Contacts of the helix formed by residues 217 - 223 (chain C) in PDB entry 1OVM
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 217 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216C ALA* 1.3 72.6 - - - +
218C PHE* 1.3 74.9 + - - +
219C LEU 2.9 3.3 + - - -
220C VAL* 2.7 31.0 - - - +
221C LEU 4.1 0.9 + - - -
243C MET* 3.1 40.4 + - + +
245C MET* 2.9 25.5 - - - +
246C GLY* 2.8 25.4 + - - -
249C ILE* 5.0 2.4 - - - +
283C VAL 2.9 9.3 + - - -
284C GLY 3.4 14.3 - - - +
285C THR* 4.1 10.3 - - - -
286C ARG 5.0 0.9 + - - -
291C LEU* 4.0 6.1 - - - +
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Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ALA 4.9 3.1 - - - -
92C GLU* 3.4 32.8 - - - -
93C HIS* 4.0 8.5 - + - -
217C ASP* 1.3 97.9 - - - +
219C LEU* 1.3 88.3 + - + +
220C VAL 3.1 0.2 - - - -
221C LEU* 2.8 27.1 + - - +
222C ARG* 3.0 31.3 + - + +
245C MET* 3.6 48.9 - - + +
246C GLY* 3.4 9.0 - - - -
284C GLY 4.0 3.6 - - - -
286C ARG* 3.7 33.9 - - + -
406C LEU* 5.3 3.4 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C HIS* 3.8 39.5 - - + +
217C ASP 2.9 4.8 + - - -
218C PHE* 1.3 90.3 - - + +
220C VAL* 1.3 61.7 + - - +
222C ARG* 4.3 2.5 - - + -
223C HIS* 3.1 34.3 + - + +
284C GLY* 3.4 26.0 - - - +
286C ARG* 3.2 39.9 - - - +
308C GLN* 3.5 11.0 - - - +
309C PRO* 4.1 15.3 - - + -
324C MET* 4.1 9.6 - - + +
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Residues in contact with VAL 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA* 4.1 10.5 - - + -
217C ASP 2.7 22.2 - - - +
219C LEU* 1.3 72.8 - - - +
221C LEU* 1.3 65.0 + - - +
223C HIS 3.5 0.7 + - - -
224C GLY 3.3 3.1 + - - -
225C LEU* 2.9 62.7 + - + +
226C LYS* 3.9 7.8 + - - +
229C LEU* 4.1 17.7 - - + -
249C ILE* 4.4 13.0 - - + -
283C VAL* 3.8 26.7 - - + +
284C GLY* 4.5 0.2 - - - -
324C MET* 4.7 5.4 - - - -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE* 2.8 16.6 + - - +
220C VAL* 1.3 80.1 - - + +
222C ARG* 1.3 77.2 + - - +
224C GLY* 3.3 13.4 + - - -
226C LYS* 4.1 31.6 - - + +
245C MET 4.1 20.0 - - - +
246C GLY* 4.2 9.0 - - - +
247C LYS 4.6 6.1 - - - +
248C GLY 4.9 1.1 - - - -
249C ILE* 3.5 29.6 - - + +
400C ASN* 5.9 4.9 - - - +
401C PHE 5.2 5.4 - - - +
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Residues in contact with ARG 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ARG* 3.3 49.5 - - - +
92C GLU* 2.7 30.0 + - - +
93C HIS* 2.9 31.8 + - + +
94C VAL* 3.8 10.1 - - - +
95C PRO* 5.2 3.4 - - - -
160C ARG* 3.0 35.0 + - + -
218C PHE* 3.0 29.6 + - + +
219C LEU* 3.9 7.6 - - - +
221C LEU* 1.3 103.2 - - - +
223C HIS* 1.3 63.7 + - + +
224C GLY 3.3 2.0 + - - -
245C MET* 4.9 2.0 + - - +
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Residues in contact with HIS 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C HIS* 5.1 1.1 - + - -
158C ARG 3.9 13.9 + - - -
159C GLU* 4.6 5.1 + - - -
160C ARG* 3.6 35.7 - - + +
187C GLN* 4.5 15.5 - - - -
219C LEU* 3.1 34.2 + - + +
220C VAL 3.5 0.2 + - - -
221C LEU 3.3 0.2 - - - -
222C ARG* 1.3 78.9 - - + +
224C GLY* 1.3 62.8 + - - +
225C LEU* 3.3 27.5 + - + +
309C PRO* 4.0 35.2 - - + +
310C HIS* 5.4 2.1 - + - -
324C MET* 4.4 12.2 - - + -
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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