Contacts of the helix formed by residues 239 - 249 (chain A) in PDB entry 2YBE
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 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU* 3.9 22.9 - - + +
212A GLY 3.4 25.4 - - - +
213A GLY 4.1 0.6 + - - +
215A LYS 4.6 1.8 - - - +
216A VAL* 3.9 30.7 - - - -
219A LYS* 4.0 15.9 - - - -
220A ILE* 3.7 38.9 - - + +
223A ILE* 4.1 12.1 - - + -
235A ILE* 3.6 14.6 - - + -
236A GLY 3.3 11.2 - - - +
238A GLY* 1.3 78.5 - - - +
240A ALA* 1.3 61.2 + - - +
241A PHE 3.3 1.0 + - - -
242A THR* 4.0 7.7 + - - -
243A PHE* 3.5 20.4 - - - -
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Residues in contact with ALA 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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235A ILE 3.9 6.3 - - - +
236A GLY* 3.7 2.2 + - - -
237A GLY 3.4 13.6 + - - +
238A GLY 3.2 1.8 - - - -
239A MET* 1.3 80.4 - - - +
241A PHE* 1.3 63.9 + - + +
243A PHE* 3.3 5.4 + - - +
244A LEU* 2.9 34.2 + - + +
281A LEU* 4.1 9.2 - - - -
282A PRO* 3.2 41.3 - - + -
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Residues in contact with PHE 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 GLY 3.6 19.5 - - - -
238A GLY* 3.9 17.0 + - - -
239A MET 3.3 1.0 - - - -
240A ALA* 1.3 77.9 - - + +
242A THR* 1.3 65.3 + - - +
244A LEU* 4.4 4.3 - - + +
245A LYS* 3.0 26.5 + - - +
250A MET* 4.5 8.3 - - + -
252A ILE* 4.1 12.5 - - + +
255A SER* 3.7 23.3 - - - -
256A LEU 3.3 22.4 - - - +
257A PHE* 4.5 2.4 - - - -
285A PHE* 3.4 36.1 - + - -
306A ILE* 3.8 17.7 - - + -
312A GLY* 3.4 34.5 - - - -
314A ASP 5.6 0.9 - - - -
1419A LA8 5.0 1.6 - - - -
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Residues in contact with THR 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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216A VAL* 4.2 5.9 - - - +
220A ILE* 4.1 17.0 - - + -
238A GLY 5.1 0.2 + - - -
239A MET 4.0 4.3 + - - -
240A ALA 3.4 0.2 - - - -
241A PHE* 1.3 77.7 - - - +
243A PHE* 1.3 63.6 + - - +
245A LYS* 3.9 1.4 - - - +
246A VAL* 3.2 26.6 + - - +
256A LEU 4.3 1.5 + - - -
257A PHE* 3.6 13.4 - - + -
258A ASP* 2.8 35.1 + - - +
261A GLY 3.8 4.0 - - - -
262A ALA* 3.2 45.1 - - + +
265A VAL* 4.2 1.8 - - + -
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Residues in contact with PHE 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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220A ILE* 3.7 23.1 - - + -
223A ILE* 3.6 28.9 - - + -
235A ILE* 3.6 28.0 - - + -
239A MET* 3.5 15.5 - - + -
240A ALA 3.3 7.9 + - - +
242A THR* 1.3 80.3 - - - +
244A LEU* 1.3 58.0 + - - +
246A VAL* 3.3 1.4 + - - +
247A LEU* 2.8 36.6 + - + +
265A VAL* 3.8 35.0 - - + -
268A LEU* 4.1 15.9 - - + -
269A MET* 4.1 23.6 - - - -
281A LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ALA* 2.9 40.8 + - + +
241A PHE* 4.2 6.1 - - + +
242A THR 3.4 0.4 - - - -
243A PHE* 1.3 74.3 - - - +
245A LYS* 1.3 59.7 + - - +
247A LEU* 4.9 0.2 - - - -
248A ASN* 3.0 48.4 + - - +
250A MET* 3.5 22.3 + - + +
281A LEU* 4.4 17.3 - - + -
282A PRO* 3.6 30.7 - - + +
285A PHE* 3.9 17.3 - - + -
302A VAL* 3.7 18.6 - - + -
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A PHE 3.0 18.1 + - - +
242A THR 3.9 3.6 - - - +
244A LEU* 1.3 76.1 - - - +
246A VAL* 1.3 63.4 + - + +
249A ASN* 3.1 27.6 - - - +
250A MET* 3.9 18.3 - - - +
252A ILE* 4.1 23.4 - - + +
257A PHE* 3.6 38.9 - - + -
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Residues in contact with VAL 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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242A THR 3.2 15.7 - - - +
243A PHE 3.3 5.5 + - - +
245A LYS* 1.3 85.5 - - + +
247A LEU* 1.3 61.7 + - - +
248A ASN 3.6 0.2 + - - -
249A ASN* 4.2 9.4 + - - +
257A PHE* 5.2 0.2 - - + -
262A ALA* 3.7 39.9 - - + +
265A VAL* 3.9 19.3 - - + -
266A LYS* 4.1 31.9 + - + +
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Residues in contact with LEU 247 (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 PHE* 2.8 24.3 + - + +
246A VAL* 1.3 73.4 - - - +
248A ASN* 1.3 70.8 + - - +
249A ASN* 3.7 4.1 + - - -
265A VAL* 3.8 20.6 - - + -
266A LYS* 4.2 22.4 - - + +
269A MET* 3.8 45.1 - - + -
281A LEU* 4.0 18.6 - - + -
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Residues in contact with ASN 248 (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 LEU* 3.0 29.3 + - - +
247A LEU* 1.3 92.3 + - - +
249A ASN* 1.3 74.7 + - - +
250A MET* 3.1 3.5 + - - +
281A LEU* 5.7 1.2 - - - +
302A VAL* 3.9 30.4 - - + +
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Residues in contact with ASN 249 (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 LYS* 3.1 20.1 + - - +
246A VAL 4.4 6.8 + - - +
247A LEU 3.7 3.6 + - - -
248A ASN* 1.3 81.0 + - - +
250A MET* 1.3 63.8 + - - +
251A GLU* 3.5 3.8 + - - +
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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