Contacts of the helix formed by residues 252 - 257 (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 ASN 252 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196Z ARG* 3.5 18.9 + - - -
227Z MET* 5.7 1.6 - - - -
230Z ALA* 3.3 42.3 + - + +
233Z SER* 5.0 2.6 + - - -
236Z LEU* 3.9 11.4 - - - +
237Z GLU* 4.0 9.7 + - - +
251Z GLY* 1.3 74.2 - - - +
253Z GLU* 1.4 58.3 + - - +
254Z ARG* 2.8 16.3 + - - +
255Z PHE* 3.1 36.5 + - + -
256Z ARG* 3.8 12.8 - - - +
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Residues in contact with GLU 253 (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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189Z LEU* 4.6 6.7 - - + +
192Z ILE* 3.6 27.6 - - + +
193Z LEU* 4.1 17.3 - - + -
196Z ARG* 3.3 39.8 + - - +
250Z ILE* 3.5 12.8 - - + -
251Z GLY 3.0 28.4 + - - -
252Z ASN* 1.4 70.1 + - - +
254Z ARG* 1.3 65.0 + - - +
255Z PHE 3.1 1.1 - - - -
256Z ARG* 3.0 45.7 + - - +
257Z CYS* 3.1 17.7 + - - +
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Residues in contact with ARG 254 (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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189Z LEU* 5.7 0.2 - - - -
215Z LYS 5.4 0.2 + - - -
216Z LEU* 2.9 34.0 + - + +
217Z CYS* 2.9 30.1 - - - +
218Z TYR* 3.1 59.0 + - + +
236Z LEU 3.1 21.1 + - - -
237Z GLU 4.3 0.2 + - - -
238Z LYS* 3.5 30.9 - - - +
250Z ILE* 3.6 24.8 - - + +
251Z GLY 3.1 26.9 - - - +
252Z ASN 3.5 1.1 - - - +
253Z GLU* 1.3 74.7 - - - +
255Z PHE* 1.4 59.3 + - + +
258Z PRO* 3.7 1.7 - - - +
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Residues in contact with PHE 255 (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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218Z TYR* 3.4 22.7 - - + +
220Z ALA* 4.4 3.4 - - + -
223Z PHE* 3.0 50.7 - + + -
226Z GLU* 3.4 54.3 - - + -
227Z MET* 3.3 34.3 - - + -
230Z ALA* 4.8 1.6 - - + -
236Z LEU* 4.5 9.4 - - + -
251Z GLY 5.1 0.7 - - - -
252Z ASN* 3.1 31.5 + - - -
253Z GLU 3.1 0.2 - - - -
254Z ARG* 1.4 79.1 - - + +
256Z ARG* 1.3 69.9 + - + +
257Z CYS 3.1 2.5 - - - -
258Z PRO* 3.6 1.0 - - - +
259Z GLU* 3.1 17.8 + - - +
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Residues in contact with ARG 256 (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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188Z TYR* 3.3 22.9 + - - +
192Z ILE* 3.6 43.7 + - + +
195Z GLU* 3.7 13.9 + - - -
196Z ARG* 6.0 0.4 - - - +
227Z MET* 3.7 33.0 - - + +
252Z ASN* 3.8 9.9 - - - +
253Z GLU* 3.0 45.1 + - - +
255Z PHE* 1.3 84.9 - - + +
257Z CYS* 1.3 60.0 + - - +
259Z GLU* 4.0 8.1 - - - +
260Z THR* 3.4 2.1 + - - -
266Z PHE* 3.3 21.5 - - + -
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Residues in contact with CYS 257 (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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185Z LEU* 3.2 39.3 - - - +
188Z TYR* 3.8 9.9 - - - -
189Z LEU* 3.8 16.6 - - + -
192Z ILE* 4.0 8.2 - - + +
213Z LYS* 4.2 17.7 - - - -
217Z CYS* 4.2 9.2 - - - -
253Z GLU 3.1 13.3 + - - +
255Z PHE 3.1 0.8 - - - -
256Z ARG* 1.3 75.3 - - - +
258Z PRO* 1.3 69.6 - - + +
260Z THR* 2.6 28.2 + - - -
306Z TYR* 5.1 0.7 - - - -
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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