Contacts of the strand formed by residues 275 - 285 (chain A) in PDB entry 2BU6
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 ASP 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ALA 4.0 0.3 - - - +
271A LEU* 3.7 1.2 - - - +
272A GLY* 2.7 36.7 + - - +
274A GLU* 1.3 98.4 - - - +
276A LEU* 1.3 58.5 + - - +
277A SER* 3.9 13.8 + - - +
351A TYR* 4.4 18.1 - - + -
352A LEU 3.6 7.9 - - - +
353A LYS* 4.9 8.8 + - - +
354A ALA* 3.9 1.3 - - - -
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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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189A VAL* 4.1 15.9 - - + -
228A ILE* 4.1 20.0 - - + -
229A HIS 4.6 1.1 - - - +
230A MET* 3.4 45.1 - - + -
269A VAL* 4.2 7.9 - - + -
270A ALA 3.3 9.6 - - - +
271A LEU* 4.3 13.2 - - + +
275A ASP* 1.3 74.5 - - - +
277A SER* 1.3 60.6 + - - +
278A ILE* 4.2 17.7 - - + +
350A ILE 3.8 1.7 - - - +
352A LEU* 3.0 43.4 + - + +
354A ALA* 4.2 12.3 - - + +
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Residues in contact with SER 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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268A MET 3.5 0.9 - - - +
269A VAL* 3.4 4.5 - - - +
270A ALA* 2.7 49.5 + - - +
275A ASP* 3.9 13.0 + - - +
276A LEU* 1.3 73.8 - - - +
278A ILE* 1.3 64.8 + - - +
279A LYS* 4.1 1.1 - - - -
349A VAL* 4.5 4.5 - - - -
350A ILE 3.5 4.3 - - - -
351A TYR* 3.4 32.3 - - - +
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Residues in contact with ILE 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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189A VAL* 3.5 27.8 - - + -
193A VAL* 4.5 1.8 - - + -
237A LEU* 3.8 26.0 - - + -
241A LEU* 4.1 21.8 - - + -
267A VAL* 3.8 24.5 - - + -
268A MET 3.3 3.8 - - - +
269A VAL* 4.3 6.7 - - + -
276A LEU* 4.2 10.5 - - + +
277A SER* 1.3 78.2 - - - +
279A LYS* 1.3 63.1 + - - +
280A MET* 5.6 1.5 - - + +
348A ALA 3.6 1.7 - - - +
349A VAL* 3.3 4.6 - - - -
350A ILE* 2.8 51.7 + - + +
352A LEU* 4.5 10.1 - - + -
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Residues in contact with LYS 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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266A LYS 3.6 0.9 - - - +
267A VAL* 3.0 8.9 - - - +
268A MET* 2.8 53.1 + - + +
277A SER* 4.1 1.6 - - - -
278A ILE* 1.3 74.6 - - - +
280A MET* 1.3 64.0 + - - +
281A SER* 3.7 14.8 - - - +
339A PHE* 4.7 4.6 - - + -
347A ASP* 3.3 31.7 + - + +
348A ALA 3.4 3.6 - - - +
349A VAL* 3.6 25.5 - - + +
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Residues in contact with MET 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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241A LEU* 4.9 7.0 - - + +
244A LEU* 2.7 48.9 - - + +
245A PHE* 3.6 35.9 - - - -
248A ALA* 3.2 20.4 - - + -
265A ILE* 3.6 20.0 - - + -
266A LYS 3.4 2.9 - - - -
267A VAL* 4.0 9.4 - - + -
278A ILE* 6.0 0.9 - - + -
279A LYS* 1.3 75.1 - - - +
281A SER* 1.3 59.9 + - - +
282A ASP* 4.1 3.1 + - - +
346A THR 3.5 2.6 - - - +
347A ASP* 3.4 2.1 - - - -
348A ALA* 2.8 46.7 + - + +
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Residues in contact with SER 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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264A PRO 4.2 1.6 - - - +
265A ILE* 3.6 5.0 - - - -
266A LYS* 2.7 48.3 + - - +
279A LYS* 3.7 11.4 - - - +
280A MET* 1.3 73.5 - - - +
282A ASP* 1.3 60.8 - - - +
283A ARG* 4.8 5.3 + - - -
346A THR 3.4 4.3 - - - -
347A ASP* 3.0 26.9 + - - -
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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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248A ALA* 3.6 35.6 - - + +
251A ALA* 5.0 3.1 - - - +
252A THR* 3.9 11.4 - - - +
264A PRO 4.8 5.4 - - - -
265A ILE* 4.4 4.3 - - + -
280A MET* 4.9 3.8 - - - +
281A SER* 1.3 76.6 - - - +
283A ARG* 1.3 65.0 + - - +
284A GLY* 2.9 18.9 + - - -
344A PHE* 4.9 3.3 - - - -
345A GLY* 3.1 3.3 - - - -
346A THR* 3.0 54.4 + - - +
347A ASP* 5.1 0.7 - - - +
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Residues in contact with ARG 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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252A THR* 4.3 5.2 + - - +
256A HIS* 3.0 24.9 - - + +
263A PRO* 3.6 32.3 - - + +
264A PRO* 3.5 25.6 + - - +
266A LYS* 3.2 40.9 - - - +
281A SER* 4.8 6.6 + - - -
282A ASP* 1.3 75.5 - - - +
284A GLY* 1.3 55.3 + - - +
285A GLY 3.1 3.8 + - - -
344A PHE* 3.1 53.1 - - + +
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Residues in contact with GLY 284 (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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251A ALA* 3.3 38.7 - - - +
252A THR* 3.7 5.1 + - - -
255A SER* 3.3 19.2 - - - -
282A ASP* 2.9 17.0 + - - +
283A ARG* 1.3 74.6 - - - +
285A GLY* 1.3 55.4 + - - +
286A GLY 3.3 9.7 + - - +
344A PHE 3.7 0.4 + - - -
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Residues in contact with GLY 285 (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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255A SER* 3.8 9.1 + - - -
283A ARG 3.1 3.4 + - - -
284A GLY* 1.3 74.9 - - - +
286A GLY* 1.3 57.9 + - - +
342A GLU* 4.8 0.3 - - - +
343A GLY* 2.5 38.0 + - - -
344A PHE 3.0 19.8 + - - -
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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