Contacts of the helix formed by residues 222 - 231 (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 GLN 222 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G MET 6.3 0.2 - - - -
167G GLY 2.9 27.7 + - - +
168G GLY 3.1 19.5 + - - +
169G LYS* 4.6 4.3 - - - -
172G PHE* 2.8 45.0 - - + +
187G SER 3.2 17.8 + - - -
188G ILE* 3.4 28.1 - - + +
219G ASP* 2.5 33.9 + - - +
221G ALA* 1.3 86.9 - - + +
223G ALA* 1.3 61.5 + - - +
224G ASN 3.3 0.9 - - - -
225G THR 3.3 1.9 + - - -
226G ALA 2.9 13.9 + - - -
253G ARG* 4.5 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 223 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G ILE* 4.9 0.4 - - - +
219G ASP* 2.9 28.8 + - + +
222G GLN* 1.3 71.5 - - - +
224G ASN* 1.3 58.4 + - - +
226G ALA* 3.4 9.2 + - - +
227G MET* 3.0 26.2 + - - +
243G ALA 5.3 1.6 - - - +
246G ALA* 4.5 6.3 - - - +
247G ARG* 3.6 37.9 + - - +
250G SER* 3.9 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 224 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G ASP 3.7 2.8 + - - -
220G CYS* 3.1 46.9 - - - +
222G GLN 3.3 0.6 - - - -
223G ALA* 1.3 73.1 - - - +
225G THR* 1.3 63.7 + - - +
227G MET* 3.0 6.7 + - - +
228G PHE* 2.7 47.6 + - + -
247G ARG* 2.9 29.2 + - - -
269G CYS* 2.8 32.0 + - - +
271G TYR* 3.6 9.2 - - - -
287G GLU* 5.3 0.2 + - - -
295G HIS* 6.1 0.6 + - - -
500H B13 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 225 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G PHE* 3.8 18.6 - - + -
173G ASP* 4.5 1.3 - - - +
220G CYS 3.4 9.2 + - - -
221G ALA 3.4 13.5 + - - -
222G GLN 3.3 8.7 + - - -
224G ASN* 1.3 76.5 - - - +
226G ALA* 1.3 62.8 + - - +
228G PHE* 3.1 5.3 + - - +
229G ILE* 3.0 32.2 + - + +
138H ILE* 3.7 29.8 - - + -
500H B13 3.5 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G PHE* 3.9 13.6 - - + -
176G VAL* 4.3 5.8 - - + -
222G GLN 2.9 13.7 + - - +
223G ALA 3.4 10.3 - - - +
225G THR* 1.3 77.3 - - - +
227G MET* 1.3 55.9 + - - +
229G ILE* 3.4 1.4 + - - -
230G GLY* 2.9 24.8 + - - -
238G LEU* 3.3 28.5 - - + +
243G ALA* 4.2 7.5 - - - +
246G ALA* 4.2 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 227 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223G ALA 3.0 14.4 + - - +
224G ASN* 3.0 11.4 + - - +
226G ALA* 1.3 75.1 - - - +
228G PHE* 1.3 83.1 + - + +
230G GLY* 3.4 2.1 + - - -
231G GLY* 2.8 26.0 + - - +
243G ALA* 4.6 3.3 - - + +
247G ARG* 3.4 21.5 - - - +
271G TYR* 3.9 24.5 - - + +
295G HIS* 4.1 13.7 - - + +
296G SER 4.7 4.0 - - - +
297G ASP* 4.4 10.8 - - + -
298G VAL* 5.7 2.2 - - + -
299G MET* 4.2 18.2 - - - +
366G GLN* 3.1 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 228 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220G CYS* 6.1 0.9 - - - -
224G ASN* 2.7 42.4 + - + -
225G THR* 3.1 7.4 + - - +
227G MET* 1.3 89.2 - - + +
229G ILE* 1.3 58.8 + - + +
230G GLY 3.1 1.3 - - - -
231G GLY* 2.8 24.1 + - - -
235G ASN* 4.5 2.1 + - - -
295G HIS* 3.3 52.0 - + + -
296G SER 4.9 4.3 - - - -
500H B13 3.6 69.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 229 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176G VAL* 4.1 17.3 - - + +
177G LEU* 3.9 23.8 - - + -
225G THR* 3.0 24.7 + - + +
226G ALA 3.8 3.8 - - - +
228G PHE* 1.3 75.4 - - + +
230G GLY* 1.3 61.0 + - - +
235G ASN* 4.3 2.9 + - - -
237G ASN* 3.1 57.4 + - + +
238G LEU* 3.8 8.1 - - + -
95H LEU* 4.9 3.8 - - + -
138H ILE* 3.7 37.9 - - + -
142H ILE* 5.7 2.2 - - + -
500H B13 4.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 230 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ALA 2.9 15.5 + - - -
227G MET* 3.4 5.4 + - - -
228G PHE 3.1 0.2 - - - -
229G ILE* 1.3 76.8 - - - +
231G GLY* 1.3 60.5 + - - +
235G ASN* 3.1 15.7 - - - +
238G LEU* 3.7 24.6 + - - +
240G HIS* 2.7 26.9 + - - -
243G ALA* 5.5 2.0 - - - -
366G GLN* 5.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 231 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227G MET* 2.8 15.1 + - - +
228G PHE* 2.8 14.2 + - - -
230G GLY* 1.3 80.5 - - - +
232G GLY* 1.3 62.2 + - - +
235G ASN* 3.1 14.1 - - - -
240G HIS* 3.3 9.0 + - - -
298G VAL* 6.0 1.9 - - - +
366G GLN* 4.8 2.4 + - - -
----------------------------------------------------------
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