Contacts of the strand formed by residues 261 - 267 (chain C) in PDB entry 3MDY
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 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180C ILE* 4.6 1.4 - - - +
190C SER* 3.3 28.7 - - - -
191C GLY* 3.6 10.3 - - - +
197C GLN* 3.9 4.0 - - - -
245C THR* 4.1 10.5 - - + -
248C TYR* 3.7 36.1 - + + +
249C GLN* 3.4 33.4 - - + -
254C ARG* 3.0 28.2 + - - +
259C LEU 3.4 3.6 + - - -
260C GLY* 1.3 73.8 - - - -
262C ILE* 1.3 68.6 + - - +
263C ALA* 3.6 31.9 - - - -
264C ALA 3.8 3.4 - - - -
277C LEU* 3.5 34.1 - - + -
278C ILE 4.0 3.6 - - - -
279C THR* 4.4 3.6 - - + +
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Residues in contact with ILE 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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176C LEU* 4.3 16.2 - - + -
180C ILE* 3.9 17.3 - - + -
191C GLY* 3.6 1.9 - - - -
192C LEU* 2.9 53.2 + - + +
197C GLN* 4.0 0.7 - - - +
200C ILE* 4.7 2.5 - - + -
228C VAL* 3.7 22.9 - - + -
261C PHE* 1.3 83.5 - - - +
263C ALA* 1.3 64.5 + - + +
278C ILE* 2.8 20.8 + - + +
279C THR* 3.5 31.0 - - - +
280C ASP* 3.7 14.1 - - - +
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Residues in contact with ALA 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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197C GLN* 3.5 23.3 - - + +
200C ILE* 3.3 32.8 - - + -
261C PHE* 3.6 12.2 - - - -
262C ILE* 1.3 84.4 - - + +
264C ALA* 1.3 58.4 + - - +
278C ILE* 2.6 46.6 + - + +
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Residues in contact with ALA 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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197C GLN* 3.0 14.4 + - - +
198C ARG* 3.4 5.5 - - - -
241C TRP* 3.9 13.7 - - + -
245C THR* 3.6 37.0 - - + +
261C PHE* 4.4 0.7 - - + -
263C ALA* 1.3 75.3 - - - +
265C ASP* 1.3 63.3 + - - +
276C TYR 3.1 13.5 - - - +
277C LEU* 4.8 0.7 - - - -
88D HIS* 3.2 24.0 - - + -
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Residues in contact with ASP 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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197C GLN 3.4 6.2 - - - +
198C ARG* 2.9 44.8 + - - +
199C THR 3.9 0.3 - - - -
200C ILE 3.2 11.8 + - - -
201C ALA* 2.7 40.5 + - + +
202C LYS 4.4 0.7 + - - -
241C TRP* 4.0 2.6 - - - -
264C ALA* 1.3 75.0 - - - +
266C ILE* 1.3 76.8 + - - +
275C LEU* 3.8 0.2 - - - -
276C TYR* 2.8 38.1 + - + +
278C ILE* 4.8 6.9 - - + +
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Residues in contact with ILE 266 (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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269A THR* 3.9 17.0 + - - +
198C ARG* 3.7 23.9 + - - +
201C ALA* 3.8 7.2 - - - +
241C TRP* 3.9 13.0 - - + -
265C ASP* 1.3 91.9 + - - +
267C LYS* 1.3 65.9 + - - +
273C THR* 3.6 28.0 - - + -
274C GLN 3.4 5.6 - - - +
275C LEU* 3.5 23.1 - - + -
86D THR* 3.8 30.1 - - + +
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Residues in contact with LYS 267 (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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269A THR* 3.6 10.5 - - + -
54B GLN* 5.8 1.6 + - - -
201C ALA* 4.1 25.6 - - + +
202C LYS* 5.3 4.5 - - - +
266C ILE* 1.3 77.7 - - - +
268C GLY* 1.3 69.6 + - - +
272C TRP 5.3 1.6 + - - -
273C THR* 3.6 2.8 - - - +
274C GLN* 2.8 61.6 + - - +
276C TYR* 3.1 31.2 - - + +
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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