Contacts of the strand formed by residues 265 - 271 (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 ILE 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A TYR* 5.3 1.1 - - + -
212A PRO* 3.8 17.3 - - + -
213A ASP 3.0 10.7 + - - +
214A LEU* 3.5 7.6 - - + +
215A GLU* 3.2 21.8 + - - +
245A PHE* 4.0 22.7 - - + +
248A ALA* 3.6 28.5 - - + -
249A MET* 3.7 30.5 - - + -
252A THR* 4.3 8.7 - - - +
264A PRO* 1.3 75.4 - - - +
266A LYS* 1.3 63.5 - - - +
267A VAL* 4.7 0.4 - - + -
280A MET* 3.6 30.3 - - + -
281A SER 3.6 7.2 - - - +
282A ASP* 4.4 4.5 - - + +
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Residues in contact with LYS 266 (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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215A GLU* 3.6 34.3 + - + +
264A PRO* 4.1 18.8 - - - +
265A ILE* 1.3 76.2 - - - +
267A VAL* 1.3 63.2 + - - +
279A LYS 3.6 0.9 - - - +
280A MET* 3.4 2.4 - - - +
281A SER* 2.7 49.0 + - - +
283A ARG* 3.2 38.5 - - - +
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Residues in contact with VAL 267 (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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193A VAL* 4.2 15.5 - - + -
214A LEU* 4.0 8.3 - - + -
215A GLU 2.8 11.4 + - - +
216A ILE* 3.2 7.4 - - + +
217A GLN* 2.9 26.0 + - - +
241A LEU* 5.6 2.0 - - + -
245A PHE* 4.0 27.1 - - + -
265A ILE* 4.7 0.2 - - + -
266A LYS* 1.3 80.0 - - - +
268A MET* 1.3 66.3 + - - +
269A VAL* 4.2 9.2 - - + -
278A ILE* 3.8 24.0 - - + -
279A LYS 3.0 11.0 - - - +
280A MET* 4.0 15.9 - - + -
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Residues in contact with MET 268 (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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217A GLN* 3.2 22.9 - - + +
219A ILE* 3.6 26.9 - - + -
267A VAL* 1.3 76.0 - - - +
269A VAL* 1.3 64.4 + - - +
270A ALA* 3.3 30.5 - - + -
277A SER 3.5 1.2 - - - +
278A ILE* 3.3 5.0 - - - +
279A LYS* 2.8 49.8 + - + +
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Residues in contact with VAL 269 (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* 3.9 31.4 - - + -
190A SER* 4.1 16.4 - - - +
193A VAL* 4.3 5.6 - - + -
216A ILE* 4.6 4.9 - - + -
217A GLN 2.8 8.2 + - - +
218A GLU* 3.2 7.9 - - + -
219A ILE 2.8 24.3 + - - -
228A ILE* 3.3 32.2 - - + +
267A VAL* 4.2 15.5 - - + -
268A MET* 1.3 77.8 - - - +
270A ALA* 1.3 60.7 + - - +
276A LEU* 4.2 11.0 - - + -
277A SER 3.4 3.6 - - - +
278A ILE* 4.3 5.8 - - + -
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Residues in contact with ALA 270 (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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219A ILE* 3.5 13.0 - - + +
228A ILE* 4.5 0.9 - - - -
268A MET* 3.3 30.0 - - + -
269A VAL* 1.3 74.0 - - - +
271A LEU* 1.3 62.6 + - - +
272A GLY 4.1 0.4 - - - -
275A ASP 4.0 0.5 - - - +
276A LEU* 3.3 4.7 - - - +
277A SER* 2.7 50.5 + - - +
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Residues in contact with LEU 271 (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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219A ILE 3.0 9.5 + - - +
220A ASN* 3.9 27.3 - - - +
221A ALA* 3.2 27.4 + - - +
222A ALA 4.7 0.9 + - - -
228A ILE* 4.1 30.7 - - + +
229A HIS 4.7 9.9 - - - +
270A ALA* 1.3 74.1 - - - +
272A GLY* 1.3 77.8 + - - +
275A ASP 3.7 1.8 - - - +
276A LEU* 4.3 12.1 - - + +
354A ALA* 3.7 22.9 - - + -
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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