Contacts of the helix formed by residues 76 - 82 (chain A) in PDB entry 2P2B
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP 5.0 0.2 + - - -
49A ILE* 4.1 9.6 - - + +
75A LEU* 1.3 77.2 - - - +
77A LEU* 1.3 64.2 + - - +
78A ALA* 3.0 39.0 - - - +
79A ALA* 3.1 23.0 - - + +
80A ASN* 2.9 29.6 + - - +
153A ALA 4.1 2.6 + - - +
154A ARG* 3.0 25.1 - - - +
250A PRO* 3.8 16.5 - - + +
251A GLU 2.9 23.3 - - - +
253A MET* 4.0 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU 4.3 0.6 - - - -
76A ASN* 1.3 73.2 - - - +
78A ALA* 1.3 59.5 + - - +
80A ASN* 3.1 2.9 + - - +
81A CYS* 2.9 31.2 + - - -
150A LEU* 3.9 11.7 - - + -
153A ALA* 3.7 23.6 + - + +
253A MET* 5.8 0.6 - - - +
259A LEU* 3.5 39.0 - - + -
278A THR* 4.6 13.1 - - + +
282A LEU* 3.8 40.6 - - + -
318A TYR* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN* 3.0 14.0 - - - +
77A LEU* 1.3 82.0 - - - +
79A ALA* 1.3 58.1 + - - +
81A CYS 3.2 0.7 + - - +
82A LEU* 2.8 48.7 + - + +
83A ASP* 3.9 2.5 - - - -
117A VAL* 4.6 0.2 - - + -
150A LEU* 3.8 12.8 - - + +
153A ALA* 4.9 1.2 - - - +
154A ARG* 3.5 38.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 6.3 0.7 - - + -
49A ILE* 5.9 3.1 - - + -
76A ASN* 3.1 28.8 - - + +
77A LEU 3.3 0.2 - - - -
78A ALA* 1.3 76.4 - - - +
80A ASN* 1.3 61.8 + - - +
83A ASP* 3.3 25.1 + - + -
84A ARG* 3.1 31.0 + - - +
154A ARG* 4.2 0.6 - - - +
250A PRO* 4.3 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.4 16.5 - - + -
47A ASP* 2.7 51.0 + - - +
75A LEU* 4.2 11.7 - - - +
76A ASN 2.9 29.7 + - - +
77A LEU 3.1 7.4 + - - +
79A ALA* 1.3 80.3 - - - +
81A CYS* 1.3 59.6 + - - +
84A ARG* 3.0 22.5 + - - +
85A HIS* 2.9 22.4 + - - -
282A LEU* 3.9 14.4 - - + -
322A ALA* 3.5 5.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 2.9 38.9 + - - +
78A ALA 3.2 1.1 + - - +
80A ASN* 1.3 77.9 - - - +
82A LEU* 1.3 63.7 + - + +
85A HIS* 3.6 3.8 - - - -
110A TYR* 3.2 24.6 - - - -
150A LEU* 3.8 18.4 - - + -
282A LEU* 4.6 3.1 - - - -
318A TYR* 3.8 19.3 - - - -
321A LEU* 3.5 23.2 - - + +
322A ALA* 3.7 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ALA* 2.8 19.3 + - + +
80A ASN 3.4 1.6 - - - -
81A CYS* 1.3 91.9 - - + +
83A ASP* 1.3 70.9 + - - +
84A ARG 3.3 1.3 - - - -
85A HIS* 3.0 21.1 + - - +
86A LEU* 3.6 12.0 + - - +
110A TYR* 4.3 10.8 - - + +
113A LEU* 3.5 40.6 - - + -
114A HIS* 4.2 17.5 - - + +
117A VAL* 3.8 36.8 - - + -
150A LEU* 4.1 15.9 - - + -
154A ARG* 4.6 3.4 - - - +
321A LEU* 4.9 1.1 - - + -
----------------------------------------------------------
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