Contacts of the helix formed by residues 223 - 231 (chain C) in PDB entry 2GRA
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 HIS 223 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C GLN* 1.3 74.3 + - - +
224C PRO* 1.3 87.4 - - + +
225C GLY* 2.6 19.3 + - - +
226C GLN* 2.6 38.3 + - + +
227C LEU* 3.1 9.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 224 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 3.7 36.5 - - + -
222C GLN 3.9 5.1 - - - +
223C HIS* 1.3 100.8 - - + +
225C GLY* 1.3 56.1 + - - +
227C LEU* 3.4 7.2 + - + +
228C LYS* 2.8 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C HIS* 2.6 22.6 + - - -
224C PRO* 1.3 71.4 - - - +
226C GLN* 1.3 49.2 + - - -
227C LEU 2.9 4.3 - - - -
228C LYS* 2.8 11.3 + - - +
229C ASP* 2.6 45.2 + - - +
251C ARG* 6.4 0.4 - - - -
186D ASP* 6.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 226 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C GLN* 3.7 25.6 - - - +
223C HIS* 2.6 30.1 + - + +
225C GLY* 1.3 71.8 - - - +
227C LEU* 1.3 55.5 + - - +
229C ASP* 3.6 20.6 + - - +
230C ASN* 2.4 52.3 + - - +
199D ARG* 5.7 1.8 - - - +
200D ARG* 3.5 29.2 + - - +
204D ARG* 5.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ALA 5.7 0.2 - - - +
216C MET* 4.8 21.1 - - + +
217C LEU* 3.5 42.2 - - + +
220C SER* 4.2 7.0 - - - +
222C GLN* 3.4 37.2 - - + -
223C HIS 3.1 4.5 + - - +
224C PRO* 3.5 8.1 - - + +
225C GLY 2.9 0.6 - - - -
226C GLN* 1.3 80.0 - - - +
228C LYS* 1.3 65.2 + - - +
229C ASP 3.2 0.2 - - - -
230C ASN* 3.5 13.0 - - + +
231C VAL* 3.0 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C PRO 2.8 14.0 + - - +
225C GLY* 2.8 11.1 + - - +
227C LEU* 1.3 76.7 - - - +
229C ASP* 1.3 102.7 + - - +
231C VAL* 3.2 9.2 + - - +
232C SER* 3.5 12.3 + - - -
238C THR* 5.4 0.9 - - + +
239C ILE* 6.1 0.4 - - - -
242C LEU* 3.7 33.4 - - + -
246C GLU* 5.8 1.3 - - - +
251C ARG* 4.7 20.4 - - - +
186D ASP* 4.9 4.2 + - - -
190D ASP* 3.4 26.5 - - - -
199D ARG* 3.5 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C GLY* 2.6 25.5 + - - +
226C GLN* 3.6 22.5 + - - +
228C LYS* 1.3 112.9 + - - +
230C ASN* 1.3 66.1 + - - +
232C SER* 2.7 20.8 + - - +
186D ASP* 4.8 2.1 - - - +
199D ARG* 2.8 53.1 + - + +
203D VAL* 5.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C GLN* 4.6 9.9 - - - +
226C GLN* 2.4 40.9 + - - +
227C LEU* 3.5 19.7 - - + +
229C ASP* 1.3 78.9 - - - +
231C VAL* 1.3 61.1 + - + +
232C SER 3.2 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C MET* 5.8 8.3 - - - -
227C LEU* 3.0 23.0 + - + +
228C LYS* 3.6 4.9 - - - +
229C ASP 2.8 3.6 + - - -
230C ASN* 1.3 76.0 - - + +
232C SER* 1.3 57.7 + - - +
238C THR* 3.7 20.0 + - + +
----------------------------------------------------------
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