Contacts of the helix formed by residues 249 - 253 (chain C) in PDB entry 2I5N
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 249 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 3.6 23.7 - - - +
19C MET* 3.8 23.9 - - + +
248C HIS* 1.3 70.6 - - - +
250C ALA* 1.3 55.9 + - - +
251C GLN* 3.0 39.2 + - + +
252C THR* 3.0 23.2 + - - +
253C PHE 3.9 0.3 + - - -
258C LYS 5.1 3.1 + - - +
259C LYS* 3.0 34.5 + - + +
155L ASP* 5.0 1.2 - - - +
159L ASN* 3.0 18.3 + - - -
305M TYR* 4.3 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C CYS* 6.0 0.4 - - + -
245C THR* 5.6 0.4 - - + -
248C HIS 3.7 2.4 - - - -
249C ASN* 1.3 66.8 - - - +
251C GLN* 1.3 65.2 + - - +
252C THR* 3.0 3.0 + - - -
253C PHE* 3.6 44.0 + - + -
158L ASN* 2.8 33.9 + - - +
159L ASN* 2.9 24.4 + - - +
162L TYR* 3.8 10.1 - - + -
193M ASN* 3.5 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ASN* 3.1 22.9 + - - +
250C ALA* 1.3 76.3 - - - +
252C THR* 1.3 59.5 + - + +
259C LYS* 2.8 32.1 + - - +
155L ASP* 3.0 22.4 + - - +
158L ASN* 3.5 4.9 - - - +
159L ASN* 4.6 1.8 - - - +
193M ASN* 3.0 29.5 + - - +
196M TYR* 2.8 30.5 + - + +
293M TYR* 3.7 28.5 - - + -
303M PRO* 3.1 24.9 + - - +
305M TYR* 3.9 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C HIS* 5.1 0.2 + - - -
249C ASN 3.0 9.9 + - - +
250C ALA 3.0 0.4 - - - -
251C GLN* 1.3 83.4 - - + +
253C PHE* 1.3 63.5 + - - +
254C GLU* 2.8 25.6 + - - -
255C SER* 2.6 33.0 + - - +
259C LYS* 3.5 40.6 - - + +
193M ASN* 5.7 0.9 - - - -
293M TYR* 3.7 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C VAL* 5.5 0.7 - - + -
244C CYS* 4.4 6.1 - - + -
248C HIS* 3.2 32.9 + + + -
249C ASN 3.9 1.9 + - - -
250C ALA* 3.6 29.2 - - + -
252C THR* 1.3 72.2 - - - +
254C GLU* 1.3 61.5 + - - +
264C ARG* 3.0 28.8 + - - -
403C HEC 3.5 66.6 - + + +
158L ASN* 5.6 0.2 - - - -
162L TYR* 3.6 44.6 - + - -
189M ILE* 4.5 11.9 - - + -
193M ASN* 6.5 0.4 - - + -
----------------------------------------------------------
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