Contacts of the helix formed by residues 223 - 232 (chain D) in PDB entry 2IZZ
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ASP* 3.6 23.5 + - - -
199C ARG* 3.7 16.4 + - - -
221D GLU 4.3 0.2 + - - -
222D GLN* 1.3 76.0 - - - +
224D PRO* 1.3 77.8 - - + +
225D GLY* 3.1 27.2 + - - +
226D GLN* 2.9 21.8 + - + +
227D LEU* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C PHE* 3.7 28.1 - - + +
185C LEU 5.2 0.4 - - - -
186C ASP* 4.1 11.7 - - + +
199C ARG* 3.8 21.8 - - - +
203C VAL* 5.1 8.5 - - + -
217D LEU* 4.0 33.9 - - + -
222D GLN 3.7 4.0 - - - +
223D HIS* 1.3 97.0 - - + +
225D GLY* 1.3 55.3 + - - +
227D LEU* 3.3 7.0 + - + +
228D LYS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ASP* 5.3 4.1 - - - -
223D HIS* 3.1 18.5 + - - -
224D PRO* 1.3 76.1 - - - +
226D GLN* 1.3 57.2 + - - +
228D LYS* 3.4 18.3 - - - +
229D ASP* 3.1 34.8 + - - +
251D ARG* 6.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D GLN* 3.9 30.0 - - + +
223D HIS* 2.9 24.6 + - + +
225D GLY* 1.3 73.5 - - - +
227D LEU* 1.3 65.9 + - - +
229D ASP* 3.2 19.6 + - - +
230D ASN* 2.8 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C PHE* 3.7 34.5 - - + -
216D MET* 4.3 18.1 - - + +
217D LEU* 3.6 41.3 - - + +
220D SER* 3.9 17.3 - - - +
222D GLN* 3.6 25.1 - - + +
223D HIS 3.1 9.8 + - - +
224D PRO* 3.6 6.3 - - + +
226D GLN* 1.3 73.0 - - - +
228D LYS* 1.3 66.2 + - - +
230D ASN* 3.2 24.7 + - - +
231D VAL* 3.5 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ALA* 4.6 7.5 - - + +
182C PHE* 3.6 17.1 - - + -
183C THR* 4.3 17.0 - - - +
224D PRO 3.0 13.7 + - - +
225D GLY* 3.4 17.9 + - - +
227D LEU* 1.3 76.7 - - - +
229D ASP* 1.3 88.9 + - - +
231D VAL* 3.1 12.5 + - - +
232D SER* 2.9 22.9 + - - -
239D ILE* 5.7 4.7 - - - -
242D LEU* 3.9 28.7 - - + -
251D ARG* 4.7 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D GLY 3.1 13.1 + - - +
226D GLN* 3.2 27.6 + - - +
228D LYS* 1.3 101.2 + - - +
230D ASN* 1.3 62.2 + - - +
232D SER* 3.4 22.5 + - - +
1272D EDO 3.9 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLN* 3.5 40.3 + - + +
124C THR* 4.7 5.0 - - + +
350C NAD 3.6 4.2 + - - -
216D MET* 6.1 2.3 - - + +
222D GLN* 4.1 12.1 + - - +
226D GLN* 2.8 39.1 + - - +
227D LEU* 3.2 26.8 + - + +
229D ASP* 1.3 75.1 - - - +
231D VAL* 1.3 55.4 + - + +
1272D EDO 2.6 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C THR* 3.7 30.1 - - + +
175C GLY 4.1 12.1 - - - +
176C SER 4.6 0.2 - - - +
178C PRO* 4.6 5.8 - - + -
179C ALA* 4.1 12.8 - - + +
182C PHE* 4.3 11.9 - - + -
350C NAD 3.5 15.4 - - - +
1277C EDO 3.1 18.2 + - - +
227D LEU 3.7 13.0 - - - +
228D LYS 3.1 8.3 + - - +
230D ASN* 1.3 77.3 - - + +
232D SER* 1.3 60.0 + - - +
233D SER* 3.3 6.7 + - - -
238D THR* 3.8 26.0 + - + +
1272D EDO 4.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LYS* 2.9 19.7 + - - +
229D ASP* 3.4 18.5 + - - +
230D ASN 3.5 0.2 - - - -
231D VAL* 1.3 74.9 - - - +
233D SER* 1.3 66.7 + - - +
234D PRO* 3.5 5.0 - - - +
238D THR* 3.9 10.0 - - - +
239D ILE* 4.4 23.4 - - - +
242D LEU* 3.4 23.9 - - - +
1272D EDO 4.2 2.9 + - - -
----------------------------------------------------------
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