Contacts of the helix formed by residues 222 - 234 (chain I) in PDB entry 1SXG
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 THR 222 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 6.4 2.0 - - - -
220I ASP* 2.5 39.6 + - - +
221I TYR* 1.3 81.6 - - - +
223I TYR* 1.3 65.3 + - - +
224I ASP* 3.6 7.0 + - - +
225I SER* 2.7 43.0 + - - -
226I GLY 3.2 2.6 + - - -
249I GLU* 4.4 4.3 - - - -
250I MET* 3.6 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 223 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 5.5 6.3 - - + +
281B THR* 3.1 26.4 + - + -
282B MET* 3.6 41.1 - - + -
284B ARG* 3.1 16.0 + - - -
221I TYR 4.1 0.8 + - - -
222I THR* 1.3 73.5 - - - +
224I ASP* 1.3 73.8 + - - +
226I GLY* 2.8 22.5 + - - -
227I ILE* 3.3 22.3 + - + +
249I GLU* 3.4 23.6 + - + +
252I LEU* 3.5 14.6 - - + -
253I GLY* 3.3 34.5 - - - -
256I HIS* 3.0 34.2 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 224 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR* 4.8 10.0 - - - +
222I THR* 3.2 6.9 + - - +
223I TYR* 1.3 92.0 - - - +
225I SER* 1.3 61.6 + - - +
226I GLY 2.8 6.6 + - - -
227I ILE* 3.2 13.0 + - - +
228I GLU* 3.1 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 225 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I VAL* 4.9 0.3 - - - +
218I GLU 5.1 0.7 - - - +
219I GLY* 3.5 13.0 - - - -
220I ASP* 3.0 48.8 + - - -
222I THR* 2.7 27.3 + - - -
224I ASP* 1.3 72.9 - - - +
226I GLY* 1.3 56.0 + - - +
228I GLU* 4.0 9.2 - - - +
229I ALA* 3.3 23.2 + - - +
250I MET* 3.7 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 226 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I VAL* 5.2 0.7 - - - -
222I THR 3.2 3.0 + - - -
223I TYR 2.8 9.9 + - - -
224I ASP 2.8 3.2 - - - -
225I SER* 1.3 80.3 + - - +
227I ILE* 1.3 64.4 + - - +
228I GLU 3.1 0.7 - - - -
229I ALA* 3.1 14.0 + - - +
230I VAL* 3.3 18.0 + - - +
250I MET* 3.8 22.0 - - - -
253I GLY 3.4 6.9 - - - -
254I VAL* 3.8 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B ARG* 5.1 1.6 - - - +
223I TYR* 3.3 53.6 + - + +
224I ASP* 3.2 15.7 + - - +
226I GLY* 1.3 73.7 - - - +
228I GLU* 1.3 68.3 + - - +
229I ALA 3.0 0.9 + - - -
230I VAL* 3.0 4.2 + - - +
231I GLU* 2.9 45.3 + - + +
253I GLY 3.2 16.2 + - - +
257I GLY* 3.8 22.4 - - - +
260I ASP* 4.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I VAL* 5.1 0.7 - - - +
224I ASP* 3.1 18.0 + - + +
225I SER* 4.0 9.2 - - - +
227I ILE* 1.3 90.7 - - + +
229I ALA* 1.3 58.4 + - - +
231I GLU* 4.1 14.6 - - - +
232I LYS* 3.6 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I VAL* 3.4 39.7 - - + -
217I VAL* 4.1 20.2 - - + +
218I GLU 5.5 1.8 - - - +
225I SER 3.3 13.3 + - - +
226I GLY 3.1 6.7 + - - +
227I ILE 3.0 1.0 + - - -
228I GLU* 1.3 77.5 - - - +
230I VAL* 1.3 64.3 + - - +
232I LYS* 3.7 2.9 + - - +
233I LEU* 3.2 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I VAL* 5.6 1.1 - - + -
226I GLY 3.3 7.0 - - - +
227I ILE 3.0 3.3 + - - +
229I ALA* 1.3 74.1 - - - +
231I GLU* 1.3 55.2 + - - +
232I LYS 3.1 1.8 - - - -
233I LEU* 2.8 8.1 + - + +
234I LEU* 2.5 60.9 + - + +
243I ILE* 5.3 5.6 - - + -
253I GLY 4.2 2.2 - - - +
254I VAL* 3.1 53.4 - - + +
257I GLY 4.6 1.1 - - - -
258I ALA* 3.8 25.8 - - + +
269I LEU* 4.8 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 231 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I ILE* 2.9 37.8 + - + +
228I GLU* 4.3 17.3 - - - +
229I ALA 3.4 0.2 - - - -
230I VAL* 1.3 77.0 - - - +
232I LYS* 1.3 60.5 + - - +
233I LEU 3.5 0.2 + - - -
234I LEU* 3.6 6.2 + - - +
235I GLU* 3.6 25.7 + - - +
257I GLY* 3.3 22.9 - - - +
260I ASP* 4.9 4.2 - - - +
261I ARG* 3.5 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I VAL* 4.4 25.1 - - + -
228I GLU 3.6 16.5 + - - +
229I ALA* 3.9 5.4 - - - +
230I VAL 3.1 0.8 - - - -
231I GLU* 1.3 81.2 - - - +
233I LEU* 1.3 60.4 + - - +
235I GLU* 3.8 12.5 + - - +
236I GLU* 4.0 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181I ALA* 3.5 25.8 - - + -
183I VAL* 4.4 14.6 - - + -
214I SER 3.4 26.2 - - - +
215I TYR* 4.1 10.8 - - + +
217I VAL* 3.4 20.4 - - + -
229I ALA 3.2 19.4 + - - +
230I VAL* 2.8 9.0 + - + +
232I LYS* 1.3 76.2 - - - +
234I LEU* 1.3 58.3 + - + +
235I GLU 2.8 11.4 + - - -
236I GLU* 3.2 18.0 + - - +
239I LYS* 4.0 2.6 - - - -
240I PRO* 3.6 29.8 - - + +
243I ILE* 3.9 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I VAL* 2.5 42.9 + - + +
231I GLU* 3.6 0.6 + - - +
232I LYS 3.5 0.4 - - - -
233I LEU* 1.3 70.7 - - - +
235I GLU* 1.3 64.8 + - - +
236I GLU 3.8 0.4 - - - -
239I LYS* 2.7 49.8 + - + +
240I PRO* 5.7 3.8 - - + +
257I GLY 4.3 0.7 - - - +
258I ALA* 4.0 11.0 - - - +
261I ARG* 3.1 54.6 + - + +
263I LEU* 3.6 26.9 - - + -
269I LEU* 5.4 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