Contacts of the helix formed by residues 66 - 72 (chain A) in PDB entry 2Y96
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 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 2.7 42.0 + - - +
65A GLY* 1.3 75.8 - - - -
67A GLU* 1.3 64.7 + - - +
68A ALA* 3.5 6.9 + - - +
69A THR* 2.7 42.7 + - - -
70A ALA 3.2 9.5 + - - -
146A HIS* 3.9 4.7 - - - +
147A CYS 3.9 4.7 - - - -
148A VAL 3.3 14.1 - - - +
149A MET* 3.5 20.2 - - - +
150A GLY 4.2 0.4 - - - +
151A ARG* 5.9 0.6 + - - +
181A ARG* 4.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 1.3 69.5 - - - +
68A ALA* 1.3 67.1 + - - +
70A ALA* 3.1 7.8 + - - +
71A LEU* 3.0 43.4 + - + +
93A ASN 5.3 1.3 - - - +
94A VAL* 3.9 31.2 - - + +
146A HIS* 4.5 0.4 - - - -
147A CYS 3.4 11.7 + - - +
148A VAL* 2.9 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 4.4 14.1 - - + +
66A ASP* 3.4 15.0 + - - +
67A GLU* 1.3 77.3 - - - +
69A THR* 1.3 63.8 + - - +
71A LEU* 3.2 10.7 + - - +
72A ASP* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 3.5 20.4 + - - +
55A VAL* 3.6 32.4 - - + +
65A GLY* 4.5 0.4 - - - -
66A ASP* 2.7 30.7 + - - -
67A GLU 3.1 0.6 - - - -
68A ALA* 1.3 79.0 - - - +
70A ALA* 1.3 62.6 + - - +
71A LEU 3.3 0.7 + - - -
72A ASP* 3.5 11.5 + - - +
76A LEU* 3.6 23.0 - - + +
81A PHE* 5.8 2.2 - - + -
144A LEU* 4.1 14.6 - - + -
1208A SO4 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP 3.2 1.8 + - - +
67A GLU 3.1 8.8 + - - +
69A THR* 1.3 78.6 - - - +
71A LEU* 1.3 60.0 + - + +
76A LEU* 3.6 5.0 - - - +
94A VAL* 5.0 4.3 - - + -
96A THR* 5.3 1.3 - - + -
100A TYR* 3.9 1.4 - - - -
101A TYR* 2.7 35.3 + - - +
144A LEU* 3.8 11.3 - - + +
146A HIS* 3.3 49.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.0 44.6 + - + +
68A ALA* 3.2 7.8 + - - +
70A ALA* 1.3 79.0 - - + +
72A ASP* 1.3 59.4 + - - +
73A ARG* 3.0 10.8 + - - +
94A VAL* 5.0 3.6 - - + -
95A ASP 5.7 1.3 - - - +
96A THR* 3.8 19.7 - - + -
100A TYR* 2.6 45.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 3.1 15.7 + - - +
69A THR* 3.5 6.3 + - - +
71A LEU* 1.3 73.1 - - - +
73A ARG* 1.3 58.3 + - - +
74A TYR* 3.7 9.0 + - - +
75A ARG* 3.2 56.6 + - + +
76A LEU* 3.1 30.8 + - - +
----------------------------------------------------------
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