Contacts of the strand formed by residues 40 - 43 (chain C) in PDB entry 2I2X
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 ILE 40 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.6 18.4 - - + -
33C GLU 3.3 26.5 - - - +
34C ILE* 3.8 23.1 - - + -
38C TYR* 3.7 18.8 - - + +
39C THR* 1.3 79.4 - - - +
41C PRO* 1.4 82.3 - - + +
80C ALA* 4.3 4.0 - - + -
81C ILE* 4.1 9.4 - - - +
82C ILE* 3.7 28.0 - - + +
308C ASP 3.0 9.7 + - - +
309C CYS* 3.1 7.5 - - - +
310C TRP 2.9 24.4 + - - -
337C CYS* 3.4 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR 4.4 1.3 - - - +
40C ILE* 1.4 87.4 - - + +
42C GLU* 1.3 58.9 - - - +
43C ILE* 4.1 0.9 - - + +
73C MET* 3.8 17.3 - - + -
80C ALA* 3.3 28.3 - - + +
81C ILE* 3.7 5.9 - - + +
82C ILE 2.9 24.7 + - - +
310C TRP 3.5 7.0 - - - +
330C SER* 4.5 3.4 - - - +
333C LEU* 3.8 10.5 - - + -
334C ALA* 3.7 28.0 - - + +
337C CYS* 3.4 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE 3.6 0.2 + - - -
41C PRO* 1.3 73.0 - - - +
43C ILE* 1.3 61.1 + - - +
44C ASN* 4.3 2.9 - - - +
82C ILE* 3.2 31.2 - - + +
84C GLU* 3.5 21.4 - - + +
123C ARG* 2.8 52.7 + - - -
285C THR* 2.8 22.9 + - + +
309C CYS* 4.0 11.8 - - + +
310C TRP 2.8 13.3 + - - +
311C SER* 3.2 30.0 + - - -
312C ASN 3.7 0.3 + - - -
333C LEU* 3.6 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PRO* 4.1 1.0 - - + -
42C GLU* 1.3 73.6 - - - +
44C ASN* 1.3 70.6 + - - +
45C TYR* 3.4 9.7 - - + -
69C VAL* 3.9 15.0 - - + -
81C ILE* 3.6 21.3 - - + -
82C ILE 2.9 18.5 + - - +
83C LEU* 3.8 14.4 - - + -
84C GLU 3.0 24.4 + - - -
312C ASN* 3.5 24.9 - - - +
326C VAL* 3.7 22.0 - - + +
329C TRP* 4.0 4.5 - - + -
330C SER* 3.7 33.2 - - - +
333C LEU* 4.2 3.4 - - + -
----------------------------------------------------------
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