Contacts of the strand formed by residues 275 - 283 (chain A) in PDB entry 6BHG
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 TRP 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A THR* 4.1 30.7 - - + -
214A HIS* 6.4 0.7 - + - -
267A LYS* 3.5 3.3 - - - -
268A TYR* 2.8 50.9 + + + +
270A ASP* 6.5 0.9 - - + -
274A VAL* 1.3 87.8 + - - +
276A LEU* 1.3 66.3 + - - +
277A TYR* 5.4 2.9 - - + -
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Residues in contact with LEU 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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205A LEU* 4.0 26.7 - - + -
212A THR* 3.3 9.6 - - - +
213A TRP* 2.9 51.7 + - + +
214A HIS* 5.3 2.0 - - - -
215A LYS* 5.4 8.5 - - + -
265A VAL* 3.7 10.3 - - + -
266A ALA 3.5 2.5 - - - +
267A LYS* 3.7 37.2 - - + +
274A VAL* 5.9 0.7 - - + -
275A TRP* 1.3 75.0 - - - +
277A TYR* 1.3 61.2 + - - +
311A TYR* 3.9 23.1 - - + +
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Residues in contact with TYR 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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210A THR 5.0 1.6 - - - -
211A LYS* 3.5 41.6 - - + +
212A THR* 4.5 10.8 - - + -
213A TRP* 3.9 6.5 - - - -
265A VAL* 4.0 2.6 - - - +
266A ALA 2.9 29.7 + - - +
268A TYR* 3.8 31.9 - + + -
275A TRP* 5.1 2.2 - - + -
276A LEU* 1.3 74.8 - - - +
278A ALA* 1.3 82.9 + - + +
297A PHE* 3.6 14.7 - + + -
298A ASP* 4.0 12.4 - - + +
299A ASP* 3.8 43.2 + - + +
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Residues in contact with ALA 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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207A LYS* 5.4 4.5 - - - +
211A LYS 4.9 0.4 + - - -
213A TRP* 3.6 32.1 - - + +
263A ARG* 3.7 9.0 - - - +
264A VAL 3.3 9.6 - - - +
265A VAL* 4.3 1.6 - - - +
277A TYR* 1.3 87.2 - - + +
279A GLY* 1.3 59.5 + - - +
297A PHE* 3.5 3.9 - - - -
298A ASP* 3.0 41.2 + - + +
313A ILE* 4.4 2.9 - - + -
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Residues in contact with GLY 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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263A ARG* 3.0 19.4 + - - +
264A VAL* 2.8 32.5 + - - +
277A TYR 3.9 0.4 + - - -
278A ALA* 1.3 76.6 - - - +
280A ILE* 1.3 60.6 + - - +
295A ILE* 4.1 7.8 - - - +
296A PHE 3.3 12.3 - - - -
297A PHE* 3.8 2.9 - - - -
298A ASP* 3.5 7.4 - - - -
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Residues in contact with ILE 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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261A GLY* 3.8 17.7 - - - +
262A SER 3.3 2.0 - - - +
263A ARG* 3.6 27.6 - - - +
264A VAL* 4.6 0.4 - - - -
279A GLY* 1.3 75.7 - - - -
281A VAL* 1.3 78.9 + - - +
282A ALA* 3.3 2.4 + - + -
295A ILE* 3.5 6.7 - - - +
296A PHE* 2.8 38.2 + - + +
320A THR* 3.7 24.5 - - - +
321A TRP 4.5 0.2 - - - +
324A ILE* 4.2 14.6 - - + -
333A ILE* 3.9 39.0 - - + -
336A TYR* 6.0 1.3 - - + -
337A VAL* 4.4 4.3 - - + -
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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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258A LEU* 4.3 11.9 - - + -
259A TYR 3.4 25.4 - - - +
260A VAL* 3.3 4.2 - - - +
261A GLY 2.8 28.1 + - - -
262A SER* 2.9 24.3 + - - +
264A VAL* 3.8 26.7 - - + -
280A ILE* 1.3 73.5 - - - +
282A ALA* 1.3 60.4 + - - +
283A GLU 3.6 24.5 - - - +
284A THR* 4.1 3.6 - - + -
293A PHE* 3.9 15.5 - - + -
294A LEU 3.6 5.2 - - - +
295A ILE* 4.1 8.3 - - + -
310A LEU* 4.4 0.4 - - + -
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Residues in contact with ALA 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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260A VAL* 3.6 12.3 - - - +
280A ILE* 3.3 2.1 + - - +
281A VAL* 1.3 72.0 - - - +
283A GLU* 1.4 57.5 + - - +
294A LEU* 2.7 22.1 + - + +
296A PHE* 3.5 51.1 - - + -
336A TYR* 2.6 35.0 + - + +
340A TYR* 4.4 1.9 - - - -
343A ARG* 3.8 2.1 + - - -
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Residues in contact with GLU 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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260A VAL* 4.0 6.1 - - - -
281A VAL* 3.6 8.5 - - - +
282A ALA* 1.4 79.8 - - - +
284A THR* 1.3 67.1 + - - +
286A ASN* 4.4 8.4 + - - +
289A ASN* 2.9 25.9 + - - +
292A ARG 4.7 0.2 - - - -
293A PHE* 3.4 5.2 - - - -
294A LEU* 3.0 35.8 + - + +
304A TYR* 2.6 26.6 + - - -
340A TYR* 5.5 3.4 - - - +
343A ARG* 2.8 30.2 + - - +
373A SER* 2.6 28.2 + - - -
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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