Contacts of the helix formed by residues 222 - 234 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B ASP* 3.0 23.3 + - - +
221B TYR* 1.3 81.3 + - - +
223B TYR* 1.3 63.2 + - - +
224B ASP* 3.0 33.2 - - + +
225B SER* 2.9 28.7 + - - +
226B GLY 3.2 3.6 + - - -
249B GLU* 4.5 1.3 - - - -
250B MET* 3.6 7.9 - - - +
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Residues in contact with TYR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR* 1.3 73.4 - - - +
224B ASP* 1.3 71.7 + - - +
226B GLY* 3.0 14.6 + - - -
227B ILE* 3.3 26.8 + - + +
249B GLU* 3.6 21.5 - - + +
252B LEU* 3.5 21.5 - - + -
253B GLY* 3.3 41.9 - - - -
256B HIS* 2.7 28.6 + + - +
278I ARG* 5.6 0.9 - - - +
281I THR* 3.1 24.8 + - - -
282I MET* 3.7 39.3 - - + -
284I ARG* 2.9 18.1 + - - -
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR* 3.0 14.0 - - + +
223B TYR* 1.3 89.8 - - - +
225B SER* 1.3 58.7 + - - +
226B GLY 2.8 10.1 + - - -
227B ILE* 2.9 22.5 + - + +
228B GLU* 3.2 20.8 + - - +
281I THR* 5.3 2.3 + - - -
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B VAL* 5.1 0.3 - - - +
219B GLY* 3.3 12.9 - - - -
220B ASP* 2.7 48.4 + - - -
222B THR* 2.9 18.1 + - - +
224B ASP* 1.3 78.0 - - - +
226B GLY* 1.3 59.8 + - - +
228B GLU* 3.8 16.9 + - - +
229B ALA* 3.2 22.9 + - - +
250B MET* 3.8 4.7 - - - -
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Residues in contact with GLY 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B THR 3.2 7.2 + - - -
223B TYR 3.0 9.4 + - - -
224B ASP 2.8 1.4 - - - -
225B SER* 1.3 77.4 - - - +
227B ILE* 1.3 65.5 + - - +
229B ALA* 3.1 15.8 + - - +
230B VAL* 3.3 13.7 + - - +
250B MET* 3.5 26.9 - - - -
253B GLY 3.6 6.5 - - - -
254B VAL* 3.6 5.0 - - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TYR* 3.3 36.4 + - + +
224B ASP* 2.9 13.5 + - + +
226B GLY* 1.3 76.6 - - - +
228B GLU* 1.3 59.9 + - + +
230B VAL* 3.0 20.1 - - - +
231B GLU* 3.0 38.3 + - + +
253B GLY* 3.5 21.9 + - - +
257B GLY* 4.1 10.8 - - - +
260B ASP* 4.8 8.7 - - - +
284I ARG* 4.5 9.9 - - - +
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ASP* 3.2 20.3 + - + +
225B SER* 3.8 14.7 + - - +
227B ILE* 1.3 76.9 - - + +
229B ALA* 1.3 65.6 + - - +
231B GLU* 4.1 8.1 - - + +
232B LYS* 3.1 25.1 + - - +
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B VAL* 3.6 34.1 - - + -
217B VAL* 3.6 16.3 - - + +
218B GLU 5.8 0.4 - - - -
219B GLY* 5.5 3.4 - - - +
225B SER 3.2 16.0 + - - +
226B GLY 3.1 10.7 + - - +
228B GLU* 1.3 76.4 - - - +
230B VAL* 1.3 59.3 + - - +
232B LYS* 3.5 4.7 - - - +
233B LEU* 3.0 33.3 + - - +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B GLY 3.4 8.3 - - - +
227B ILE 3.0 17.9 - - - +
229B ALA* 1.3 76.2 - - - +
231B GLU* 1.3 64.5 + - - +
232B LYS 3.0 1.3 - - - -
233B LEU* 3.6 3.9 - - - +
234B LEU* 2.8 36.3 + - + +
243B ILE* 3.4 18.4 - - + -
254B VAL* 3.1 43.3 - - + +
257B GLY* 3.4 30.7 - - - -
258B ALA* 4.4 4.5 - - + +
269B LEU* 5.0 6.1 - - + -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ILE* 3.0 43.4 + - + +
228B GLU* 4.1 6.7 - - - +
229B ALA 3.6 0.2 - - - -
230B VAL* 1.3 77.8 - - + +
232B LYS* 1.3 65.8 + - - +
234B LEU* 3.2 5.9 + - - -
235B GLU* 3.4 13.1 + - - +
257B GLY 3.7 9.5 - - - +
260B ASP* 4.8 5.4 - - - +
261B ARG* 2.8 68.1 + - - +
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B VAL* 3.7 29.0 - - + +
228B GLU 3.1 17.9 + - - +
229B ALA* 3.5 5.2 - - - +
231B GLU* 1.3 78.1 - - - +
233B LEU* 1.3 56.2 + - + +
235B GLU* 2.8 44.7 + - + +
236B GLU* 3.6 13.0 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ALA* 3.8 26.2 - - + -
183B VAL* 3.8 15.0 - - + -
214B SER 3.8 13.2 - - - +
215B TYR* 4.4 4.0 - - + +
217B VAL* 3.5 26.7 - - + -
229B ALA 3.0 19.4 + - - +
230B VAL* 3.2 5.6 + - - +
232B LYS* 1.3 79.5 - - + +
234B LEU* 1.3 60.4 - - + +
235B GLU 3.1 2.0 + - - -
236B GLU* 3.5 28.2 - - + +
239B LYS* 4.2 2.1 - - - -
240B PRO* 3.6 22.4 - - + +
243B ILE* 3.5 30.5 - - + -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B VAL* 2.8 30.3 + - + +
232B LYS 2.9 1.0 + - - -
233B LEU* 1.3 79.6 - - + +
235B GLU* 1.3 59.3 + - - +
236B GLU 3.4 0.4 - - - +
239B LYS* 3.3 34.3 - - + +
240B PRO* 5.8 4.3 - - + +
243B ILE* 6.5 0.2 - - + -
258B ALA* 4.3 8.5 - - - -
261B ARG* 3.2 55.4 + - + +
263B LEU* 3.4 36.1 - - + -
269B LEU* 4.9 11.9 - - + -
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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