Contacts of the helix formed by residues 258 - 263 (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 PRO 258 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185Y LEU* 5.1 1.1 - - + -
217Y CYS* 4.1 3.1 - - + -
218Y TYR 3.2 22.0 - - - +
219Y VAL* 3.3 26.2 - - + -
223Y PHE* 4.1 2.7 - - - -
254Y ARG 3.7 7.9 - - - +
255Y PHE 3.6 3.6 - - - +
257Y CYS* 1.3 89.0 - - + +
259Y GLU* 1.4 58.6 + - - +
260Y THR 2.9 5.4 - - - -
261Y LEU* 2.9 26.5 + - + +
262Y PHE* 3.8 7.7 - - - -
306Y TYR* 3.6 43.7 - - + -
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Residues in contact with GLU 259 (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* 3.1 60.1 - - + +
224Y GLU* 5.2 0.2 - - - -
227Y MET* 3.9 23.0 - - - +
255Y PHE* 3.1 24.6 + - - +
256Y ARG* 3.9 1.6 - - - +
257Y CYS 3.3 0.4 - - - -
258Y PRO* 1.4 73.6 - - - +
260Y THR* 1.4 60.3 + - - +
262Y PHE* 3.2 1.9 + - - -
263Y GLN* 2.7 60.2 + - - +
266Y PHE* 3.6 28.2 - - + -
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Residues in contact with THR 260 (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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180Y LEU* 4.4 3.7 - - + +
185Y LEU* 4.3 15.7 - - + -
188Y TYR* 3.2 25.4 - - + -
256Y ARG 3.4 1.3 + - - -
257Y CYS 2.6 21.2 + - - -
258Y PRO 2.9 1.0 - - - -
259Y GLU* 1.4 76.3 - - - +
261Y LEU* 1.3 61.6 + - - +
263Y GLN 2.7 28.6 - - - +
264Y PRO* 3.4 5.4 - - - +
266Y PHE* 3.9 7.0 - - + -
267Y ILE* 3.6 46.9 - - + -
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Residues in contact with LEU 261 (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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155Y SER* 4.8 4.0 - - - +
178Y LEU* 5.1 0.9 - - - +
180Y LEU* 3.5 31.0 - - + +
185Y LEU* 4.0 17.0 - - + -
219Y VAL* 5.6 0.7 - - + -
258Y PRO* 2.9 14.2 + - + +
260Y THR* 1.3 77.7 - - - +
262Y PHE* 1.4 64.1 + - + +
263Y GLN 4.9 0.2 - - - -
264Y PRO* 4.7 1.8 - - - +
273Y GLY* 3.8 3.3 - - - -
274Y ILE* 3.2 52.5 + - + +
303Y THR* 4.1 17.3 - - + +
304Y THR* 6.5 0.2 - - + -
306Y TYR* 4.0 30.5 - - + -
309Y ILE* 4.3 13.5 - - + -
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Residues in contact with PHE 262 (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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219Y VAL* 3.5 29.2 - - + -
223Y PHE* 3.9 4.5 - + - -
258Y PRO 3.8 14.1 - - - -
259Y GLU* 3.2 2.0 + - - -
261Y LEU* 1.4 79.6 - - + +
263Y GLN* 1.3 74.0 + - - +
264Y PRO* 3.6 7.6 - - - +
273Y GLY* 4.0 4.9 + - - -
274Y ILE* 3.6 27.1 - - + -
275Y HIS* 3.4 40.9 - - + +
309Y ILE* 4.6 11.0 - - + -
312Y ARG* 3.3 49.8 - - + +
313Y MET* 4.2 17.3 - - + -
316Y GLU* 4.0 2.2 - - + -
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Residues in contact with GLN 263 (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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259Y GLU* 2.7 63.7 + - - +
260Y THR* 2.7 24.3 - - - +
262Y PHE* 1.3 93.4 - - - +
264Y PRO* 1.3 58.3 - - - +
265Y SER* 3.1 19.9 + - - +
266Y PHE* 3.5 25.7 + - + +
312Y ARG* 3.4 10.9 + - - +
39Z ARG* 5.8 3.4 - - - +
40Z HIS* 6.0 3.6 - - + +
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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