Contacts of the strand formed by residues 259 - 265 (chain C) in PDB entry 3MY0
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 259 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B THR* 5.7 5.2 - - - -
195C GLN* 6.5 0.4 - - + -
242C GLU 5.3 0.2 - - - -
243C THR* 5.3 2.0 - - - -
246C TYR* 3.4 54.9 - + + +
247C ASN* 3.7 29.2 - - - -
257C LEU 3.6 1.6 + - - -
258C GLY* 1.3 73.6 - - - -
260C ILE* 1.3 69.0 + - - +
261C ALA* 3.3 38.4 - - - -
262C SER* 3.8 12.1 - - - -
275C LEU* 3.3 24.0 - - + -
276C ILE 4.2 1.6 - - - -
277C THR* 4.5 2.7 - - + +
278C HIS* 5.2 2.1 + - - -
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B THR* 5.7 0.7 + - - -
195C GLN* 4.5 8.3 - - - +
198C VAL* 3.7 35.2 - - + +
221C TRP* 4.1 13.5 - - + -
226C VAL* 3.6 30.3 - - + -
259C PHE* 1.3 84.9 - - - +
261C ALA* 1.3 63.2 + - + +
276C ILE* 2.9 15.1 + - + +
277C THR 3.7 20.4 - - - +
278C HIS* 4.0 20.4 - - + +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C GLN* 3.8 34.3 - - + +
198C VAL* 4.2 6.3 - - + -
199C ALA* 5.4 0.4 - - + -
259C PHE* 3.5 10.9 - - - -
260C ILE* 1.3 84.5 - - + +
262C SER* 1.3 62.2 + - - +
275C LEU* 3.3 10.6 - - - +
276C ILE* 2.9 46.0 + - + -
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Residues in contact with SER 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLN* 5.1 7.6 - - - +
239C TRP* 3.2 17.9 + - - -
243C THR* 2.6 44.6 + - - +
247C ASN* 4.8 1.6 - - - -
259C PHE* 3.8 13.2 - - - -
261C ALA* 1.3 79.2 - - - +
263C ASP* 1.3 62.5 + - - +
274C TRP 3.4 7.0 - - - -
275C LEU* 4.6 1.8 - - - -
276C ILE* 5.7 0.4 - - - -
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Residues in contact with ASP 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C GLN 5.8 0.7 - - - +
196C ARG* 4.7 11.8 - - - +
199C ALA* 3.1 35.1 - - + +
200C ARG* 5.0 0.5 + - - +
239C TRP* 3.8 9.8 + - - -
262C SER* 1.3 75.9 + - - +
264C MET* 1.3 91.7 + - - +
265C THR* 4.1 9.4 - - + -
273C LEU* 3.6 3.5 - - - -
274C TRP* 2.8 43.8 + - + +
276C ILE* 5.4 0.8 - - + +
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Residues in contact with MET 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C TRP* 4.6 13.2 - - + -
263C ASP* 1.3 93.3 + - - +
265C THR* 1.3 62.0 + - - +
271C THR* 5.0 15.0 - - - +
272C GLN 3.6 9.6 - - - +
273C LEU* 4.4 27.1 - - + -
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Residues in contact with THR 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ALA* 5.6 2.8 + - - -
263C ASP* 4.1 13.5 - - + -
264C MET* 1.3 76.6 - - - +
266C SER* 1.3 63.5 + - - +
267C ARG* 2.8 26.3 + - - +
268C ASN 4.4 0.5 - - - +
270C SER 3.7 1.6 - - - +
271C THR* 3.2 5.9 - - - -
272C GLN* 3.0 34.6 + - - +
274C TRP* 3.5 52.7 - - + +
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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