Contacts of the strand formed by residues 265 - 272 (chain B) in PDB entry 4BGG
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 265 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B THR* 5.3 2.5 - - - -
252B TYR* 3.4 63.9 - + + -
253B ASN* 4.9 12.8 - - + -
256B MET* 6.4 0.9 - - + -
257B LEU 5.5 1.5 + - - +
263B LEU 3.6 3.8 + - - -
264B GLY* 1.3 73.4 - - - -
266B ILE* 1.3 76.5 + - - +
267B ALA* 3.4 35.7 - - - -
268B SER* 3.7 11.4 - - - -
281B LEU* 3.7 17.7 - - + -
282B ILE 4.2 2.7 - - - -
283B THR* 4.5 4.0 - - - -
284B HIS* 4.8 4.0 - - - -
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.8 3.3 - - + +
227B TRP* 4.2 28.0 - - + -
232B VAL* 3.8 21.1 - - + -
265B PHE* 1.3 90.3 - - - +
267B ALA* 1.3 70.9 + - + +
282B ILE* 3.0 19.1 + - + +
283B THR* 3.8 27.4 - - - +
284B HIS* 3.8 28.3 - - + +
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 4.1 32.3 - - + -
265B PHE* 3.4 16.2 - - - -
266B ILE* 1.3 87.8 - - + +
268B SER* 1.3 60.0 + - - +
269B ASP* 4.8 2.7 - - - +
281B LEU 3.7 0.3 - - - -
282B ILE* 2.7 43.9 + - + +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B TRP* 3.0 22.7 + - - -
249B THR* 2.8 39.0 + - - -
265B PHE* 3.7 14.3 - - - -
267B ALA* 1.3 77.6 - - - +
269B ASP* 1.3 68.3 + - - +
280B TRP 3.3 6.1 + - - -
281B LEU* 4.5 2.9 - - - +
282B ILE* 4.8 0.7 - - - +
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B THR* 3.7 20.2 + - - +
204B VAL* 4.0 9.5 + - - +
205B ALA* 3.3 41.7 + - + +
245B TRP* 4.0 4.2 + - - -
267B ALA* 4.8 2.6 - - - +
268B SER* 1.3 79.5 + - - +
270B MET* 1.3 62.9 + - - +
271B THR* 6.4 0.4 - - + -
278B GLN 4.1 0.3 - - - +
279B LEU* 3.7 0.7 - - - -
280B TRP* 2.8 42.6 + - + +
282B ILE* 4.6 4.7 - - + +
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Residues in contact with MET 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU* 3.7 23.6 - - + +
245B TRP* 3.7 30.0 - - + -
269B ASP* 1.3 76.8 + - - +
271B THR* 1.3 73.1 + - - +
272B SER* 3.8 24.5 - - - -
277B THR* 4.4 4.0 - - + -
278B GLN 3.3 7.4 - - - +
279B LEU* 3.3 23.1 - - + -
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Residues in contact with THR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B ASP* 6.4 0.7 - - + -
270B MET* 1.3 80.9 - - - +
272B SER* 1.3 60.0 + - - +
273B ARG* 5.7 2.5 - - - -
276B SER 3.9 1.0 - - - +
277B THR* 3.2 3.8 - - - +
278B GLN* 2.9 65.0 + - - +
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Residues in contact with SER 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLU* 5.5 0.3 + - - -
270B MET* 3.8 20.5 - - - +
271B THR* 1.3 75.9 - - - +
273B ARG* 1.3 71.6 + - - +
276B SER 3.4 4.5 - - - -
277B THR* 2.8 21.9 + - - +
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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