Contacts of the helix formed by residues 218 - 230 (chain B) in PDB entry 1S0O
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 GLY 218 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B LYS* 2.8 23.0 + - - -
215B GLY 4.9 0.2 + - - -
216B MET 3.8 0.8 - - - -
217B ILE* 1.3 75.2 - - - +
219B GLU* 1.3 66.0 + - - -
220B ALA 3.4 2.6 + - - -
221B LYS 4.1 0.4 - - - -
222B ALA* 3.1 24.6 + - - +
1912F T 3.6 18.2 - - - -
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Residues in contact with GLU 219 (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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210B PHE* 4.8 2.1 - - + -
214B LYS* 2.9 52.9 + - + +
218B GLY* 1.3 70.3 - - - +
220B ALA* 1.3 58.4 + - - +
222B ALA* 3.9 1.1 - - - +
223B LYS* 2.9 73.9 + - + +
1912F T 3.1 9.4 + - - +
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Residues in contact with ALA 220 (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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219B GLU* 1.3 75.1 - - - +
221B LYS* 1.3 57.6 + - - +
223B LYS* 3.9 6.0 - - - +
224B TYR* 3.0 28.4 + - - +
1911F C 3.2 50.3 - - - +
1912F T 2.9 13.3 + - - +
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Residues in contact with LYS 221 (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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185B GLY* 3.2 24.2 + - - -
186B ILE* 4.5 14.6 - - + -
190B THR* 4.2 17.3 + - + +
217B ILE* 3.6 34.8 - - + +
218B GLY 3.5 1.6 + - - -
219B GLU 3.4 0.2 - - - -
220B ALA* 1.3 77.5 - - - +
222B ALA* 1.3 67.2 + - - +
224B TYR* 3.2 12.5 + - + +
225B LEU* 3.0 27.7 + - - +
1810E A 4.5 12.1 + - - -
1811E C 3.7 22.0 + - - -
1911F C 5.0 8.0 + - - -
1912F T 4.5 0.6 + - - -
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Residues in contact with ALA 222 (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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210B PHE* 4.1 11.2 - - + -
213B LEU* 3.6 29.8 - - + -
214B LYS* 4.1 13.9 - - - +
217B ILE* 3.5 10.2 - - + +
218B GLY 3.1 17.7 + - - +
219B GLU 3.9 2.9 - - - +
221B LYS* 1.3 78.0 - - - +
223B LYS* 1.3 64.3 + - - +
224B TYR 3.2 0.2 + - - -
225B LEU* 3.9 1.9 - - - +
226B ILE* 3.0 30.4 + - - +
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Residues in contact with LYS 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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210B PHE* 3.9 22.9 - - + -
219B GLU* 2.9 58.0 + - + +
220B ALA* 3.9 5.6 - - - +
222B ALA* 1.3 75.5 - - - +
224B TYR* 1.3 57.5 + - - +
226B ILE* 3.7 5.2 + - - +
227B SER* 3.1 30.0 + - - -
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Residues in contact with TYR 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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149B VAL* 3.6 18.8 - - + +
183B VAL* 3.8 12.8 - - + +
184B PRO* 2.8 32.4 + - - +
185B GLY* 5.0 3.1 - - - -
186B ILE* 5.0 3.1 - - + -
220B ALA 3.0 19.5 + - - +
221B LYS* 3.3 17.3 - - + +
222B ALA 3.1 0.2 - - - -
223B LYS* 1.3 76.5 - - - +
225B LEU* 1.3 72.7 + - + +
227B SER* 2.8 21.9 + - - -
228B LEU* 3.2 26.6 + - + +
233B TYR* 3.7 31.6 - + - -
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Residues in contact with LEU 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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180B ILE* 4.1 18.2 - - + -
183B VAL* 4.2 7.6 - - + -
186B ILE* 3.8 34.5 - - + -
194B LEU* 4.1 11.2 - - + -
202B LEU* 3.8 23.4 - - + +
205B THR* 4.1 18.4 - - + -
213B LEU* 5.4 0.4 - - + -
217B ILE* 3.9 26.2 - - + -
221B LYS 3.0 14.7 + - - +
222B ALA* 4.0 3.6 - - - +
224B TYR* 1.3 85.2 - - + +
226B ILE* 1.3 60.7 + - - +
228B LEU* 3.1 5.5 + - + +
229B ALA* 2.8 28.1 + - - +
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Residues in contact with ILE 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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205B THR* 4.0 28.0 - - - +
206B LEU* 4.1 6.1 - - + -
208B ILE 6.0 0.7 - - - +
210B PHE* 3.5 36.1 - - + -
213B LEU* 4.0 15.3 - - + -
222B ALA 3.0 21.0 + - - +
223B LYS* 3.9 4.9 - - - +
225B LEU* 1.3 75.4 - - - +
227B SER* 1.3 54.3 + - - +
229B ALA* 2.9 3.3 + - - +
230B ARG* 2.7 74.7 + - - +
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Residues in contact with SER 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 LYS 3.1 15.7 + - - -
224B TYR* 2.8 21.5 + - - -
226B ILE* 1.3 77.6 - - - +
228B LEU* 1.3 57.6 + - - +
230B ARG* 3.6 6.7 + - - +
231B ASP 3.2 1.4 + - - -
232B GLU* 2.7 39.7 + - - -
233B TYR* 3.1 29.6 + - - -
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Residues in contact with LEU 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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147B ASN* 4.7 0.2 - - - +
149B VAL* 3.9 23.3 - - + -
150B PHE* 4.0 19.3 - - + -
175B ILE* 3.4 12.7 - - - +
183B VAL* 3.8 20.4 - - + -
202B LEU* 4.2 19.5 - - + -
224B TYR* 3.2 41.9 + - + +
225B LEU* 3.1 8.6 + - - +
226B ILE 3.1 0.6 - - - -
227B SER* 1.3 79.6 + - - +
229B ALA* 1.3 59.7 + - - +
231B ASP* 2.9 20.4 + - - +
233B TYR* 3.5 32.5 - - + -
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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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175B ILE* 3.6 26.5 - - - +
202B LEU* 3.3 31.6 - - - +
203B VAL* 4.5 0.7 - - - +
205B THR* 3.5 7.4 - - - +
206B LEU* 3.6 25.0 - - + +
225B LEU 2.8 13.1 + - - +
226B ILE 3.4 7.2 - - - +
228B LEU* 1.3 78.7 - - - +
230B ARG* 1.3 57.5 + - - +
231B ASP 3.2 2.8 + - - -
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Residues in contact with ARG 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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206B LEU* 3.7 20.6 - - + +
226B ILE* 2.7 45.6 + - - +
227B SER* 4.0 4.0 - - - +
229B ALA* 1.3 70.3 - - - +
231B ASP* 1.3 71.0 + - - +
232B GLU* 3.2 42.1 + - + +
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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