Contacts of the strand formed by residues 237 - 243 (chain B) in PDB entry 6EBT
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 GLN 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B ARG* 3.2 5.6 - - - -
234B THR* 2.8 31.9 + - - +
235B HIS* 4.2 12.8 - - + +
236B THR* 1.3 87.2 + - - +
238B ASP* 1.3 72.8 + - - +
239B ALA* 4.1 0.2 - - - +
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Residues in contact with ASP 238 (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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231B ILE* 4.2 11.6 - - + +
232B GLY 3.7 5.4 - - - -
233B ARG* 4.9 7.8 + - - +
234B THR* 4.8 1.6 + - - -
236B THR 4.8 2.3 - - - +
237B GLN* 1.3 82.8 - - - +
239B ALA* 1.3 59.4 + - - +
452B SER* 4.9 7.2 + - - -
453B LEU 5.5 3.1 + - - -
454B MET* 3.6 28.9 - - + +
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Residues in contact with ALA 239 (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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278A ALA* 5.8 1.8 - - + -
279A VAL* 3.7 17.5 - - + -
231B ILE* 3.3 18.0 - - - +
232B GLY 2.7 22.7 + - - +
234B THR* 3.7 23.1 - - + +
238B ASP* 1.3 75.9 - - - +
240B VAL* 1.3 70.4 + - - +
241B PRO 3.8 0.2 - - - -
454B MET* 3.5 18.5 - - - +
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Residues in contact with VAL 240 (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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278A ALA* 4.2 16.6 - - + +
279A VAL* 3.6 32.0 - - + +
281A THR* 4.8 2.9 - - - +
283A LEU* 3.7 28.5 - - + -
284A ASN* 5.4 3.8 - - - +
232B GLY* 3.2 13.3 + - - -
239B ALA* 1.3 78.2 - - - +
241B PRO* 1.3 77.4 - - + +
454B MET* 3.7 20.3 - - + +
457B THR* 6.0 1.3 - - - +
506B MET* 5.5 3.4 - - + -
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Residues in contact with PRO 241 (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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279A VAL* 3.9 2.8 - - - +
281A THR* 3.6 14.6 + - - +
229B ILE* 3.9 17.9 - - + -
230B LYS 3.3 15.9 - - - +
231B ILE* 4.4 4.9 - - + -
232B GLY 4.1 1.3 - - - +
240B VAL* 1.3 97.1 - - + +
242B LEU* 1.3 63.7 + - - +
449B MET* 4.6 4.5 - - + -
454B MET* 5.7 0.4 - - + -
455B LEU* 3.5 31.2 - - + -
503B PRO* 4.9 2.5 - - + -
506B MET* 3.9 33.0 - - + +
507B LEU* 4.2 6.5 - - + -
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Residues in contact with LEU 242 (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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279A VAL* 4.5 3.6 - - + +
281A THR* 3.8 9.2 - - + -
312A PHE* 3.9 22.4 - - + -
404A GLU* 3.7 35.0 - - + +
230B LYS* 2.9 39.9 + - - +
232B GLY* 3.2 33.2 - - - +
240B VAL 4.3 1.1 - - - +
241B PRO* 1.3 76.0 - - - +
243B THR* 1.3 67.4 + - - +
246B GLN* 3.5 13.0 - - - +
247B GLU* 4.0 20.4 - - + +
507B LEU* 3.9 7.6 - - - -
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Residues in contact with THR 243 (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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225B PHE 4.0 0.4 - - - -
226B ALA* 3.5 26.3 + - - +
227B GLN* 4.5 1.1 - - - -
228B ILE 3.1 16.2 - - - +
229B ILE* 3.9 21.3 - - + -
230B LYS* 4.2 1.6 - - - -
242B LEU* 1.3 77.3 - - - +
244B LEU* 1.3 64.6 + - - +
245B GLY 3.6 3.4 + - - -
246B GLN* 2.9 38.4 + - - +
247B GLU* 3.0 22.0 + - - +
507B LEU* 3.9 17.3 - - + -
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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