Contacts of the helix formed by residues 301 - 305 (chain O) 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 ASN 301 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335M TYR* 2.9 30.4 + - - +
339M LEU* 3.9 10.8 + - - +
289O LYS* 3.1 39.2 - - - +
300O GLY* 1.3 72.4 - - - -
302O LEU* 1.3 57.8 - - - +
303O VAL 3.2 2.5 - - - -
304O MET* 2.8 42.3 + - + +
356O MET* 3.6 23.7 - - + +
359O SER* 3.0 21.2 + - - +
360O ASP* 2.8 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 302 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299O MET* 3.4 15.2 + - + +
301O ASN* 1.3 76.9 - - - +
303O VAL* 1.3 61.3 - - + +
305O GLN* 2.9 57.3 + - - +
356O MET 3.4 16.3 + - - +
357O MET* 3.5 19.5 - - + +
360O ASP* 3.1 19.4 + - + +
361O ARG 4.1 10.5 - - - +
367O ALA* 3.5 20.6 - - + +
370O LEU* 3.8 24.0 - - + -
371O ALA* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 303 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271O TYR* 3.6 31.4 - - + +
286O MET* 3.2 46.6 - - + +
287O GLU 3.2 20.6 - - - +
288O GLY* 3.6 7.0 - - - -
299O MET* 3.4 28.4 + - + +
300O GLY 3.7 3.1 - - - +
302O LEU* 1.3 81.7 - - + +
304O MET* 1.3 61.7 + - - +
305O GLN* 3.2 4.2 + - - +
306O CYS 4.4 0.9 + - - -
307O CYS* 3.7 2.3 + - - +
310O TRP* 3.6 18.4 - - + -
370O LEU* 5.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M LEU* 5.2 3.6 - - + -
19O PHE* 3.5 13.0 - - - +
289O LYS* 3.4 21.1 - - + +
301O ASN* 2.8 50.2 + - + +
303O VAL* 1.3 76.9 - - - +
305O GLN* 1.3 66.0 + - - +
306O CYS 2.8 3.9 + - - -
307O CYS* 3.1 18.6 + - - -
310O TRP* 3.3 45.1 - - + -
336O ASP* 4.7 5.6 - - - +
339O LEU* 6.5 0.4 - - + -
340O MET* 4.3 18.8 - - - +
356O MET* 3.5 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 305 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O PHE* 3.3 19.3 + - - -
274O ILE* 3.6 16.5 - - + +
286O MET* 5.8 0.6 - - - +
301O ASN 3.9 0.6 + - - -
302O LEU* 2.9 31.8 + - - +
303O VAL* 3.2 4.4 - - - +
304O MET* 1.3 76.5 - - - +
306O CYS* 1.3 78.0 + - - +
353O ARG* 3.4 29.3 - - + +
356O MET* 3.7 13.8 - - - +
357O MET* 3.4 15.9 - - + +
370O LEU 2.7 26.9 + - - -
371O ALA* 3.5 1.0 - - - -
372O TYR* 2.7 34.3 + - + +
----------------------------------------------------------
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