Contacts of the helix formed by residues 218 - 229 (chain K) 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 K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K VAL* 6.0 2.0 - - + -
217K VAL* 1.3 71.5 - - - +
219K ILE* 1.3 62.6 + - - +
220K GLU* 3.4 11.3 + - - +
221K LEU* 3.0 42.3 + - + +
222K VAL* 2.9 24.0 + - + +
350K ILE* 3.7 32.7 - - + +
353K LYS* 3.0 31.8 + - - +
354K GLN* 3.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 219 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208K SER* 4.5 3.8 - - - +
217K VAL* 2.6 15.2 + - + +
218K ASP* 1.3 69.2 - - - +
220K GLU* 1.3 57.8 + - - +
222K VAL* 4.0 5.5 - - - +
223K SER* 2.8 43.8 + - - +
233K VAL* 5.7 0.4 - - + -
235K ILE* 4.1 25.8 - - + -
245K GLN* 4.2 20.9 - - - +
247K ALA* 3.9 22.2 - - + +
250K LEU* 3.3 44.9 - - + +
252K ALA* 4.2 8.1 - - + +
354K GLN* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 220 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218K ASP* 3.3 8.2 + - - +
219K ILE* 1.3 79.1 - - - +
221K LEU* 1.3 63.8 + - - +
223K SER* 3.7 2.9 - - - -
224K LYS* 3.3 44.0 + - - +
250K LEU* 3.1 33.3 - - + +
353K LYS* 4.0 21.2 + - - +
354K GLN* 4.6 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 221 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K VAL* 4.0 30.3 - - + -
218K ASP* 3.0 35.0 + - + +
220K GLU* 1.3 73.2 - - - +
222K VAL* 1.3 70.1 + - + +
223K SER 3.0 1.3 - - - -
224K LYS* 2.8 23.7 + - + +
225K LEU* 3.1 36.4 + - + +
353K LYS* 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 222 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K PRO 5.9 0.9 - - - +
189K VAL* 5.4 9.4 - - + -
192K LEU* 3.6 24.0 - - + +
204K PHE* 3.2 38.4 - - + -
217K VAL* 3.5 26.7 - - + -
218K ASP* 2.9 17.6 + - + +
219K ILE* 4.0 4.0 - - - +
221K LEU* 1.3 76.5 - - + +
223K SER* 1.3 65.2 + - - +
225K LEU* 3.5 5.8 + - + +
226K CYS* 3.1 24.5 + - - -
233K VAL* 4.6 7.0 - - + -
235K ILE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 223 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219K ILE* 2.8 23.4 + - - +
220K GLU 3.7 5.6 - - - -
222K VAL* 1.3 77.5 - - - +
224K LYS* 1.3 56.5 + - - +
226K CYS* 3.3 2.4 + - - +
227K HIS* 2.9 39.7 + - - -
233K VAL* 3.9 19.0 - - - +
251K GLY* 3.3 39.0 - - - -
252K ALA* 3.3 8.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 224 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220K GLU* 3.3 34.8 + - - +
221K LEU* 2.8 19.0 + - + +
223K SER* 1.3 74.8 - - - +
225K LEU* 1.3 67.9 + - + +
227K HIS* 3.3 6.3 + - - +
228K GLU* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 225 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189K VAL* 3.5 36.3 - - + +
192K LEU* 4.0 18.8 - - + -
193K GLU* 4.7 25.6 - - + +
196K LEU* 4.2 8.7 - - + +
221K LEU* 3.1 31.3 + - + +
222K VAL* 3.8 4.5 - - - +
224K LYS* 1.3 77.7 - - + +
226K CYS* 1.3 64.4 + - - +
228K GLU* 3.2 27.1 - - - +
229K LYS* 3.5 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 226 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192K LEU* 4.3 4.7 - - - -
196K LEU* 3.9 23.1 - - - -
201K VAL* 5.8 0.2 - - - -
204K PHE* 3.7 34.5 - - - -
222K VAL 3.1 18.3 + - - +
223K SER 3.6 2.9 - - - +
225K LEU* 1.3 75.2 - - - +
227K HIS* 1.3 54.3 - - - +
228K GLU 2.9 4.0 - - - -
229K LYS* 2.8 24.6 + - - +
230K GLY 3.0 8.7 + - - -
231K ALA* 3.1 25.6 + - + +
233K VAL* 3.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 227 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223K SER* 2.9 29.2 + - - +
224K LYS* 3.9 5.5 - - - +
226K CYS* 1.3 73.4 - - - +
228K GLU* 1.3 61.0 + - - +
229K LYS 3.2 0.2 - - - -
230K GLY* 3.5 9.4 + - - +
231K ALA 3.6 14.6 - - - -
232K LEU* 5.3 0.9 - - + -
233K VAL* 4.4 4.9 - - + +
251K GLY* 3.3 27.1 - - - -
253K ASP* 2.8 37.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224K LYS* 3.0 17.2 + - - +
225K LEU* 3.2 21.7 - - - +
226K CYS 2.9 0.4 + - - -
227K HIS* 1.3 79.2 - - - +
229K LYS* 1.3 80.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 229 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196K LEU* 3.6 49.8 - - + +
197K ASN* 3.3 31.9 + - - +
200K LYS* 5.6 7.4 - - - +
201K VAL 4.9 4.3 + - - +
225K LEU 3.9 10.5 - - - +
226K CYS 2.8 2.6 + - - -
228K GLU* 1.3 100.6 + - + +
230K GLY* 1.3 60.9 + - - +
231K ALA 3.4 1.0 + - - -
----------------------------------------------------------
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