Contacts of the helix formed by residues 219 - 226 (chain A) 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 MET 219 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLY* 3.4 35.4 - - - +
198A LEU 3.1 5.1 + - - +
199A ARG* 3.6 26.2 - - + -
218A SER* 1.3 74.5 - - - +
220A ARG* 1.3 57.0 + - - +
222A ILE* 3.2 8.4 + - + +
223A ASP* 2.8 35.5 + - - +
269A GLY 3.5 14.4 - - - +
270A GLY 3.5 13.7 - - - -
271A LEU* 3.8 18.6 - - + +
274C ARG* 3.3 42.0 - - - +
327C ARG* 3.8 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 3.1 10.6 + - - +
219A MET* 1.3 76.9 - - - +
221A ASP* 1.3 68.9 + - - +
223A ASP* 3.2 4.4 + - - +
224A ARG* 3.1 46.5 + - - +
278C TYR* 3.4 19.6 - - + -
281C GLU* 3.1 40.8 + - - +
282C GLU* 2.6 31.7 + - - -
285C ASN* 3.6 14.7 - - - +
327C ARG* 3.7 31.7 - - + +
328C GLU* 5.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 3.5 12.7 - - - +
217A PHE* 3.4 25.9 - - + -
218A SER* 2.9 35.1 + - - +
220A ARG* 1.3 78.9 + - - +
222A ILE* 1.3 58.4 + - - +
224A ARG* 3.2 14.8 + - - +
225A LEU* 2.8 40.7 + - + +
230A VAL* 4.6 0.9 - - - -
328C GLU* 4.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A ILE* 3.9 18.8 - - + -
197A GLY 4.2 3.6 - - - +
217A PHE* 4.5 3.1 - - + +
218A SER 3.0 14.6 + - - +
219A MET* 3.2 17.7 + - - +
221A ASP* 1.3 75.0 - - - +
223A ASP* 1.3 61.0 + - - +
226A GLY* 2.8 27.8 + - - -
227A ILE* 4.2 22.0 - - + +
230A VAL* 3.9 22.0 - - + -
271A LEU* 3.7 26.7 - - + -
275A GLU* 3.4 28.5 - - - +
274C ARG* 3.6 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET 2.8 13.8 + - - +
220A ARG* 3.4 8.1 - - - +
222A ILE* 1.3 75.7 - - - +
224A ARG* 1.3 61.2 + - - +
226A GLY 4.6 0.7 + - - -
227C ILE* 4.8 17.0 + - + +
228C GLN* 5.0 3.3 + - - +
274C ARG* 2.7 48.9 + - - +
275C GLU* 5.9 0.7 - - - -
278C TYR* 4.3 14.6 - - + -
327C ARG* 2.9 37.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.1 43.9 + - - +
221A ASP* 3.6 15.0 + - - +
223A ASP* 1.3 79.8 - - - +
225A LEU* 1.3 69.1 + - + +
226A GLY 3.5 0.4 + - - -
228C GLN* 3.1 50.6 - - - +
232C GLU* 5.4 0.4 + - - -
278C TYR* 3.0 45.9 + - + +
282C GLU* 5.0 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A PHE* 4.0 30.3 - - + -
221A ASP* 2.8 24.3 + - + +
224A ARG* 1.3 82.3 - - + +
226A GLY* 1.3 70.4 + - - +
229A LYS* 3.6 36.6 + - + +
230A VAL* 4.1 6.5 - - + +
233A ARG* 3.7 46.2 - - - +
228C GLN* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 2.8 19.9 + - - -
223A ASP 4.5 0.6 - - - -
224A ARG 3.5 1.4 - - - -
225A LEU* 1.3 83.6 - - - +
227A ILE* 1.3 65.8 + - - -
228A GLN 3.3 3.9 + - - -
229A LYS 3.4 0.3 + - - -
230A VAL* 3.1 21.6 + - - +
223B ASP 6.0 0.9 - - - -
----------------------------------------------------------
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