Contacts of the strand formed by residues 234 - 246 (chain A) in PDB entry 1BY7
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 MET 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS* 4.1 0.3 - - - -
215A LYS* 3.1 17.3 + - + +
220A TYR* 3.4 50.4 - - + -
221A PRO 5.4 0.2 - - - +
222A PHE* 4.4 0.7 - - + -
232A VAL* 3.4 24.1 + - + -
233A GLN* 1.3 92.6 + - - +
235A MET* 1.3 64.4 + - - +
308A TYR* 4.1 13.0 - - + -
309A ILE* 3.4 32.1 - - - -
310A PRO* 3.5 4.5 - - + -
389A VAL* 5.8 0.4 - - + -
390A ALA 3.5 21.5 - - - +
391A ASP* 3.8 22.2 - - + -
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Residues in contact with MET 235 (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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212A PHE* 3.5 25.5 - - + -
213A GLU 3.2 7.9 - - - +
214A LYS* 5.1 7.6 - - + -
233A GLN* 5.3 0.7 - - + -
234A MET* 1.3 78.9 - - - +
236A TYR* 1.3 61.8 - - - +
307A VAL 3.6 0.7 - - - +
308A TYR* 3.4 7.1 - - - +
309A ILE* 2.9 52.7 + - + +
310A PRO 3.4 21.5 - - - +
311A GLN* 4.0 19.5 - - + +
362A VAL* 4.2 5.6 - - + -
363A ASN* 3.5 40.2 - - - +
364A GLU* 3.5 12.8 - - + +
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Residues in contact with TYR 236 (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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212A PHE* 3.5 1.6 - - - -
213A GLU* 2.7 57.2 + - + +
215A LYS* 3.5 39.9 - - + -
235A MET* 1.3 77.2 - - - +
237A LEU* 1.3 68.0 + - - +
238A ARG* 3.4 28.2 + - + +
306A GLU* 2.3 46.5 + - + +
307A VAL 3.3 6.5 - - - -
308A TYR* 3.4 39.9 - + + -
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Residues in contact with LEU 237 (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* 3.5 30.5 - - + +
211A PRO 3.3 25.6 - - - +
212A PHE* 3.4 27.8 - - + -
236A TYR* 1.3 84.0 - - - +
238A ARG* 1.3 66.2 + - - +
239A GLU* 3.8 21.8 - - + -
241A LEU* 3.9 20.0 - - + -
256A LEU* 4.5 7.6 - - + -
305A VAL 3.7 0.9 - - - +
306A GLU* 3.5 0.9 - - - -
307A VAL* 2.6 40.9 + - + +
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Residues in contact with ARG 238 (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* 5.5 1.0 - - - +
236A TYR* 3.4 34.9 + - + +
237A LEU* 1.3 76.7 - - - +
239A GLU* 1.3 67.2 + - - +
304A GLU* 2.9 32.7 + - + +
305A VAL 3.4 5.8 - - - +
306A GLU* 3.4 34.6 + - + +
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Residues in contact with GLU 239 (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* 2.9 32.9 + - - +
237A LEU* 3.8 22.6 - - + -
238A ARG* 1.3 81.4 - - - +
240A LYS* 1.3 96.4 + - - +
241A LEU* 3.5 18.5 + - + +
303A ASP 3.4 0.3 - - - +
304A GLU* 4.2 6.5 - - - -
305A VAL 2.9 30.2 + - - +
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Residues in contact with LYS 240 (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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239A GLU* 1.3 93.2 + - - +
241A LEU* 1.3 67.7 + - - +
302A GLU* 3.3 36.2 - - + +
303A ASP 3.1 9.4 - - - +
304A GLU* 4.4 27.1 + - + +
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Residues in contact with LEU 241 (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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237A LEU* 3.9 14.4 - - + -
239A GLU* 3.8 20.9 - - + +
240A LYS* 1.3 82.8 - - - +
242A ASN* 1.3 66.5 + - - +
243A ILE 3.6 0.5 + - - -
254A LEU* 4.0 10.5 - - + -
255A GLU 3.6 15.0 - - - +
256A LEU* 3.7 23.1 - - + -
257A PRO* 3.7 21.5 - - + -
301A ALA 3.6 0.3 - - - +
302A GLU* 4.0 1.5 - - - +
303A ASP* 2.8 29.8 + - - +
305A VAL* 3.9 16.1 - - + +
307A VAL* 3.7 22.7 - - + -
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Residues in contact with ASN 242 (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* 1.3 73.5 - - - +
243A ILE* 1.3 59.6 + - - +
254A LEU* 3.4 4.5 - - - +
255A GLU* 3.1 59.2 + - + +
300A MET* 3.4 22.2 + - + +
301A ALA 3.4 3.8 - - - -
302A GLU* 3.4 32.1 + - - +
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Residues in contact with ILE 243 (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 4.4 0.2 - - - +
242A ASN* 1.3 77.3 - - - +
244A GLY* 1.3 67.1 - - - +
252A GLN* 3.7 25.6 - - + +
253A ILE 3.3 13.9 - - - +
254A LEU* 4.1 11.2 - - + -
300A MET* 4.1 5.2 - - - -
301A ALA* 2.9 33.0 + - - +
303A ASP* 4.2 19.3 - - + +
305A VAL* 3.8 33.2 - - + -
386A PRO* 4.2 13.2 - - + -
388A PHE* 4.5 5.8 - - + -
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Residues in contact with GLY 244 (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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243A ILE* 1.3 78.7 - - - +
245A TYR* 1.3 61.4 + - - +
252A GLN* 3.4 9.0 - - - +
253A ILE* 2.8 43.4 + - - +
299A LYS 3.6 18.2 - - - -
300A MET* 4.2 0.4 - - - -
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Residues in contact with TYR 245 (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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244A GLY* 1.3 75.4 - - - +
246A ILE* 1.3 73.0 - - - +
247A GLU* 3.6 27.7 + - + +
250A LYS* 3.5 24.4 - - + +
251A ALA 3.4 18.4 - - - -
252A GLN* 3.8 16.6 - - + -
253A ILE* 5.4 0.2 - - - -
270A ASP* 2.7 38.7 + - + -
299A LYS* 4.4 8.5 + - - +
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Residues in contact with ILE 246 (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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245A TYR* 1.3 73.2 - - - +
247A GLU* 1.3 56.9 + - - +
248A ASP* 2.9 26.7 - - - +
249A LEU* 3.6 18.6 - - + -
250A LYS* 2.9 25.8 + - - -
251A ALA* 2.9 31.3 + - + +
252A GLN 5.1 0.4 - - - -
253A ILE* 4.4 21.1 - - + -
267A LEU* 4.9 3.8 - - + -
282A LEU* 4.6 5.2 - - + -
294A TRP* 3.6 61.5 - - + +
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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