Contacts of the helix formed by residues 223 - 233 (chain Y) 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 PHE 223 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219Y VAL* 3.5 21.8 - - + -
220Y ALA* 3.2 39.7 - - + -
221Y LEU 3.5 0.4 - - - -
222Y ASP* 1.3 74.8 - - - +
224Y GLU* 1.4 60.7 + - - +
226Y GLU* 3.6 5.9 - - - +
227Y MET* 3.4 27.5 + - - +
255Y PHE* 3.0 54.3 - + + -
259Y GLU* 3.1 50.5 - - + +
262Y PHE* 3.9 2.5 - + - -
312Y ARG* 2.9 38.2 - - - +
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Residues in contact with GLU 224 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222Y ASP* 3.0 17.6 - - - +
223Y PHE* 1.4 75.7 - - - +
225Y ASN* 1.3 83.2 + - - +
226Y GLU 3.1 8.0 + - - -
227Y MET* 3.5 6.7 + - - +
228Y ALA* 3.5 14.6 + - - +
259Y GLU* 5.2 1.1 - - - -
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Residues in contact with ASN 225 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222Y ASP* 3.2 24.5 + - - +
224Y GLU* 1.3 111.4 + - - +
226Y GLU* 1.3 56.0 + - - +
228Y ALA* 3.8 18.2 - - + +
229Y THR* 2.6 22.6 + - - -
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Residues in contact with GLU 226 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220Y ALA* 3.7 23.0 - - + +
221Y LEU 5.1 2.7 - - - +
222Y ASP 3.2 17.5 - - - +
223Y PHE* 3.6 11.4 - - - +
224Y GLU 3.1 0.6 - - - -
225Y ASN* 1.3 79.4 - - - +
227Y MET* 1.3 61.9 + - - +
228Y ALA 3.4 0.7 - - - -
229Y THR* 3.1 23.5 + - - +
230Y ALA* 2.9 21.5 + - - +
236Y LEU* 4.6 7.1 - - - +
255Y PHE* 3.4 37.4 - - + -
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Residues in contact with MET 227 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223Y PHE 3.4 15.9 - - - +
224Y GLU* 3.6 8.5 - - - +
226Y GLU* 1.3 75.4 - - - +
228Y ALA* 1.4 57.6 + - - +
230Y ALA* 2.9 29.9 + - - +
231Y ALA* 3.2 8.0 + - - +
252Y ASN* 5.7 1.8 - - - -
255Y PHE* 3.3 22.2 - - + -
256Y ARG* 3.7 30.7 - - + +
259Y GLU* 3.9 16.4 - - - +
266Y PHE* 5.6 4.9 - - + -
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Residues in contact with ALA 228 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224Y GLU 3.5 4.0 + - - +
225Y ASN* 3.8 31.2 - - + +
227Y MET* 1.4 78.2 - - - +
229Y THR* 1.3 61.6 + - - +
231Y ALA* 3.4 20.0 + - - +
232Y SER* 3.5 11.1 + - - -
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Residues in contact with THR 229 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225Y ASN 2.6 24.9 + - - -
226Y GLU* 3.1 22.5 + - - +
227Y MET 3.2 0.4 - - - -
228Y ALA* 1.3 77.0 - - - +
230Y ALA* 1.3 62.9 + - - +
231Y ALA 3.3 0.5 + - - -
232Y SER* 3.4 10.9 + - - -
233Y SER* 3.3 16.5 + - - -
234Y SER* 4.1 22.5 + - - +
236Y LEU* 4.9 3.6 - - + -
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Residues in contact with ALA 230 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226Y GLU 2.9 13.7 + - - +
227Y MET* 2.9 20.0 + - - +
229Y THR* 1.3 73.6 - - - +
231Y ALA* 1.4 51.9 - - - +
233Y SER* 2.9 33.3 + - - -
236Y LEU* 3.8 17.5 - - + +
252Y ASN* 3.3 36.5 + - + +
255Y PHE* 4.8 2.2 - - + -
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Residues in contact with ALA 231 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227Y MET 3.2 5.5 + - - +
228Y ALA* 3.4 13.7 - - - +
230Y ALA* 1.4 75.9 - - - +
232Y SER* 1.3 60.8 + - - +
233Y SER* 2.9 11.0 + - - -
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Residues in contact with SER 232 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228Y ALA 3.5 9.1 + - - -
229Y THR* 3.4 13.4 + - - -
231Y ALA* 1.3 75.9 - - - +
233Y SER* 1.4 68.6 + - - +
234Y SER* 5.1 1.8 - - - -
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Residues in contact with SER 233 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229Y THR 3.3 1.6 + - - -
230Y ALA 2.9 22.1 + - - -
231Y ALA* 2.9 7.7 + - - -
232Y SER* 1.4 86.0 - - - +
234Y SER* 1.3 69.1 - - - +
236Y LEU* 4.1 3.5 - - - +
237Y GLU* 5.7 4.7 + - - +
252Y ASN* 5.0 2.3 + - - -
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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