Contacts of the helix formed by residues 202 - 212 (chain C) in PDB entry 4IXU
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 202 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 2.7 26.1 + - - +
155C SER* 4.8 2.9 + - - -
200C ASP 4.9 0.7 - - - +
201C VAL* 1.3 75.2 - - - +
203C PRO* 1.3 76.5 - - + +
204C PRO* 3.9 11.9 - - + -
205C GLU* 2.8 33.4 + - + +
206C HIS* 3.0 10.4 + - - +
406C 38I 2.9 64.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLY* 4.4 15.5 - - - +
201C VAL 4.3 2.2 - - - +
202C ASP* 1.3 83.3 - - + +
204C PRO* 1.3 73.1 - - + +
206C HIS* 3.1 5.2 + - + +
207C PHE* 3.0 21.2 + - - +
406C 38I 3.9 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 3.7 14.8 - - - +
153C THR* 3.6 39.3 - - + +
202C ASP* 3.6 6.3 - - + -
203C PRO* 1.3 99.4 - - + +
205C GLU* 1.3 56.5 + - - +
207C PHE* 3.4 9.2 + - + +
208C ILE* 3.0 33.6 + - - +
406C 38I 4.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ALA* 3.7 7.7 + - + +
147C ASP* 3.1 13.7 + - - -
148C ILE* 3.0 43.0 + - + +
149C ASN* 3.4 33.1 + - - +
161C GLY 4.1 0.3 - - - +
200C ASP 4.4 1.7 - - - +
201C VAL* 3.7 14.2 - - + -
202C ASP* 2.8 38.5 + - + +
204C PRO* 1.3 74.6 - - - +
206C HIS* 1.3 61.6 + - - +
208C ILE* 3.1 4.5 + - - +
209C LEU* 2.8 34.1 + - - +
406C 38I 3.9 6.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 3.1 30.4 + - + +
329B GLY* 3.6 27.6 + - - +
201C VAL* 3.6 6.0 - - + +
202C ASP 3.0 9.7 + - - +
203C PRO 3.5 8.0 + - - +
205C GLU* 1.3 76.5 - - - +
207C PHE* 1.3 65.6 + - - +
209C LEU* 3.3 6.2 + - + +
210C LYS* 2.9 55.5 + - + +
216C TYR* 4.2 13.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LYS* 5.9 4.5 - - - -
203C PRO 3.0 12.9 + - - +
204C PRO* 3.5 14.1 - - + +
206C HIS* 1.3 80.0 + - - +
208C ILE* 1.3 62.0 + - + +
210C LYS* 4.0 3.4 - - + +
211C ASN* 2.7 70.9 + - + +
212C TYR* 5.1 3.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C ILE* 3.4 50.3 - - + +
149C ASN* 5.0 0.2 - - - -
150C THR* 4.2 18.8 - - + -
153C THR* 4.8 11.0 - - + +
171C LEU* 4.1 14.4 - - + -
204C PRO 3.0 22.7 + - - +
205C GLU* 3.1 8.3 + - - +
207C PHE* 1.3 85.6 - - + +
209C LEU* 1.3 64.3 + - - +
212C TYR* 3.0 51.3 + - + +
214C ILE* 4.3 1.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU 5.4 1.6 - - - +
146C ALA* 4.2 9.9 - - + -
148C ILE* 4.4 11.7 - - + -
195C TYR* 3.8 29.6 - - + -
198C LEU* 4.0 24.5 - - + -
201C VAL* 4.3 13.9 - - + -
205C GLU 2.8 23.5 + - - +
206C HIS* 3.7 7.2 - - + +
208C ILE* 1.3 72.5 - - - +
210C LYS* 1.3 64.3 + - + +
213C ASP* 3.2 3.1 + - - -
214C ILE* 3.0 50.8 + - + +
216C TYR* 4.1 26.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLU* 5.1 2.3 + - - -
206C HIS* 2.9 45.8 + - + +
207C PHE* 4.0 3.6 - - + +
209C LEU* 1.3 77.0 - - + +
211C ASN* 1.3 64.6 + - - +
213C ASP* 3.1 16.3 + - - +
216C TYR* 3.3 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LYS* 5.7 2.2 - - - +
207C PHE* 2.7 51.9 + - + +
210C LYS* 1.3 74.7 - - - +
212C TYR* 1.3 94.4 + - + +
213C ASP* 3.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C GLU* 3.3 43.5 + - + -
171C LEU* 3.7 24.8 - - + +
173C ASP* 5.0 0.9 + - - -
174C LYS* 3.6 34.8 + - - +
190C SER* 3.4 23.1 + - - +
207C PHE* 5.1 4.0 - + - -
208C ILE* 3.0 41.9 + - + +
211C ASN* 1.3 100.4 + - + +
213C ASP* 1.3 70.9 + - - +
214C ILE* 3.3 15.1 + - + -
----------------------------------------------------------
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