104C ILE* 4.2 11.0 - - + -
105C ALA* 3.5 34.8 - - + -
263C SER* 3.5 20.2 - - - -
265C GLY* 3.6 14.4 - - - -
332C ASN* 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C HIS 4.0 1.0 + - - -
65C ASP 3.5 4.8 + - - -
66C ARG 3.2 1.6 - - - -
67C PHE* 1.3 78.1 - - - +
69C GLY* 1.3 59.6 + - - +
71C ALA 3.5 0.2 + - - -
72C GLN* 3.1 21.2 + - - +
99C TYR* 3.4 18.4 - - - -
332C ASN* 3.3 41.8 - - - +
334C PRO* 6.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 69 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ASP 4.7 1.0 + - - -
66C ARG* 3.3 10.5 + - - -
67C PHE 3.2 0.2 - - - -
68C GLY* 1.3 72.0 - - - +
70C TYR* 1.3 66.6 + - - +
72C GLN* 3.5 6.4 + - - +
73C SER* 2.9 30.1 + - - -
332C ASN 4.4 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 3.1 32.8 + - - +
47C PHE* 4.1 29.2 - + + +
48C PRO* 4.1 18.0 - - + +
60C ILE* 4.7 10.9 - - + +
62C TRP* 5.3 1.9 - - + -
66C ARG* 3.5 40.0 - - + +
67C PHE* 3.0 41.2 + + - +
69C GLY* 1.3 76.8 - - - +
71C ALA* 1.3 66.1 + - - +
73C SER* 3.1 6.8 + - - -
75C LEU* 3.0 41.6 + - + +
76C LEU* 3.7 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE 2.7 19.7 + - - +
70C TYR* 1.3 73.9 - - - +
72C GLN* 1.3 57.2 + - - +
74C GLY* 3.1 17.9 + - - +
75C LEU 4.7 0.4 - - - +
76C LEU* 4.1 13.7 - - + +
99C TYR* 3.8 36.3 - - + -
104C ILE* 4.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ASP* 5.6 0.2 - - - +
362A ALA* 3.4 18.9 - - - +
366A THR* 3.2 35.3 - - + +
68C GLY 3.1 14.9 + - - +
69C GLY* 3.9 6.6 - - - +
71C ALA* 1.3 75.0 - - - +
73C SER* 1.3 59.5 + - - +
74C GLY 3.1 2.5 - - - -
99C TYR* 2.7 37.2 + - + +
334C PRO* 4.1 21.6 - - - +
379C LYS* 4.4 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 3.3 27.3 - - - +
362A ALA* 3.7 8.0 - - - +
363A ALA* 5.7 1.1 - - - +
69C GLY 2.9 17.8 + - - -
70C TYR 3.1 5.9 + - - -
72C GLN* 1.3 78.8 - - - +
74C GLY* 1.3 59.5 + - - -
75C LEU* 3.2 20.9 + - - +
----------------------------------------------------------
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