Contacts of the helix formed by residues 364 - 369 (chain G) 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 ASP 364 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233G LEU* 3.6 4.2 - - - +
240G HIS* 2.8 26.0 + - - +
298G VAL* 3.7 26.9 - - + -
361G ARG 3.9 1.7 - - - +
362G TYR 3.2 2.4 - - - -
363G ARG* 1.3 79.5 - - + +
365G PRO* 1.4 71.8 - - - +
366G GLN* 2.9 41.0 + - - +
367G ALA* 3.1 5.4 + - + +
368G TYR* 2.9 26.7 + - - +
412G LEU* 4.2 6.1 - - - -
15H ARG* 3.0 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 365 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G HIS* 3.9 23.6 - - + +
241G THR* 3.9 18.4 - - + -
244G VAL* 3.3 21.1 - - + +
364G ASP* 1.4 98.3 - - - +
366G GLN* 1.3 62.7 + - - +
367G ALA 3.0 1.4 + - - -
368G TYR* 4.1 4.5 - - + -
369G MET 3.1 20.1 + - - -
404G ILE* 3.7 24.7 - - + +
412G LEU* 4.3 3.3 - - + -
414G LEU* 4.0 14.4 - - + -
418G GLU* 5.1 0.7 - - - +
15H ARG* 3.8 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 366 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G MET* 3.1 41.8 + - - +
230G GLY* 5.3 0.2 - - - -
231G GLY 4.8 3.8 + - - -
240G HIS* 3.4 45.4 + - - +
243G ALA* 3.7 16.3 - - + +
244G VAL* 4.0 16.3 - - + +
247G ARG* 5.1 2.7 + - - +
298G VAL* 4.1 15.0 - - + +
299G MET* 3.5 9.9 - - + +
364G ASP* 2.9 23.1 + - - +
365G PRO* 1.3 77.0 - - - +
367G ALA* 1.3 56.9 + - - +
369G MET 4.6 0.2 - - - -
370G LEU* 3.3 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 367 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G VAL* 3.8 19.9 - - - +
299G MET* 4.0 17.7 - - + +
302G LEU* 3.6 10.7 - - + +
360G ASP 3.4 25.4 - - - +
361G ARG 4.2 0.9 - - - -
364G ASP* 3.1 11.4 + - + +
365G PRO 3.0 0.2 - - - -
366G GLN* 1.3 77.1 - - - +
368G TYR* 1.3 66.7 + - - +
369G MET 3.2 1.6 - - - -
370G LEU* 2.9 15.6 + - - +
371G ALA 3.2 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G ARG* 3.2 62.5 + - + +
362G TYR* 3.9 22.0 + + - -
364G ASP 2.9 16.8 + - - +
365G PRO* 3.8 10.1 - - + +
367G ALA* 1.3 74.1 - - - +
369G MET* 1.3 61.6 + - - +
371G ALA* 3.3 8.5 + - - +
374G ASN* 2.9 35.0 + - - -
403G ILE* 3.6 33.2 - - + -
404G ILE* 4.0 9.4 - - + -
406G GLU* 4.7 1.4 - - - +
407G GLY* 3.4 23.1 + - - -
412G LEU* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 369 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G VAL* 3.4 35.2 - - + +
247G ARG* 3.8 11.2 - - + -
248G ALA* 3.3 36.6 - - + +
275G ILE* 3.9 15.9 - - + -
365G PRO 3.1 4.1 + - - +
366G GLN 5.1 0.4 - - - +
368G TYR* 1.3 79.6 - - - +
370G LEU* 1.3 77.7 + - + +
371G ALA 3.2 0.2 - - - -
374G ASN* 3.3 22.1 - - - +
375G ALA* 3.4 8.7 + - - -
378G VAL* 4.2 17.7 - - + -
400G CYS* 4.0 16.4 - - + -
403G ILE* 4.4 10.8 - - + -
404G ILE* 4.2 6.7 - - + -
----------------------------------------------------------
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