Contacts of the strand formed by residues 210 - 220 (chain E) in PDB entry 5YWB
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 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299C GLN* 5.4 0.3 + - - +
181E LEU* 5.0 13.7 - - + -
204E ASP* 4.7 11.4 - - - +
209E MET* 1.3 88.0 - - - +
211E ILE* 1.3 64.2 + - - +
212E SER 3.7 1.6 + - - -
213E ALA* 4.2 20.6 + - + +
250E PHE* 5.9 1.6 - - - -
251E LEU* 4.4 29.1 + - + +
287E LEU* 4.6 9.0 - - + +
288E GLU 4.5 1.6 - - - -
289E GLY* 3.5 43.3 - - - +
290E VAL 3.7 6.7 - - - +
291E VAL* 4.6 9.6 - - + +
298E THR* 5.0 4.7 - - - +
299E GLN* 6.2 0.2 - - - -
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Residues in contact with ILE 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C GLU* 4.7 8.3 - - + -
297C THR* 3.9 17.9 - - - +
298C THR 5.8 0.2 - - - -
299C GLN* 4.3 22.7 - - + +
209E MET 4.3 0.4 - - - -
210E ILE* 1.3 69.9 - - - +
212E SER* 1.3 76.1 + - - +
213E ALA 3.3 0.5 + - - -
290E VAL* 2.7 46.2 + - + +
291E VAL 5.6 0.4 - - - -
292E GLU* 5.3 6.9 - - + +
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Residues in contact with SER 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C THR* 5.9 0.2 - - - -
216C HIS* 4.8 18.2 - - - -
288C GLU* 4.3 24.1 + - - -
299C GLN* 4.6 7.7 - - - +
210E ILE 3.7 2.0 + - - -
211E ILE* 1.3 76.6 + - - +
213E ALA* 1.3 65.8 + - - +
214E THR* 3.3 7.8 + - - +
248E GLY* 5.6 1.6 - - - -
249E ILE 4.7 5.1 + - - -
288E GLU* 4.0 7.8 + - - +
289E GLY* 4.3 2.9 - - - -
290E VAL* 4.1 9.0 + - - +
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Residues in contact with ALA 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ILE* 4.2 25.0 + - + +
211E ILE 3.3 1.2 - - - -
212E SER* 1.3 76.7 - - - +
214E THR* 1.3 52.2 + - - +
248E GLY* 3.2 1.6 - - - -
249E ILE* 2.7 58.2 + - + +
251E LEU* 5.1 3.1 - - + +
287E LEU* 3.7 14.4 - - + -
288E GLU 2.8 16.2 - - - +
289E GLY* 4.0 1.6 - - - -
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Residues in contact with THR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E SER 3.3 4.7 + - - +
213E ALA* 1.3 74.3 - - - +
215E ILE* 1.3 61.2 + - - +
216E HIS* 3.4 21.2 + - + +
247E ASN* 2.6 43.3 + - - +
248E GLY* 3.5 6.3 - - - -
249E ILE* 5.0 0.2 - - - -
286E ILE 3.5 1.4 - - - +
287E LEU* 3.4 5.0 - - - +
288E GLU* 2.9 59.2 + - + +
212G SER* 5.9 0.2 - - - -
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Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E PHE* 5.2 4.0 - - + -
202E VAL* 5.3 6.7 - - + -
214E THR* 1.3 73.5 - - - +
216E HIS* 1.3 63.7 + - - +
217E MET* 4.0 25.5 + - + +
240E MET* 3.9 24.5 - - + +
247E ASN* 2.8 37.5 + - - +
248E GLY* 4.4 0.2 - - - -
249E ILE* 4.0 23.3 - - + -
257E ILE* 5.0 15.0 - - + -
285E VAL* 4.9 13.2 - - + -
286E ILE 3.6 2.5 - - - +
287E LEU* 3.6 32.3 - - + +
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Residues in contact with HIS 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E THR* 3.4 27.1 - - + +
215E ILE* 1.3 70.5 - - - +
217E MET* 1.3 61.6 + - - +
218E GLN* 3.8 13.7 + - + +
237E ASP* 5.3 3.1 - - - -
247E ASN* 3.3 28.1 + - - -
285E VAL* 3.8 0.7 - - - -
286E ILE* 2.9 64.6 + - + +
288E GLU* 4.7 8.3 - - + +
299E GLN* 5.8 1.1 - - - -
212G SER* 4.8 18.1 - - - -
248G GLY* 5.8 11.0 + - - -
249G ILE 5.9 3.7 + - - -
250G PHE* 6.0 2.0 - - + -
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Residues in contact with MET 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E PHE* 5.5 12.8 - - - -
200E LEU* 5.8 0.2 - - - -
215E ILE* 3.8 12.2 + - + -
216E HIS* 1.3 71.6 - - - +
218E GLN* 1.3 62.1 + - - +
237E ASP* 3.1 8.1 + - - +
238E ILE* 2.9 55.3 + - + +
239E PRO 3.2 28.9 - - - +
240E MET* 4.1 10.0 - - + +
257E ILE* 4.6 21.1 - - + -
259E HIS* 4.0 17.0 - - + -
283E ILE* 4.8 8.7 - - + -
284E ILE 3.7 4.0 - - - +
285E VAL* 4.0 24.9 - - + +
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Residues in contact with GLN 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216E HIS* 3.8 17.2 + - + +
217E MET* 1.3 79.3 - - - +
219E VAL* 1.3 63.4 + - - +
235E GLN* 3.6 17.9 + - + +
236E VAL 3.3 16.7 - - - +
237E ASP* 4.5 10.4 - - + +
238E ILE* 3.9 2.5 - - - -
283E ILE* 3.6 6.6 - - - +
284E ILE* 2.9 50.5 + - + +
286E ILE* 4.5 2.8 - - - +
249G ILE* 4.5 5.7 - - - +
250G PHE* 3.2 50.3 - - - +
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Residues in contact with VAL 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E GLN* 1.3 74.8 - - - +
220E VAL* 1.3 75.6 + - - +
221E ARG* 4.8 16.6 - - + +
234E HIS 2.9 14.0 - - - +
235E GLN* 3.3 1.4 - - - -
236E VAL* 3.1 43.7 + - + +
238E ILE* 3.9 17.0 - - + -
266E PRO* 5.0 10.1 - - + -
267E LEU* 5.1 12.8 - - + -
281E LEU* 5.4 3.4 - - + -
282E GLU 3.5 5.8 - - - -
283E ILE* 3.6 26.2 - - + -
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Residues in contact with VAL 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E PHE* 4.0 20.2 - - + -
219E VAL* 1.3 81.9 - - - +
221E ARG* 1.3 72.5 + - - +
233E LEU* 3.7 31.2 - - + -
234E HIS 3.2 4.3 - - - -
235E GLN* 3.7 27.6 - - + -
280E ASP 4.4 0.3 - - - +
281E LEU* 4.0 1.0 - - - -
282E GLU* 3.0 47.5 + - + +
284E ILE* 4.9 7.9 - - + -
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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