Contacts of the helix formed by residues 213 - 224 (chain A) in PDB entry 1OV1
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 ILE 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.2 30.9 + - + +
212A PHE* 1.3 104.3 - - + +
214A ILE* 1.3 79.8 + - + +
215A PRO* 3.2 1.9 - - - -
216A LEU* 3.5 4.9 + - - +
217A ILE* 3.2 41.0 + - + +
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Residues in contact with ILE 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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209A VAL* 4.2 4.3 - - + +
210A VAL* 3.2 44.4 - - + +
213A ILE* 1.3 87.4 - - + +
215A PRO* 1.4 69.6 - - + +
217A ILE* 3.1 19.3 + - - +
218A VAL* 3.3 22.7 + - + +
261A PHE* 6.0 3.1 - - + -
265A TRP* 6.3 3.1 - - + -
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Residues in contact with PRO 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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210A VAL 3.7 1.1 - - - +
211A HIS* 3.6 20.6 - - + +
212A PHE* 3.2 29.4 - - - +
213A ILE 3.2 3.4 - - - -
214A ILE* 1.4 99.3 - - + +
216A LEU* 1.3 64.5 + - - +
217A ILE 3.3 0.2 - - - -
218A VAL* 3.5 11.0 + - + +
219A ILE* 3.1 36.4 + - + +
261A PHE* 3.7 30.7 - - + -
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Residues in contact with LEU 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 PHE* 3.5 22.4 - - + +
213A ILE* 4.0 5.2 - - - +
214A ILE 3.2 0.4 - - - -
215A PRO* 1.3 81.0 - - - +
217A ILE* 1.3 63.3 + - + +
219A ILE* 3.3 12.8 + - + +
220A PHE* 2.8 31.8 + - + +
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Residues in contact with ILE 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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213A ILE* 3.2 35.2 - - + +
214A ILE* 3.1 9.0 + - - +
216A LEU* 1.3 79.2 - - + +
218A VAL* 1.3 57.5 + - + +
220A PHE* 3.5 15.6 - - + -
221A PHE* 2.7 36.1 + - + +
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Residues in contact with VAL 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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132A ALA* 4.5 20.0 - - + -
214A ILE* 3.3 24.9 - - + +
215A PRO* 3.6 13.9 - - + +
216A LEU 3.2 0.6 - - - -
217A ILE* 1.3 79.3 - - + +
219A ILE* 1.3 64.3 + - + +
221A PHE* 3.3 13.9 - - + +
222A CYS* 3.2 18.7 - - - -
257A MET* 5.8 1.6 - - + -
261A PHE* 5.7 11.2 - - + -
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Residues in contact with ILE 219 (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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135A ARG* 3.1 38.0 + - - +
215A PRO* 3.1 25.7 + - + +
216A LEU* 3.3 12.1 + - + +
217A ILE 3.2 0.4 - - - -
218A VAL* 1.3 76.8 - - + +
220A PHE* 1.3 64.6 + - - +
221A PHE 3.1 0.2 - - - -
222A CYS* 3.3 11.6 + - - +
223A TYR* 3.3 3.0 + - + +
254A VAL* 4.6 10.8 - - + -
257A MET* 3.9 22.7 - - + -
258A VAL* 3.9 30.7 - - + -
261A PHE* 6.1 6.1 - - + -
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Residues in contact with PHE 220 (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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216A LEU* 2.8 21.4 + - + +
217A ILE* 3.6 18.4 - - + +
219A ILE* 1.3 76.0 - - - +
221A PHE* 1.3 57.7 + - - +
222A CYS 3.1 0.4 - - - -
223A TYR* 3.3 19.9 + + + -
224A GLY* 2.7 38.6 + - - -
227A VAL* 5.2 10.8 - - + -
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Residues in contact with PHE 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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136A TYR* 3.7 44.7 - + + -
217A ILE* 2.7 23.6 + - + +
218A VAL* 3.3 14.8 - - + +
220A PHE* 1.3 78.4 - - - +
222A CYS* 1.3 65.8 + - - +
224A GLY* 3.6 10.0 + - - +
225A CYS 4.1 1.7 + - - -
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Residues in contact with CYS 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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132A ALA* 3.3 35.2 - - - -
135A ARG* 3.3 32.3 - - - +
136A TYR* 4.1 18.6 - - - -
139A VAL* 3.1 26.6 - - - +
218A VAL 3.2 19.7 - - - -
219A ILE* 3.3 5.8 + - - +
220A PHE 3.1 0.4 - - - -
221A PHE* 1.3 80.9 - - - +
223A TYR* 1.3 62.6 + - - +
224A GLY 3.1 1.3 - - - -
225A CYS* 3.3 6.9 + - - +
226A LEU 3.8 0.2 + - - -
257A MET* 5.9 2.0 - - - -
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Residues in contact with TYR 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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135A ARG* 3.8 24.1 - - - +
219A ILE* 3.3 10.6 + - + +
220A PHE* 3.3 21.0 + + + +
222A CYS* 1.3 75.2 - - - +
224A GLY* 1.3 56.6 + - - +
225A CYS 3.0 5.8 - - - -
226A LEU* 2.9 21.6 + - + +
227A VAL* 2.9 42.7 + - + +
230A VAL* 2.9 30.6 + - + +
231A LYS 2.6 31.0 + - - -
232A GLU* 4.9 0.9 - - - -
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Residues in contact with GLY 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 PHE* 2.7 25.3 + - - -
221A PHE* 3.6 6.7 + - - -
222A CYS 3.1 1.4 - - - -
223A TYR* 1.3 78.2 - - - +
225A CYS* 1.3 56.9 + - - +
227A VAL* 3.0 28.0 - - - +
228A PHE* 4.3 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