Contacts of the helix formed by residues 223 - 239 (chain A) in PDB entry 1OIK
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 SER 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR* 1.3 77.1 - - - +
224A LEU* 1.3 58.7 + - - +
225A ALA* 3.6 6.4 + - - +
226A ASP* 3.1 32.9 + - - +
227A SER* 2.9 27.5 + - - -
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG* 6.2 1.8 - - - -
223A SER* 1.3 72.5 - - - +
225A ALA* 1.3 66.4 + - + +
227A SER* 3.6 6.7 - - - -
228A GLN* 3.0 54.3 + - + +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A SER* 3.3 6.5 + - - +
224A LEU* 1.3 83.8 - - + +
226A ASP* 1.3 65.2 + - - +
228A GLN* 3.3 15.1 + - - +
229A HIS* 3.1 37.2 + - + +
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Residues in contact with ASP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A TYR* 4.0 23.7 - - + -
223A SER* 3.1 22.3 + - - +
225A ALA* 1.3 76.1 - - - +
227A SER* 1.3 61.1 + - - +
229A HIS* 3.1 9.6 + - - +
230A LEU* 2.9 37.1 + - + +
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Residues in contact with SER 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG* 3.5 13.3 - - - +
219A ILE* 2.8 49.8 + - - +
222A TYR* 4.0 4.5 - - - +
223A SER 2.9 23.1 + - - -
224A LEU* 3.6 7.6 - - - -
226A ASP* 1.3 72.2 - - - +
228A GLN* 1.3 56.4 + - - +
230A LEU* 3.8 1.9 - - - -
231A PHE* 2.8 33.9 + - - +
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Residues in contact with GLN 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.0 46.6 + - + +
225A ALA* 3.5 15.3 - - - +
226A ASP 3.2 0.2 - - - -
227A SER* 1.3 75.8 - - - +
229A HIS* 1.3 61.1 + - + +
231A PHE* 3.6 6.5 + - - +
232A ALA* 2.9 29.8 + - - +
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Residues in contact with HIS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ALA* 3.1 31.1 + - + +
226A ASP* 3.7 10.4 + - - +
228A GLN* 1.3 78.6 - - + +
230A LEU* 1.3 64.9 + - + +
232A ALA* 3.3 7.5 + - + +
233A VAL* 3.1 28.7 + - + +
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 5.8 3.4 - - + -
154A LEU* 4.0 25.4 - - + -
158A LEU* 4.7 17.9 - - + -
219A ILE* 4.6 9.9 - - + -
222A TYR* 3.9 42.8 - - + -
226A ASP* 2.9 20.4 + - + +
227A SER 3.9 3.6 - - - +
229A HIS* 1.3 75.0 - - + +
231A PHE* 1.3 67.1 + - - +
233A VAL* 3.4 8.5 + - + +
234A LEU* 3.2 31.9 + - + +
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Residues in contact with PHE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LEU* 3.9 26.9 - - + -
213A GLY 3.6 18.8 - - - -
214A HIS* 5.5 0.9 - - - -
216A VAL* 3.6 37.9 - - + -
219A ILE* 4.7 10.2 - - + +
227A SER* 2.8 20.8 + - - +
228A GLN* 3.9 5.6 - - - +
230A LEU* 1.3 77.4 - - - +
232A ALA* 1.3 61.7 + - + +
234A LEU* 3.2 3.7 + - - +
235A GLN* 2.8 66.0 + - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A GLN 2.9 20.4 + - - +
229A HIS* 3.3 8.9 + - + +
231A PHE* 1.3 82.8 - - + +
233A VAL* 1.3 61.7 + - + +
235A GLN* 4.8 1.3 - - - -
236A GLY* 3.0 21.5 + - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 3.7 33.2 - - + -
229A HIS* 3.1 16.7 + - + +
230A LEU* 3.8 11.9 - - + +
231A PHE 3.2 0.4 - - - -
232A ALA* 1.3 77.1 - - + +
234A LEU* 1.3 70.9 + - + +
236A GLY* 3.8 0.7 - - - -
237A HIS* 3.0 38.9 + - + +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.9 32.3 - - + -
151A LEU* 4.2 20.6 - - + -
154A LEU* 6.2 0.7 - - + -
155A ALA* 4.4 9.2 - - + -
158A LEU* 4.0 27.6 - - + -
198A VAL* 4.0 20.2 - - + -
210A LEU* 3.8 9.4 - - + +
212A LEU* 3.5 19.7 - - + -
219A ILE* 6.1 1.8 - - + -
230A LEU* 3.2 19.7 + - + +
231A PHE* 4.1 1.6 - - - +
233A VAL* 1.3 79.1 - - + +
235A GLN* 1.3 64.3 + - - +
237A HIS* 3.2 16.1 + - - +
238A VAL* 3.2 15.2 + - - +
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TRP* 3.7 11.3 + - - +
212A LEU* 3.3 8.9 - - + +
213A GLY* 3.1 17.4 + - - -
231A PHE* 2.8 45.0 + - + +
232A ALA* 4.6 1.3 - - - +
234A LEU* 1.3 76.4 - - - +
236A GLY* 1.3 61.9 + - - +
238A VAL* 3.2 6.8 + - - +
239A THR* 3.1 46.2 + - + +
263A GLN* 2.9 41.4 + - - -
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Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ALA 3.0 21.8 + - - -
233A VAL 3.8 1.3 - - - -
235A GLN* 1.3 76.0 - - - +
237A HIS* 1.3 58.5 + - - +
239A THR* 3.6 7.4 + - - -
240A ARG* 3.1 27.7 + - - +
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Residues in contact with HIS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ALA* 3.8 10.3 - - + +
146A GLU* 2.6 34.2 + - + +
147A LEU* 3.6 34.0 - - + +
148A PRO* 5.2 4.9 - - + +
151A LEU* 4.9 4.4 - - - +
210A LEU* 5.0 0.2 - - + -
233A VAL* 3.0 38.1 + - + +
234A LEU 3.2 8.0 + - - +
236A GLY* 1.3 73.4 - - - +
238A VAL* 1.3 64.4 + - - +
239A THR 3.5 0.2 + - - -
240A ARG* 3.5 14.0 + - - +
243A ASN* 2.8 26.9 + - - -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA* 3.3 32.4 - - + +
139A ASN 4.9 0.4 + - - -
140A THR* 3.9 13.7 - - + -
143A ALA* 3.6 11.9 - - + -
210A LEU* 3.8 27.4 - - + -
212A LEU* 4.7 1.6 - - + -
234A LEU 3.2 13.9 + - - +
235A GLN* 3.2 12.7 + - - +
237A HIS* 1.3 81.0 - - - +
239A THR* 1.3 64.0 + - + +
240A ARG 3.5 0.5 + - - +
243A ASN* 3.7 12.0 - - - +
244A THR* 4.2 0.3 - - - +
263A GLN* 3.7 36.3 - - - +
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TRP* 3.6 42.0 - - + +
138A ALA* 4.8 0.4 - - - -
235A GLN* 3.1 41.2 + - + +
236A GLY* 3.6 8.5 + - - -
237A HIS 3.3 0.2 - - - -
238A VAL* 1.3 79.3 - - + +
240A ARG* 1.3 67.0 + - - +
241A LEU* 3.3 5.7 + - - +
244A THR* 4.0 12.0 - - - +
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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