Contacts of the helix formed by residues 258 - 263 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185Z LEU* 5.1 0.9 - - + -
217Z CYS* 4.1 2.9 - - + -
218Z TYR 3.2 22.0 - - - +
219Z VAL* 3.3 26.0 - - + -
223Z PHE* 4.1 2.9 - - - -
254Z ARG 3.7 7.6 - - - +
255Z PHE 3.6 3.6 - - - +
257Z CYS* 1.3 89.0 - - + +
259Z GLU* 1.4 59.4 + - - +
260Z THR 2.9 5.2 - - - -
261Z LEU* 2.9 26.6 + - + +
262Z PHE* 3.8 7.5 - - - -
306Z TYR* 3.6 43.3 - - + -
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Residues in contact with GLU 259 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223Z PHE* 3.1 60.3 - - + +
224Z GLU* 5.2 0.3 - - - -
227Z MET* 3.9 23.7 - - - +
255Z PHE* 3.1 24.4 + - - +
256Z ARG* 3.9 1.8 - - - +
257Z CYS 3.3 0.6 - - - -
258Z PRO* 1.4 73.2 - - - +
260Z THR* 1.4 60.0 + - - +
262Z PHE* 3.2 2.0 + - - -
263Z GLN* 2.7 59.3 + - - +
266Z PHE* 3.6 28.3 - - + -
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Residues in contact with THR 260 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Z LEU* 4.4 3.9 - - + +
185Z LEU* 4.3 15.0 - - + -
188Z TYR* 3.2 25.7 - - + -
256Z ARG 3.4 1.9 + - - -
257Z CYS 2.6 21.6 + - - -
258Z PRO 2.9 1.0 - - - -
259Z GLU* 1.4 76.2 - - - +
261Z LEU* 1.3 57.9 + - - +
263Z GLN 2.7 32.1 - - - +
264Z PRO* 3.4 5.4 - - - +
266Z PHE* 3.9 6.6 - - + -
267Z ILE* 3.6 47.1 - - + -
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Residues in contact with LEU 261 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155Z SER* 4.8 4.7 - - - +
178Z LEU* 5.1 0.9 - - - +
180Z LEU* 3.5 32.1 - - + +
185Z LEU* 4.0 16.4 - - + -
219Z VAL* 5.6 0.7 - - + -
258Z PRO* 2.9 14.4 + - + +
260Z THR* 1.3 77.7 - - - +
262Z PHE* 1.4 64.4 + - + +
263Z GLN 4.9 0.2 - - - -
264Z PRO* 4.7 2.0 - - - +
273Z GLY* 3.8 3.3 - - - -
274Z ILE* 3.2 51.9 + - + +
303Z THR* 4.1 17.3 - - + +
304Z THR* 6.5 0.2 - - + -
306Z TYR* 4.0 30.5 - - + -
309Z ILE* 4.3 13.5 - - + -
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Residues in contact with PHE 262 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Z VAL* 3.5 29.4 - - + -
223Z PHE* 3.9 4.5 - + - -
258Z PRO 3.8 13.5 - - - -
259Z GLU* 3.2 2.5 + - - -
261Z LEU* 1.4 79.5 - - + +
263Z GLN* 1.3 75.0 + - - +
264Z PRO* 3.6 7.6 - - - +
273Z GLY* 4.0 4.9 + - - -
274Z ILE* 3.6 27.1 - - + -
275Z HIS* 3.4 40.8 - - + +
309Z ILE* 4.6 10.5 - - + -
312Z ARG* 3.3 50.7 - - + +
313Z MET* 4.2 16.8 - - + -
316Z GLU* 4.0 2.5 - - + -
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Residues in contact with GLN 263 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259Z GLU* 2.7 63.6 + - - +
260Z THR* 2.7 24.1 - - - +
262Z PHE* 1.3 93.4 - - - +
264Z PRO* 1.3 58.7 - - - +
265Z SER* 3.1 20.4 + - - +
266Z PHE* 3.5 26.0 + - + +
312Z ARG* 3.4 10.3 + - - +
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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