Contacts of the helix formed by residues 205 - 218 (chain A) in PDB entry 1OH7
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 GLU 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.7 3.9 + - - +
202A TRP* 3.2 22.8 + - + +
203A GLU 3.5 1.8 - - - +
204A PHE* 1.3 77.4 - - - +
206A ILE* 1.3 72.6 + - - +
207A ASP* 3.2 36.0 + - + +
208A THR* 3.7 20.3 + - - +
209A ALA* 3.2 18.9 + - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A PHE 3.3 2.6 + - - -
205A GLU* 1.3 81.3 + - - +
207A ASP* 1.3 70.5 + - - +
209A ALA* 3.1 2.1 + - + -
210A ARG* 3.0 49.8 + - + +
231A PRO* 3.6 40.8 - - + +
234A LEU* 3.7 22.2 - - + -
235A CYS* 3.6 15.0 - - - +
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Residues in contact with ASP 207 (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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205A GLU* 3.2 18.0 + - + +
206A ILE* 1.3 83.6 - - - +
208A THR* 1.3 58.5 + - - +
210A ARG* 3.6 11.1 + - - +
211A GLN* 3.1 26.5 + - - +
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Residues in contact with THR 208 (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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202A TRP* 5.0 8.2 + - + +
203A GLU 5.7 0.7 - - - +
205A GLU* 3.7 24.4 + - - +
207A ASP* 1.3 77.1 - - - +
209A ALA* 1.3 59.4 + - - +
211A GLN* 3.5 10.6 - - - +
212A GLN* 2.9 34.1 + - + +
242A GLN* 3.7 27.4 - - - +
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Residues in contact with ALA 209 (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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203A GLU 5.7 0.7 - - - +
205A GLU 3.2 13.9 + - - +
206A ILE* 3.1 12.1 + - + +
208A THR* 1.3 74.4 - - - +
210A ARG* 1.3 67.4 + - - +
212A GLN* 4.7 1.3 - - - -
213A LEU* 3.0 32.9 + - + +
234A LEU* 3.5 31.2 - - + +
235A CYS* 4.3 4.7 - - - +
238A GLY* 3.7 20.4 - - - -
242A GLN* 5.9 0.4 - - - -
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Residues in contact with ARG 210 (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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206A ILE* 3.0 34.4 + - + +
207A ASP* 3.9 11.2 + - - +
209A ALA* 1.3 75.2 - - - +
211A GLN* 1.3 56.1 + - - +
213A LEU* 4.2 0.4 - - - +
214A ASN* 2.5 48.2 + - - +
222A LEU* 4.6 8.4 - - + +
228A GLU* 3.1 63.0 + - - +
231A PRO* 4.2 19.8 - - - +
234A LEU* 3.5 26.6 - - + +
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Residues in contact with GLN 211 (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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207A ASP 3.1 18.9 + - - +
208A THR* 3.5 11.5 - - - +
209A ALA 3.1 0.2 - - - -
210A ARG* 1.3 73.5 - - - +
212A GLN* 1.3 90.5 + - - +
213A LEU 3.2 0.3 + - - -
214A ASN* 4.0 2.6 - - - +
215A LEU* 2.9 41.4 + - - +
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Residues in contact with GLN 212 (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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208A THR* 2.9 25.3 + - + +
209A ALA* 4.1 4.5 - - - +
211A GLN* 1.3 101.8 + - - +
213A LEU* 1.3 58.7 + - + +
215A LEU* 3.3 12.2 - - - +
216A GLN* 2.9 30.7 + - - +
238A GLY* 5.0 3.8 - - - +
241A LEU* 3.8 16.9 - - + +
242A GLN* 3.8 30.5 - - + +
245A LYS* 3.4 32.5 + - + +
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Residues in contact with LEU 213 (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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155A PHE* 3.6 36.1 - - + -
209A ALA 3.0 27.3 + - - +
210A ARG 4.2 1.1 - - - +
212A GLN* 1.3 68.9 - - + +
214A ASN* 1.3 60.8 + - - +
216A GLN* 3.2 1.4 + - - +
217A PHE* 2.8 55.4 + - + -
222A LEU* 4.3 7.9 - - + -
234A LEU* 3.6 35.0 - - + +
237A ALA* 4.0 18.4 - - + +
238A GLY* 4.2 4.3 - - - +
241A LEU* 3.6 18.2 - - + -
258A ILE* 4.9 2.7 - - + -
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Residues in contact with ASN 214 (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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210A ARG* 2.5 44.1 + - - +
211A GLN* 4.0 2.9 - - - +
213A LEU* 1.3 71.2 - - - +
215A LEU* 1.3 68.4 + - - +
217A PHE 3.2 0.5 + - - -
218A GLY* 2.7 21.3 + - - -
219A THR* 3.0 42.8 + - - +
220A ARG 3.5 12.8 + - - +
221A ASP* 3.1 27.6 + - - +
222A LEU* 3.6 14.1 + - - +
228A GLU* 5.4 1.0 + - - -
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Residues in contact with LEU 215 (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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211A GLN* 2.9 26.7 + - - +
212A GLN* 3.3 23.3 - - - +
214A ASN* 1.3 77.8 - - - +
216A GLN* 1.3 63.8 + - - +
218A GLY* 3.1 10.6 + - - -
245A LYS* 4.0 23.8 - - - +
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Residues in contact with GLN 216 (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 GLN 2.9 18.5 + - - +
213A LEU 3.5 4.3 - - - +
215A LEU* 1.3 78.9 - - - +
217A PHE* 1.3 72.9 + - + +
218A GLY 3.4 1.0 + - - -
241A LEU* 4.0 32.6 - - + +
245A LYS* 4.3 13.5 + - - +
252A LEU* 3.5 30.7 + - - +
253A PRO* 5.1 2.4 - - - +
255A ILE* 2.8 31.7 + - + +
256A ARG* 5.1 0.7 - - - +
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Residues in contact with PHE 217 (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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155A PHE* 3.8 19.1 - + - -
213A LEU* 2.8 40.4 + - + +
216A GLN* 1.3 82.2 - - + +
218A GLY* 1.3 62.6 + - - +
219A THR* 3.9 11.7 - - - +
222A LEU* 3.8 8.1 - - + -
225A PHE* 3.7 30.6 - + + -
255A ILE 3.9 13.2 - - - -
256A ARG* 3.5 23.3 - - - +
257A SER* 3.3 34.5 - - - -
258A ILE* 3.7 28.0 - - + -
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Residues in contact with GLY 218 (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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214A ASN 2.7 14.3 + - - -
215A LEU* 3.1 12.5 + - - -
216A GLN 3.2 1.2 + - - -
217A PHE* 1.3 75.3 - - - +
219A THR* 1.3 57.6 + - - +
220A ARG* 5.0 8.5 + - - -
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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