Contacts of the strand formed by residues 316 - 325 (chain B) in PDB entry 2BTO
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 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300B PHE* 5.2 3.4 - + - -
311B PRO* 3.7 24.9 - - + -
312B MET* 3.9 11.9 - - + -
315B ARG* 1.3 72.9 - - - +
317B LEU* 1.3 62.6 + - - +
318B SER 4.3 2.0 - - - +
319B THR* 3.7 24.0 - - - +
344B LEU* 3.7 31.0 - - + -
345B PRO* 2.8 44.3 + - + +
346B LEU* 3.9 7.6 - - + -
347B THR* 3.4 21.4 + - - -
352B THR* 3.9 8.3 + - + +
372B LEU* 5.1 11.2 - - + -
374B ALA* 3.8 24.2 - - + -
375B ASN 3.6 2.5 - - - -
376B ASN* 3.4 20.6 - - + -
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Residues in contact with LEU 317 (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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265B PRO* 4.1 20.1 - - + +
269B LEU* 3.5 42.0 - - + -
315B ARG 3.8 5.2 - - - +
316B PHE* 1.3 74.4 - - - +
318B SER* 1.3 61.0 + - - +
347B THR* 3.9 22.2 - - + +
350B ILE* 4.4 6.9 - - + +
351B PRO 4.1 4.7 - - - +
352B THR* 3.4 24.6 - - - +
353B ALA 3.9 0.2 + - - -
375B ASN* 2.6 33.2 + - + +
376B ASN 4.5 0.7 - - - -
377B THR* 3.4 35.9 - - + +
427B TYR* 4.6 3.1 - - + -
430B ALA* 4.4 4.7 - - + -
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Residues in contact with SER 318 (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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262B ASN 2.6 26.5 + - - -
263B LEU* 3.5 27.1 - - - +
265B PRO* 5.1 3.4 - - - -
316B PHE* 3.4 3.0 - - - -
317B LEU* 1.3 83.3 + - - +
319B THR* 1.3 76.0 + - - +
352B THR* 4.0 1.3 - - - -
353B ALA* 3.5 18.1 - - - +
374B ALA* 3.5 3.1 - - - +
375B ASN* 3.0 26.9 + - - +
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Residues in contact with THR 319 (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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262B ASN* 6.1 0.2 - - - +
263B LEU* 3.9 5.5 - - - +
300B PHE* 4.6 5.4 - - + -
316B PHE* 3.7 21.5 - - + +
318B SER* 1.3 87.2 + - - +
320B ALA* 1.3 62.7 - - - +
321B VAL* 4.5 2.5 - - + -
344B LEU* 4.2 4.6 - - + +
352B THR* 5.4 1.1 - - - +
353B ALA* 3.1 6.3 + - - +
354B PHE* 3.4 37.2 - - + -
355B LYS* 2.8 31.4 + - - +
372B LEU* 3.6 25.4 - - + -
373B LEU 3.4 5.8 - - - -
374B ALA* 4.4 0.5 - - - +
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Residues in contact with ALA 320 (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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259B LEU* 4.5 13.7 - - + -
262B ASN* 6.4 0.2 - - + -
263B LEU* 3.8 15.7 - - + +
319B THR* 1.3 75.2 - - - +
321B VAL* 1.3 64.1 + - - +
322B LEU* 4.4 17.6 - - + +
355B LYS* 3.2 18.2 - - + +
371B VAL 3.7 1.6 - - - +
372B LEU* 3.5 4.0 - - - +
373B LEU* 2.9 38.5 + - + +
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Residues in contact with VAL 321 (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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299B LEU* 4.2 20.4 - - + -
300B PHE* 3.6 32.3 - - + -
319B THR* 4.5 1.1 - - + -
320B ALA* 1.3 76.2 - - - +
322B LEU* 1.3 65.8 + - - +
323B TYR* 4.7 4.9 - - + +
337B LEU* 4.3 22.2 - - + -
354B PHE* 4.3 13.0 - - + -
355B LYS 2.9 9.2 + - - +
356B ILE* 3.5 10.7 - - + +
357B GLY 2.9 26.9 + - - +
370B MET* 4.4 15.5 - - + -
371B VAL 3.6 3.4 - - - +
372B LEU* 4.5 3.6 - - + -
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Residues in contact with LEU 322 (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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239B GLY 4.5 9.5 - - - +
240B ILE* 3.9 34.3 - - + +
243B SER* 4.4 14.1 - - - +
254B ILE* 4.4 7.0 - - + -
259B LEU* 4.3 20.0 - - + -
320B ALA* 4.4 11.7 - - + +
321B VAL* 1.3 78.0 - - - +
323B TYR* 1.3 63.2 + - - +
324B ARG* 5.4 1.0 - - - +
355B LYS* 5.9 0.9 - - + -
357B GLY* 4.0 16.8 - - - +
369B SER 4.1 0.5 - - - +
370B MET* 3.4 3.5 - - - -
371B VAL* 2.8 43.3 + - + +
373B LEU* 4.0 24.9 - - + -
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Residues in contact with TYR 323 (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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292B ILE* 3.9 20.1 - - + +
295B MET* 5.0 2.0 - - - -
296B ILE* 5.9 0.7 - - + -
321B VAL* 3.7 6.1 + - + -
322B LEU* 1.3 75.7 - - - +
324B ARG* 1.3 86.2 + - - +
325B GLY 4.0 0.4 - - - -
326B ILE 2.7 30.1 + - - -
327B MET* 3.9 24.3 - - + -
333B ALA* 5.5 2.7 - - + -
337B LEU* 6.3 2.9 - - + -
356B ILE* 5.8 2.5 - - + -
357B GLY 3.1 15.7 + - - +
358B TYR* 3.4 31.7 + + + -
359B VAL* 2.9 24.3 + - - +
368B LYS* 3.4 20.3 - - + +
369B SER 3.7 3.8 - - - -
370B MET* 3.4 44.2 - - + -
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Residues in contact with ARG 324 (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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29B GLU* 2.8 41.2 + - - -
235B GLU 5.6 0.2 + - - -
238B ALA* 3.9 19.6 + - - +
239B GLY* 4.3 12.5 - - - +
242B ALA* 3.8 16.8 - - + +
246B PHE* 3.8 14.8 - - - -
322B LEU 5.4 1.1 - - - +
323B TYR* 1.3 84.0 - - - +
325B GLY* 1.3 63.7 + - - +
359B VAL* 3.0 20.4 - - + +
361B GLN 3.0 17.5 + - - +
362B PRO* 3.2 18.0 + - + -
363B GLY* 3.3 18.6 - - - +
368B LYS* 3.4 2.8 - - - -
369B SER* 3.1 55.4 + - - +
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Residues in contact with GLY 325 (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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324B ARG* 1.3 75.1 - - - +
326B ILE* 1.3 64.3 + - - +
358B TYR* 2.8 29.8 + - - -
359B VAL 2.9 9.9 + - - -
360B GLU 3.3 17.8 + - - +
361B GLN 3.8 1.2 + - - -
362B PRO* 3.8 12.3 - - - -
367B ARG 3.3 11.4 - - - -
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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