Contacts of the helix formed by residues 258 - 263 (chain V) in PDB entry 1MVW
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 PRO 258 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185V LEU* 5.1 0.9 - - + -
217V CYS* 4.1 2.9 - - + -
218V TYR 3.2 22.4 - - - +
219V VAL* 3.3 26.9 - - + -
223V PHE* 4.1 2.5 - - - -
254V ARG 3.7 7.4 - - - +
255V PHE 3.6 3.6 - - - +
257V CYS* 1.3 89.3 - - + +
259V GLU* 1.4 59.4 + - - +
260V THR 2.9 5.4 - - - -
261V LEU* 2.9 26.9 + - + +
262V PHE* 3.8 7.3 - - - -
306V TYR* 3.6 44.2 - - + -
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Residues in contact with GLU 259 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223V PHE* 3.1 60.0 - - + +
224V GLU* 4.5 1.0 + - - -
227V MET* 3.9 23.2 - - - +
255V PHE* 3.1 25.2 + - - +
256V ARG* 3.9 1.7 - - - +
257V CYS 3.3 0.4 - - - -
258V PRO* 1.4 72.6 - - - +
260V THR* 1.4 59.7 + - - +
262V PHE* 3.2 2.2 + - - -
263V GLN* 2.7 59.3 + - - +
266V PHE* 3.6 28.1 - - + -
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Residues in contact with THR 260 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180V LEU* 4.4 3.1 - - + +
185V LEU* 4.3 15.7 - - + -
188V TYR* 3.2 24.9 - - + -
256V ARG 3.4 2.5 + - - -
257V CYS 2.6 20.9 + - - -
258V PRO 2.9 0.8 - - - -
259V GLU* 1.4 76.1 - - - +
261V LEU* 1.3 57.9 + - - +
263V GLN 2.7 33.1 - - - +
264V PRO* 3.4 5.4 - - - +
266V PHE* 3.9 5.6 - - + -
267V ILE* 3.6 47.6 - - + -
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Residues in contact with LEU 261 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155V SER* 4.8 4.3 - - - +
178V LEU* 5.1 1.0 - - - +
180V LEU* 3.5 31.2 - - + +
185V LEU* 4.0 16.4 - - + -
219V VAL* 5.6 0.9 - - + -
258V PRO* 2.9 15.7 + - + +
260V THR* 1.3 77.5 - - - +
262V PHE* 1.4 64.2 + - + +
264V PRO* 4.7 2.1 - - - +
273V GLY* 3.8 2.8 - - - -
274V ILE* 3.2 52.8 + - + +
303V THR* 4.1 18.4 - - + +
304V THR* 6.5 0.4 - - + -
306V TYR* 4.0 30.1 - - + -
309V ILE* 4.3 13.5 - - + -
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Residues in contact with PHE 262 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219V VAL* 3.5 29.6 - - + -
223V PHE* 3.9 3.8 - + - -
258V PRO 3.8 14.8 - - - -
259V GLU* 3.2 3.0 + - - -
261V LEU* 1.4 78.5 - - + +
263V GLN* 1.3 74.7 + - - +
264V PRO* 3.6 7.7 - - - +
273V GLY* 4.0 5.2 + - - -
274V ILE* 3.6 26.0 - - + -
275V HIS* 3.4 40.8 - - + +
309V ILE* 4.6 10.5 - - + -
312V ARG* 3.3 50.9 - - + +
313V MET* 4.2 17.5 - - + -
316V GLU* 4.0 3.1 - - + -
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Residues in contact with GLN 263 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259V GLU* 2.7 64.2 + - - +
260V THR* 2.7 23.7 - - - +
262V PHE* 1.3 92.8 - - - +
264V PRO* 1.3 59.2 - - - +
265V SER* 3.1 21.0 + - - +
266V PHE* 3.5 26.8 + - + +
312V ARG* 3.4 10.7 + - - +
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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