Contacts of the helix formed by residues 222 - 235 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220F ASP* 2.9 24.3 + - - +
221F TYR* 1.3 80.5 - - - +
223F TYR* 1.3 65.1 + - - +
224F ASP* 3.7 12.0 + - - +
225F SER* 2.8 43.5 + - - -
226F GLY 3.2 5.2 + - - -
249F GLU* 4.1 5.6 - - - -
250F MET* 3.8 6.2 - - - +
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Residues in contact with TYR 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F THR* 1.3 72.4 - - - +
224F ASP* 1.3 79.6 + - - +
226F GLY* 3.1 11.3 + - - -
227F ILE* 3.3 32.0 + - + +
249F GLU* 3.5 22.6 + - + +
250F MET* 4.5 0.2 - - - +
252F LEU* 3.7 11.7 - - + -
253F GLY* 3.3 40.4 - - - -
256F HIS* 2.9 37.5 - + - +
278P ARG* 6.1 0.2 - - + -
281P THR* 3.2 26.5 + - - -
282P MET* 3.5 39.7 - - + -
284P ARG* 4.4 9.2 + - - -
286P GLN* 5.1 3.3 + - - -
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Residues in contact with ASP 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F THR* 3.1 11.7 - - - +
223F TYR* 1.3 89.2 + - - +
225F SER* 1.3 55.2 + - - +
227F ILE* 2.7 44.6 + - + +
228F GLU* 3.3 19.1 + - - +
281P THR* 6.1 0.5 - - - -
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Residues in contact with SER 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F GLY* 4.2 7.1 - - - -
220F ASP* 2.7 47.5 + - - -
222F THR* 2.8 26.3 + - - -
224F ASP* 1.3 76.5 - - - +
226F GLY* 1.3 59.2 + - - +
228F GLU* 3.6 17.7 + - - +
229F ALA* 3.2 22.7 + - - +
250F MET* 3.4 6.0 - - - +
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Residues in contact with GLY 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F THR 3.2 3.8 + - - -
223F TYR 3.1 9.1 + - - -
224F ASP 2.9 1.6 - - - -
225F SER* 1.3 80.7 + - - +
227F ILE* 1.3 60.9 - - - +
229F ALA* 3.6 2.5 + - - +
230F VAL* 2.9 26.9 + - - +
250F MET* 3.7 26.0 - - - -
254F VAL* 2.9 18.6 - - - +
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Residues in contact with ILE 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F TYR* 3.3 38.6 + - + +
224F ASP* 2.7 24.4 + - + +
226F GLY* 1.3 76.5 - - - +
228F GLU* 1.3 66.2 + - + +
230F VAL* 3.0 18.0 + - - +
231F GLU* 3.2 28.7 + - - +
253F GLY* 3.4 19.7 - - - +
256F HIS* 5.7 0.4 - - + -
257F GLY* 4.0 18.8 - - - +
260F ASP* 5.4 4.3 - - - +
284P ARG* 6.3 1.1 - - - +
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Residues in contact with GLU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F ASP* 3.3 24.7 + - - +
225F SER* 3.8 14.2 + - - +
226F GLY 3.4 0.2 - - - -
227F ILE* 1.3 82.2 - - + +
229F ALA* 1.3 53.0 + - - +
231F GLU* 2.8 21.0 + - - +
232F LYS* 2.7 40.9 + - + +
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Residues in contact with ALA 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F VAL* 3.8 35.0 - - + -
217F VAL* 4.0 21.6 - - + +
219F GLY* 5.6 2.2 - - - -
225F SER 3.2 15.5 + - - +
226F GLY 3.7 6.3 - - - +
227F ILE 3.3 0.4 - - - -
228F GLU* 1.3 77.5 - - - +
230F VAL* 1.3 52.6 + - - +
232F LYS* 3.4 3.7 + - - +
233F LEU* 2.7 40.0 + - - +
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Residues in contact with VAL 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F GLY 2.9 22.2 - - - +
227F ILE* 3.0 11.7 - - - +
229F ALA* 1.3 71.4 - - - +
231F GLU* 1.3 57.3 + - - +
233F LEU* 4.0 6.3 - - - +
234F LEU* 2.7 56.7 + - + +
243F ILE* 3.9 15.7 - - + -
253F GLY 3.9 1.6 - - - +
254F VAL* 3.1 47.3 - - + +
257F GLY* 4.4 8.3 - - - -
258F ALA* 4.1 9.4 - - + -
269F LEU* 4.9 0.9 - - + -
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Residues in contact with GLU 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F ILE* 3.3 27.1 - - + +
228F GLU* 2.8 23.7 + - - +
230F VAL* 1.3 77.4 - - - +
232F LYS* 1.3 63.0 + - + +
234F LEU* 3.4 0.8 + - - -
235F GLU* 3.1 33.8 + - - +
257F GLY* 5.0 7.6 - - - +
261F ARG* 3.6 34.9 + - - +
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Residues in contact with LYS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F VAL* 5.0 13.0 - - + +
228F GLU* 2.7 22.3 + - + +
229F ALA* 3.8 6.1 - - - +
231F GLU* 1.3 74.0 - - + +
233F LEU* 1.3 59.4 + - - +
235F GLU* 3.0 53.7 + - - +
236F GLU* 4.5 2.8 - - - +
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Residues in contact with LEU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F ALA* 3.4 30.7 - - + -
182F PHE 5.2 0.2 - - - +
183F VAL* 3.9 20.6 - - + -
214F SER 4.3 9.0 - - - +
215F TYR* 4.3 9.5 - - + +
217F VAL* 3.5 25.5 - - + +
229F ALA 2.7 29.0 + - - +
230F VAL* 3.2 6.5 + - + +
232F LYS* 1.3 69.3 - - - +
234F LEU* 1.3 59.9 + - + +
235F GLU 2.9 8.9 + - - -
236F GLU* 3.1 26.6 - - - +
240F PRO* 4.2 14.7 - - + +
243F ILE* 3.5 30.5 - - + -
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Residues in contact with LEU 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F VAL* 2.7 42.6 + - + +
231F GLU 3.8 3.6 - - - +
233F LEU* 1.3 68.6 - - + +
235F GLU* 1.3 53.0 + - - +
236F GLU* 3.0 6.9 + - - -
239F LYS* 2.8 46.1 + - + +
240F PRO* 5.1 17.9 - - + +
243F ILE* 6.0 1.6 - - + -
258F ALA* 4.5 5.2 - - + -
261F ARG* 4.0 39.5 + - + +
263F LEU* 3.6 34.5 - - + -
269F LEU* 5.3 4.3 - - + -
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Residues in contact with GLU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F GLU* 3.1 26.9 + - - +
232F LYS* 3.0 47.7 - - + +
233F LEU 2.9 0.4 - - - -
234F LEU* 1.3 74.0 - - - +
236F GLU* 1.3 64.6 + - - +
239F LYS* 4.9 0.4 - - - +
261F ARG* 4.5 9.7 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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