Contacts of the helix formed by residues 222 - 238 (chain A) in PDB entry 1O9D
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 ASP 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A PRO* 3.6 24.0 - - + +
223A SER* 1.3 68.4 + - - +
224A THR* 2.9 14.2 + - - +
225A LEU* 3.3 24.6 + - - +
226A ILE* 3.0 38.0 + - - +
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Residues in contact with SER 223 (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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172A THR* 3.2 32.4 + - - -
174A PRO* 4.6 12.0 - - - +
177A LEU* 4.0 10.6 - - - +
212A LEU* 5.0 4.9 - - - +
222A ASP* 1.3 78.0 - - - +
224A THR* 1.3 64.9 + - - +
226A ILE* 3.5 1.5 + - - -
227A MET* 3.1 47.7 + - - +
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Residues in contact with THR 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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222A ASP 3.6 8.6 + - - +
223A SER* 1.3 83.0 + - - +
225A LEU* 1.3 63.2 + - - +
227A MET* 3.5 9.5 + - - +
228A GLN* 3.1 40.4 + - - +
231A ARG* 5.7 0.3 + - - -
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Residues in contact with LEU 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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222A ASP* 3.3 24.1 + - - +
224A THR* 1.3 80.9 - - - +
226A ILE* 1.3 72.3 + - + +
228A GLN* 3.0 22.2 + - + +
229A LEU* 3.0 48.9 + - + +
5P VAL* 4.8 5.8 - - + -
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Residues in contact with ILE 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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174A PRO* 3.4 37.9 - - + +
177A LEU* 3.8 34.3 - - + +
178A GLY* 4.0 5.4 - - - +
181A LEU* 4.4 15.9 - - + -
222A ASP* 3.0 25.7 + - - +
223A SER 4.1 3.1 - - - +
225A LEU* 1.3 85.5 - - + +
227A MET* 1.3 58.0 + - - +
229A LEU* 3.0 11.9 + - - +
230A LEU* 2.8 28.5 + - + +
5P VAL* 4.3 18.4 - - + -
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Residues in contact with MET 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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172A THR* 4.9 1.6 - - + -
177A LEU* 4.0 20.0 - - + -
205A PHE* 3.7 27.8 - - + -
208A ALA* 3.5 25.8 - - + -
209A ILE* 4.7 7.9 - - - -
212A LEU* 3.3 33.0 - - + -
223A SER* 3.1 36.9 + - - +
224A THR* 3.8 7.9 - - - +
226A ILE* 1.3 75.7 - - - +
228A GLN* 1.3 62.8 + - - +
230A LEU* 3.1 9.1 + - + +
231A ARG* 3.1 27.2 + - - +
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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 THR* 3.1 35.8 + - - +
225A LEU* 3.0 26.8 + - + +
227A MET* 1.3 75.2 - - - +
229A LEU* 1.3 52.7 + - + +
231A ARG* 3.2 31.6 + - - +
232A ASP* 2.7 47.0 + - - +
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Residues in contact with LEU 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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181A LEU* 3.8 18.6 - - + -
225A LEU* 3.0 39.5 + - + +
226A ILE* 3.0 12.4 + - - +
228A GLN* 1.3 74.7 - - + +
230A LEU* 1.3 63.5 + - - +
232A ASP* 3.7 14.7 - - - +
233A ASN* 3.0 27.7 + - - +
3P TYR* 3.8 34.0 - - + -
4P TPO 4.7 1.3 - - - +
5P VAL* 3.6 31.0 - - + -
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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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177A LEU* 4.0 32.5 - - + +
180A ALA* 4.3 3.1 - - + -
181A LEU* 3.6 42.2 - - + +
184A SER* 4.7 0.7 - - - +
201A ALA* 4.0 29.7 - - + +
204A ALA* 4.7 2.7 - - + -
205A PHE* 4.3 31.0 - - + +
226A ILE 2.8 21.1 + - - +
227A MET* 3.1 11.6 + - - +
229A LEU* 1.3 72.9 - - - +
231A ARG* 1.3 57.7 + - - +
233A ASN* 3.3 3.2 + - - +
234A LEU* 2.8 36.3 + - + +
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Residues in contact with ARG 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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205A PHE* 3.8 35.0 - - + -
209A ILE* 5.8 1.8 - - - +
224A THR 5.7 0.6 + - - -
227A MET* 3.1 10.9 + - - +
228A GLN* 3.2 51.1 + - - +
230A LEU* 1.3 80.1 - - - +
232A ASP* 1.3 65.7 + - - +
234A LEU* 3.0 11.1 + - + +
235A THR* 2.9 37.4 + - + +
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Residues in contact with ASP 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* 2.7 30.6 + - - +
229A LEU* 3.3 19.8 + - - +
231A ARG* 1.3 75.1 + - - +
233A ASN* 1.3 62.9 + - - +
235A THR* 3.6 7.9 + - - +
236A LEU* 3.1 25.6 + - - +
3P TYR* 3.8 24.1 - - + -
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Residues in contact with ASN 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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181A LEU* 3.3 17.4 - - + +
185A VAL* 3.6 14.3 - - - +
229A LEU 3.0 14.6 + - - +
230A LEU* 3.7 4.7 - - + +
232A ASP* 1.3 74.1 - - - +
234A LEU* 1.3 67.7 + - - +
236A LEU* 3.2 7.9 + - - +
237A TRP* 2.8 48.4 + - + -
2P SER* 3.5 12.1 - - - -
3P TYR* 3.0 55.5 + - - -
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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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198A CYS* 3.9 42.8 - - + +
201A ALA* 4.0 14.4 - - + +
202A LYS* 4.0 36.1 - - + +
205A PHE* 5.0 7.2 - - + -
230A LEU* 2.8 29.3 + - + +
231A ARG* 3.0 9.4 + - + +
233A ASN* 1.3 73.7 - - - +
235A THR* 1.3 62.8 + - + +
237A TRP* 3.4 7.0 + - + +
238A THR* 2.7 30.6 + - - +
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Residues in contact with THR 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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231A ARG* 2.9 29.3 + - + +
232A ASP* 3.9 6.2 + - - +
234A LEU* 1.3 74.7 - - + +
236A LEU* 1.3 70.2 + - - +
238A THR* 3.2 23.2 + - - +
239A SER* 3.6 6.2 - - - -
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Residues in contact with LEU 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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188A TYR* 5.4 0.3 + - - -
232A ASP 3.1 16.4 + - - +
233A ASN* 3.4 19.3 - - - +
235A THR* 1.3 84.1 + - - +
237A TRP* 1.3 66.3 + - + +
239A SER* 3.5 21.3 + - - -
240A ASP 4.1 0.7 + - - -
1P GLN 4.1 19.3 - - - +
2P SER* 4.7 5.4 - - - +
3P TYR* 4.7 11.9 - - + -
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Residues in contact with TRP 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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184A SER* 3.5 33.0 - - - -
185A VAL* 4.0 8.7 - - + -
188A TYR* 3.5 55.8 + + + -
194A PRO* 5.7 2.9 - - + +
197A ALA* 3.7 28.3 - - + -
198A CYS* 3.9 28.9 - - - -
201A ALA* 4.3 8.5 - - + -
233A ASN* 2.8 43.2 + - + +
234A LEU* 3.8 6.3 - - - +
236A LEU* 1.3 83.6 - - + +
238A THR* 1.3 55.3 + - - +
239A SER 2.9 18.4 + - - +
2P SER* 3.2 28.4 + - - -
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Residues in contact with THR 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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198A CYS* 5.1 5.4 - - - -
234A LEU* 2.7 26.4 + - - +
235A THR* 3.2 8.8 + - - +
237A TRP* 1.3 72.0 - - - +
239A SER* 1.3 60.5 + - - +
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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