Contacts of the helix formed by residues 208 - 216 (chain A) in PDB entry 1IZC
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 GLY 208 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLN* 3.7 8.7 - - - +
184A ILE 2.9 12.5 + - - -
185A GLU* 3.5 11.1 - - - +
207A PHE* 1.3 76.1 - - - +
209A PRO* 1.3 66.7 - - - +
210A GLY 3.4 0.2 + - - -
211A ASP 3.6 0.3 + - - -
212A TYR* 3.0 24.6 + - - +
2001A PYR 3.2 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.4 30.6 - - + +
208A GLY* 1.3 83.4 - - - +
210A GLY* 1.3 56.4 + - - +
212A TYR* 3.6 0.3 - - - +
213A MET* 2.8 46.5 + - + +
232A PHE* 4.0 21.1 - - + -
236A MET* 5.8 0.9 - - - -
2001A PYR 3.4 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PRO* 1.3 80.6 - - - +
211A ASP* 1.3 61.3 + - - -
213A MET* 3.3 12.3 + - - +
214A ILE* 3.1 31.3 + - - +
220A LEU* 5.2 5.3 - - - +
2001A PYR 3.0 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A HIS* 5.2 4.5 + - - -
125A HIS* 3.3 18.4 - - + +
185A GLU* 3.1 23.0 - - + +
209A PRO 3.5 0.2 - - - -
210A GLY* 1.3 74.4 - - - +
212A TYR* 1.3 63.1 + - - +
214A ILE* 3.3 15.7 + - - +
215A ASP* 3.0 24.8 + - - +
1001A MG 2.1 28.1 - - - -
2001A PYR 3.1 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU 3.3 11.6 + - - -
186A SER 3.9 11.9 - - - -
187A VAL* 4.2 19.5 - - + +
190A VAL* 3.7 31.2 - - + +
207A PHE* 3.7 15.3 - + + -
208A GLY 3.0 20.5 + - - +
209A PRO 3.6 2.7 - - - +
211A ASP* 1.3 77.7 - - - +
213A MET* 1.3 61.2 + - - +
215A ASP* 3.1 4.9 + - - +
216A ALA* 2.8 43.0 + - + +
218A LEU* 4.0 9.2 - - + -
231A THR* 3.3 30.8 + - - +
232A PHE* 3.8 28.0 - + - -
235A ALA* 3.5 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PRO* 2.8 46.1 + - + +
210A GLY* 3.7 10.1 - - - +
212A TYR* 1.3 75.0 - - + +
214A ILE* 1.3 61.4 + - - +
216A ALA* 3.3 1.2 + - - +
217A GLY 3.0 3.3 + - - -
218A LEU* 2.9 53.5 + - + +
219A ASP 5.1 1.6 - - - +
220A LEU* 4.1 29.2 - - + -
221A ASN 4.8 4.0 - - - +
232A PHE* 4.1 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLY 3.1 19.0 + - - +
211A ASP* 3.7 16.6 - - - +
213A MET* 1.3 75.0 - - - +
215A ASP* 1.3 65.4 + - - +
217A GLY* 3.1 13.6 + - - -
218A LEU 4.8 2.5 - - - +
220A LEU* 4.1 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU 4.6 0.4 - - - +
186A SER* 3.5 17.8 - - - -
187A VAL* 2.7 38.4 + - - +
188A LYS* 4.4 0.9 + - - +
211A ASP 3.0 17.7 + - - +
212A TYR 3.6 3.6 - - - +
214A ILE* 1.3 78.6 - - - +
216A ALA* 1.3 60.4 + - - +
217A GLY 3.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A VAL* 3.8 14.1 - - + +
212A TYR* 2.8 39.1 + - + +
213A MET 3.9 0.4 - - - +
215A ASP* 1.3 76.6 - - - +
217A GLY* 1.3 63.2 + - - +
218A LEU* 3.4 27.3 + - + +
231A THR* 4.9 4.8 - - + +
----------------------------------------------------------
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