Contacts of the helix formed by residues 218 - 229 (chain A) in PDB entry 1I43
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 218 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 6.2 1.8 - - + -
217A VAL* 1.3 71.4 - - - +
219A ILE* 1.3 63.9 + - - +
220A GLU* 3.4 10.9 + - - +
221A LEU* 3.1 39.5 + - + +
222A VAL* 2.9 24.2 + - + +
350A ILE* 3.8 29.5 - - + +
353A LYS* 3.2 30.3 + - - +
354A GLN* 3.6 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 4.8 4.0 - - - +
217A VAL* 2.6 16.2 + - - +
218A ASP* 1.3 70.1 - - - +
220A GLU* 1.3 63.3 + - - +
222A VAL* 3.9 6.5 - - - +
223A SER* 2.9 40.9 + - - +
233A VAL* 5.6 0.2 - - + -
235A ILE* 4.1 26.2 - - + -
245A GLN* 4.0 20.0 - - - +
247A ALA* 3.8 24.5 - - + +
250A LEU* 3.5 38.8 - - + +
252A ALA* 4.0 8.1 - - + +
354A GLN* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASP* 3.3 8.6 + - - +
219A ILE* 1.3 81.2 - - - +
221A LEU* 1.3 66.5 + - - +
223A SER* 3.6 2.6 - - - -
224A LYS* 3.2 44.8 + - - +
250A LEU* 3.1 31.0 + - + +
353A LYS* 3.9 23.8 + - - +
354A GLN* 4.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A VAL* 4.0 33.7 - - + -
218A ASP* 3.1 31.3 + - + +
220A GLU* 1.3 75.7 - - - +
222A VAL* 1.3 70.7 + - + +
224A LYS* 2.7 25.3 + - + +
225A LEU* 3.1 30.0 + - + +
353A LYS* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO 5.9 0.7 - - - +
189A VAL* 5.5 9.0 - - + -
192A LEU* 3.8 24.4 - - + +
204A PHE* 3.3 37.0 - - + -
217A VAL* 3.4 27.6 - - + -
218A ASP* 2.9 18.1 + - + +
219A ILE* 3.9 4.3 - - - +
221A LEU* 1.3 75.9 - - + +
223A SER* 1.3 66.2 + - - +
225A LEU* 3.4 5.0 + - - +
226A CYS* 3.1 24.0 + - - -
233A VAL* 4.1 10.1 - - + -
235A ILE* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ILE* 2.9 24.9 + - - +
220A GLU 3.6 4.3 - - - -
222A VAL* 1.3 76.4 - - - +
224A LYS* 1.3 59.4 + - - +
226A CYS* 3.1 2.4 + - - +
227A HIS* 2.8 39.2 + - - -
233A VAL* 3.8 18.4 - - - +
251A GLY* 3.2 40.0 + - - -
252A ALA* 3.3 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 3.2 36.1 + - + +
221A LEU* 2.7 20.5 + - + +
223A SER* 1.3 75.6 - - - +
225A LEU* 1.3 67.7 + - + +
227A HIS* 4.0 5.2 - - - +
228A GLU* 3.1 30.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
189A VAL* 3.5 36.1 - - + +
192A LEU* 4.0 17.9 - - + -
193A GLU* 4.5 24.7 - - + +
196A LEU* 4.2 7.7 - - + +
221A LEU* 3.1 30.0 + - + +
222A VAL* 3.7 6.1 - - - +
224A LYS* 1.3 78.7 - - + +
226A CYS* 1.3 64.3 + - - +
228A GLU* 3.2 28.5 - - - +
229A LYS* 3.5 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 4.5 2.5 - - - -
196A LEU* 4.2 18.4 - - - -
201A VAL* 5.8 0.2 - - - -
204A PHE* 3.6 36.3 - - - -
222A VAL* 3.1 14.4 + - - +
223A SER 3.5 2.5 - - - +
225A LEU* 1.3 74.8 - - - +
227A HIS* 1.3 54.4 + - - +
228A GLU 2.9 4.3 - - - -
229A LYS* 2.7 24.9 + - - -
231A ALA* 3.0 36.8 + - + +
233A VAL* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A SER* 2.8 26.1 + - - +
224A LYS* 4.1 4.9 - - - +
226A CYS* 1.3 73.1 - - - +
228A GLU* 1.3 60.7 + - - +
229A LYS 3.2 0.2 - - - -
230A GLY* 3.3 11.2 + - - +
231A ALA 3.4 15.0 - - - +
232A LEU* 5.3 1.3 - - + -
233A VAL* 4.2 6.9 - - + +
251A GLY* 3.2 27.3 + - - -
253A ASP* 2.6 39.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LYS* 3.1 20.3 + - - +
225A LEU* 3.2 24.9 - - - +
226A CYS 2.9 0.6 + - - -
227A HIS* 1.3 76.7 - - - +
229A LYS* 1.3 81.2 + - + +
230A GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 3.7 50.3 - - + +
197A ASN* 3.4 29.0 + - - +
200A LYS* 5.5 7.8 - - - +
201A VAL 4.7 5.5 + - - +
225A LEU 3.9 9.9 - - - +
226A CYS 2.7 3.0 + - - +
228A GLU* 1.3 106.4 + - + +
230A GLY* 1.3 59.4 + - - +
231A ALA* 3.2 3.1 + - - +
----------------------------------------------------------
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