Contacts of the helix formed by residues 252 - 257 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196X ARG* 3.5 18.9 + - - -
227X MET* 5.7 1.6 - - - -
230X ALA* 3.3 42.1 + - + +
233X SER* 5.0 2.2 + - - -
236X LEU* 3.9 10.9 - - - +
237X GLU* 4.0 10.0 + - - +
251X GLY* 1.3 75.0 - - - +
253X GLU* 1.4 58.4 + - - +
254X ARG* 2.8 16.6 + - - +
255X PHE* 3.1 36.5 + - + -
256X ARG* 3.8 13.0 - - - +
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Residues in contact with GLU 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X LEU* 4.6 6.5 - - + +
192X ILE* 3.6 27.8 - - + +
193X LEU* 4.1 16.6 - - + -
196X ARG* 3.3 39.8 + - - +
250X ILE* 3.5 13.3 - - + -
251X GLY 3.0 28.6 + - - -
252X ASN* 1.4 69.9 + - - +
254X ARG* 1.3 64.9 - - - +
255X PHE 3.1 1.1 - - - -
256X ARG* 3.0 44.9 + - - +
257X CYS* 3.1 17.8 + - - +
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Residues in contact with ARG 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X LEU* 5.7 0.2 - - - -
215X LYS 5.4 0.2 + - - -
216X LEU* 2.9 33.7 + - + +
217X CYS* 2.9 29.4 - - - +
218X TYR* 3.1 59.7 + - + +
236X LEU 3.1 20.9 + - - -
237X GLU 4.3 0.2 + - - -
238X LYS* 3.5 30.9 - - - +
250X ILE* 3.6 25.0 - - + +
251X GLY 3.1 26.9 - - - +
252X ASN 3.5 0.9 - - - +
253X GLU* 1.3 74.2 - - - +
255X PHE* 1.4 59.5 + - + +
258X PRO* 3.7 1.7 - - - +
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Residues in contact with PHE 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218X TYR* 3.4 22.4 - - + +
220X ALA* 4.4 3.4 - - + -
223X PHE* 3.0 50.4 - + + -
226X GLU* 3.4 55.0 - - + -
227X MET* 3.3 34.3 - - + -
230X ALA* 4.8 1.6 - - + -
236X LEU* 4.5 9.6 - - + -
251X GLY 5.1 0.9 - - - -
252X ASN* 3.1 31.9 + - - -
253X GLU 3.1 0.2 - - - -
254X ARG* 1.4 79.1 - - + +
256X ARG* 1.3 69.1 + - + +
257X CYS 3.1 2.5 - - - -
258X PRO* 3.6 1.0 - - - +
259X GLU* 3.1 18.3 + - - +
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Residues in contact with ARG 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X TYR* 3.3 22.8 + - - +
192X ILE* 3.6 43.7 + - + +
195X GLU* 3.7 13.9 + - - -
196X ARG* 6.0 0.4 - - - +
227X MET* 3.7 33.0 - - + +
252X ASN* 3.8 9.9 - - - +
253X GLU* 3.0 44.7 + - - +
255X PHE* 1.3 84.6 - - + +
257X CYS* 1.3 59.4 + - - +
259X GLU* 4.0 8.1 - - - +
260X THR* 3.4 2.3 + - - -
266X PHE* 3.3 21.2 - - + -
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Residues in contact with CYS 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X LEU* 3.2 39.7 - - - +
188X TYR* 3.8 10.1 - - - -
189X LEU* 3.8 16.4 - - + -
192X ILE* 4.0 8.0 - - + +
213X LYS* 4.2 17.3 - - - -
217X CYS* 4.2 9.2 - - - -
253X GLU 3.1 13.6 + - - +
255X PHE 3.1 0.6 - - - -
256X ARG* 1.3 75.0 - - - +
258X PRO* 1.3 69.4 - - + +
260X THR* 2.6 28.1 + - - -
306X 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