Contacts of the helix formed by residues 220 - 230 (chain A) in PDB entry 1O7F
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A VAL* 1.3 72.9 - - - +
221A THR* 1.3 62.8 + - - +
223A LEU* 3.0 12.4 + - - +
224A VAL* 3.1 14.7 + - - +
262A PHE* 3.8 8.4 - - - -
263A GLN 3.7 16.8 - - - -
264A ASP* 4.4 1.8 - - - -
265A LYS 3.3 8.5 + - - -
267A LEU 2.9 14.1 + - - -
269A TYR* 3.8 15.9 - - - -
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Residues in contact with THR 221 (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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219A VAL* 3.6 14.7 - - - +
220A GLY* 1.3 71.3 - - - +
222A GLU* 1.3 59.0 + - - +
224A VAL* 3.5 0.7 + - - -
225A ASP* 2.9 36.8 + - - +
237A ARG* 3.5 9.8 + - - +
264A ASP* 3.2 37.4 + - - +
265A LYS* 3.0 17.7 + - - +
266A TYR* 4.2 3.4 + - + +
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Residues in contact with GLU 222 (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 HIS* 4.1 17.8 + - - +
203A MET* 3.4 38.0 - - + +
207A ARG* 3.9 20.3 + - - -
219A VAL* 2.8 25.5 + - + +
221A THR* 1.3 76.7 + - - +
223A LEU* 1.3 59.9 + - - +
225A ASP* 3.5 11.8 - - + +
226A TRP* 2.9 27.9 + - - +
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Residues in contact with LEU 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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196A ILE* 4.2 5.8 - - + -
203A MET* 3.9 16.4 - - + -
218A CYS* 3.8 34.8 - - + -
219A VAL 2.9 15.7 + - - +
220A GLY 3.0 4.5 + - - +
222A GLU* 1.3 74.3 - - - +
224A VAL* 1.3 61.9 + - - +
226A TRP* 3.3 1.2 + - - +
227A MET* 2.8 25.8 + - - +
244A TRP* 3.2 46.6 + - + +
253A LEU* 4.5 10.1 - - + -
262A PHE* 3.8 24.9 - - + -
269A TYR* 4.1 17.7 - - + -
271A PHE* 4.5 3.4 - - + -
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Residues in contact with VAL 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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220A GLY 3.1 10.9 + - - +
221A THR 3.6 7.6 - - - +
223A LEU* 1.3 78.5 - - - +
225A ASP* 1.3 63.1 + - - +
227A MET* 3.1 2.8 + - - +
228A ILE* 3.0 24.6 + - + +
237A ARG* 3.4 52.7 - - + +
240A ALA* 3.8 13.5 - - + -
241A VAL* 4.1 9.2 - - + -
244A TRP* 3.8 5.8 - - + +
262A PHE* 3.9 22.4 - - + -
264A ASP* 3.8 18.6 - - - +
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Residues in contact with ASP 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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221A THR* 2.9 27.0 + - - +
222A GLU* 3.5 16.8 - - + +
224A VAL* 1.3 77.7 - - - +
226A TRP* 1.3 63.0 + - - +
228A ILE* 3.4 5.0 + - - +
229A GLN* 3.2 28.7 + - - +
237A ARG* 2.9 29.2 + - - +
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Residues in contact with TRP 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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192A LEU* 4.3 20.9 - - + -
195A ALA* 3.9 28.5 - - + -
196A ILE* 3.5 40.8 - - + +
199A ARG* 4.5 6.4 - - - +
200A ALA* 4.0 16.3 - - + +
203A MET* 3.5 28.5 - - + -
222A GLU 2.9 18.5 + - - +
223A LEU 3.7 2.2 - - - +
225A ASP* 1.3 77.8 - - - +
227A MET* 1.3 71.7 + - + +
229A GLN* 3.4 17.2 + - - +
230A GLN* 2.8 73.5 + - + +
244A TRP* 4.3 9.6 - + - -
294A LEU* 4.9 7.2 - - + -
298A MET* 5.1 6.5 - - - -
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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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192A LEU* 4.1 13.7 - - + -
223A LEU 2.8 20.7 + - - +
224A VAL 3.6 4.5 - - - +
226A TRP* 1.3 85.0 - - + +
228A ILE* 1.3 65.2 + - - +
230A GLN* 3.4 13.6 + - - +
231A THR 4.3 0.2 - - - +
232A SER 4.2 1.0 - - - +
234A VAL* 3.7 15.1 - - + +
240A ALA* 4.1 15.5 - - + -
243A MET* 3.7 39.3 - - + +
244A TRP* 3.8 35.9 - - + +
298A MET* 3.3 36.7 - - + +
301A LEU* 4.6 4.0 - - + -
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Residues in contact with ILE 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 VAL* 3.0 20.2 + - + +
225A ASP* 3.7 5.2 - - - +
227A MET* 1.3 76.2 - - - +
229A GLN* 1.3 62.5 + - - +
230A GLN 3.7 0.3 - - - +
232A SER 3.4 4.5 - - - +
233A CYS* 3.1 47.5 - - + +
234A VAL* 4.3 4.3 - - + -
235A HIS 5.6 0.4 - - - -
236A SER* 3.7 34.5 - - - +
237A ARG* 3.8 27.8 - - + +
240A ALA* 4.4 4.7 - - + -
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Residues in contact with GLN 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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200A ALA* 5.6 1.7 - - - +
225A ASP* 3.2 20.1 + - - +
226A TRP* 3.4 17.6 - - - +
228A ILE* 1.3 76.4 - - - +
230A GLN* 1.3 94.1 + - - +
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Residues in contact with GLN 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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199A ARG* 2.9 34.4 + - - +
226A TRP* 2.8 76.4 + - + +
227A MET* 3.7 7.9 - - - +
228A ILE 3.3 5.3 - - - +
229A GLN* 1.3 111.1 + - - +
231A THR* 1.3 71.6 + - - +
232A SER 3.5 2.9 + - - +
233A CYS 4.4 0.3 + - - -
294A LEU* 5.3 4.7 - - + +
298A MET* 5.2 7.4 - - + -
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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