Contacts of the strand formed by residues 275 - 283 (chain A) in PDB entry 3MIB
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 TYR 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ALA* 3.6 29.3 - - + +
148A THR* 5.9 0.2 - - - -
238A ALA* 3.3 2.9 - - - -
239A TYR* 2.8 56.9 + + + +
240A ARG* 5.6 0.9 - - - -
241A VAL* 6.0 0.9 - - + -
266A GLN* 3.3 35.3 + - + -
270A LEU* 4.6 4.9 - - - +
271A PRO* 2.7 36.4 + - - +
272A GLN* 5.0 0.7 - - - -
273A ALA* 3.3 25.8 - - + -
274A PHE* 1.3 75.4 - - - +
276A PRO* 1.4 75.8 - - + +
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Residues in contact with PRO 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A THR* 3.8 33.6 - - + +
237A PHE 3.5 11.7 - - - +
238A ALA* 4.3 2.5 - - + -
239A TYR* 3.8 9.1 - - - -
274A PHE 4.3 0.9 - - - +
275A TYR* 1.4 93.5 - - + +
277A VAL* 1.3 68.6 + - - +
278A GLU 3.8 1.0 + - - -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 3.5 38.6 - - + +
237A PHE* 3.1 18.6 + - - +
238A ALA 3.8 2.0 - - - +
239A TYR* 4.0 11.9 - - + -
262A LEU 4.9 1.8 - - - +
263A ILE* 3.5 25.6 - - - +
276A PRO* 1.3 78.5 - - - +
278A GLU* 1.3 67.3 + - - +
279A HIS* 3.0 32.7 + - - +
280A PRO* 4.9 2.2 - - + +
281A VAL* 4.1 12.1 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU* 5.6 6.1 - - - +
263A ILE 5.0 0.8 + - - -
276A PRO 3.8 2.2 + - - -
277A VAL* 1.3 77.3 - - + +
279A HIS* 1.3 90.0 + - + +
280A PRO* 4.6 1.7 - - - +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A VAL* 3.0 19.7 - - - +
278A GLU* 1.3 113.1 + - + +
280A PRO* 1.4 75.7 - - + +
281A VAL* 3.0 11.2 + - + +
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Residues in contact with PRO 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A HIS* 4.8 15.7 - - + -
236A VAL 3.6 13.5 - - - +
237A PHE* 5.5 4.5 - - + -
277A VAL* 4.7 3.3 - - + +
278A GLU 4.6 2.2 - - - +
279A HIS* 1.4 83.2 - - + +
281A VAL* 1.3 61.1 + - - +
282A ASP* 3.9 3.3 + - - +
322A TYR* 5.5 6.3 - - + +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A HIS* 4.4 1.6 - - - -
236A VAL* 2.9 41.8 + - + +
254A ARG* 3.7 39.5 - - + +
261A THR* 4.3 11.4 - - + -
262A LEU 3.8 21.3 - - - +
263A ILE* 4.3 15.7 - - + -
277A VAL* 4.1 6.3 - - + -
279A HIS* 3.0 21.3 + - + +
280A PRO* 1.3 71.8 - - - +
282A ASP* 1.3 68.0 + - - +
283A VAL* 3.8 3.1 + - + -
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A NO2 3.5 21.0 + - - +
233A PRO* 5.5 2.2 - - + -
234A MET 3.3 6.5 - - - +
235A HIS* 3.4 29.7 - - + +
254A ARG* 2.8 38.6 + - - -
256A ARG* 3.0 28.5 + - - -
280A PRO 3.9 4.0 + - - +
281A VAL* 1.3 73.1 - - - +
283A VAL* 1.3 59.9 + - - +
284A THR* 3.4 12.6 + - - +
359A NI 4.2 2.6 - - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A TYR* 3.5 32.8 - - + -
233A PRO* 3.3 4.3 - - - +
234A MET* 2.9 56.8 + - + -
236A VAL* 4.3 13.7 - - + -
254A ARG* 4.3 12.8 - - + -
263A ILE* 4.8 0.9 - - + -
281A VAL* 4.4 2.7 - - + +
282A ASP* 1.3 78.0 - - - +
284A THR* 1.3 64.7 + - - +
287A ASP* 3.6 19.1 - - + -
289A LEU* 4.0 21.5 - - + -
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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