Contacts of the strand formed by residues 202 - 208 (chain E) in PDB entry 1YPO
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 PHE 202 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E PHE* 4.1 17.7 - + + -
159E SER 4.6 0.9 - - - -
195E ILE* 4.0 21.5 - - + -
198E SER* 3.7 16.4 - - - -
200E PHE 3.4 18.6 - - - -
201E PRO* 1.3 78.3 - - - +
203E TRP* 1.3 63.1 + - - +
245E TYR* 3.1 4.9 - - - -
246E ILE* 2.9 41.8 + - + +
261E PHE* 3.0 26.5 - + + -
262E SER 3.8 7.4 - - - -
263E ILE* 3.5 36.6 - - + -
197F TYR* 3.7 40.4 - + + -
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Residues in contact with TRP 203 (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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163E PHE 3.3 13.2 + - - -
165E TRP* 3.2 39.4 - + + +
168E SER* 3.6 22.2 - - - -
179E LEU* 4.1 5.2 - - + +
180E LEU* 4.7 1.0 - - - +
201E PRO 4.3 0.2 - - - -
202E PHE* 1.3 76.4 - - - +
204E MET* 1.3 59.8 + - - +
243E CYS* 3.4 33.0 - - + -
244E ALA 3.4 21.3 - - - -
245E TYR* 3.7 17.5 - + + -
254E GLU* 4.0 11.9 - - + -
255E ASN 3.4 22.2 - - - -
256E CYS 4.1 5.2 - - - -
258E LEU* 3.2 24.2 + - + -
259E ALA 5.0 0.2 - - - -
260E ALA* 3.8 21.1 - - + +
261E PHE 2.7 12.5 + - - +
262E SER* 3.7 9.3 - - - +
263E ILE* 3.4 25.6 + - - +
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Residues in contact with MET 204 (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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165E TRP* 2.8 22.2 + - - -
179E LEU* 3.8 7.9 - - - -
180E LEU* 3.3 24.0 - - + +
182E ILE* 3.9 23.8 - - + -
203E TRP* 1.3 75.4 - - - +
205E GLY* 1.3 60.0 + - - +
206E LEU* 2.9 21.9 + - + +
217E TRP* 4.0 22.7 - - - -
228E PHE* 4.5 2.9 - - - -
244E ALA 3.1 21.7 + - - +
245E TYR* 4.5 0.4 - - - -
246E ILE* 3.7 33.7 - - + +
251E VAL* 3.9 27.4 - - + -
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Residues in contact with GLY 205 (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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165E TRP* 3.9 11.8 - - - -
179E LEU* 3.3 19.9 - - - +
180E LEU 2.9 17.1 + - - -
181E LYS* 5.8 0.2 - - - -
204E MET* 1.3 69.0 - - - +
206E LEU* 1.3 57.1 + - - +
207E SER* 4.0 0.5 + - - -
216E LEU 3.4 1.6 - - - +
217E TRP* 2.9 35.0 - - - -
218E GLU* 3.1 16.5 + - - +
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Residues in contact with LEU 206 (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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165E TRP* 4.4 1.1 + - - -
204E MET* 2.9 15.4 + - - +
205E GLY* 1.3 75.5 - - - +
207E SER* 1.3 63.1 + - - +
215E TRP* 3.7 31.2 - - + -
216E LEU* 3.6 17.0 - - - +
217E TRP* 3.5 22.9 - - + -
223E LEU* 3.9 20.2 - - + -
228E PHE* 3.6 37.5 - - + -
230E VAL* 4.6 6.1 - - + -
243E CYS* 3.9 0.5 - - - -
244E ALA* 3.1 38.9 + - + +
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Residues in contact with SER 207 (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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231A ARG* 5.0 7.2 + - - -
165E TRP* 3.8 21.5 - - - -
205E GLY 4.6 0.3 + - - -
206E LEU* 1.3 77.3 - - - +
208E ARG* 1.3 66.4 + - - +
214E PRO 3.6 0.3 - - - +
215E TRP* 3.3 11.2 - - - -
216E LEU* 2.9 36.4 + - - +
217E TRP 5.6 0.7 - - - -
242E THR 3.4 14.4 - - - -
243E CYS* 3.9 16.4 - - - -
256E CYS* 5.0 0.4 - - - -
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Residues in contact with ARG 208 (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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207E SER* 1.3 84.0 + - - +
209E ARG* 1.3 61.6 + - - +
210E ASN* 4.2 5.4 - - - +
211E PRO* 3.9 31.6 + - - +
213E TYR* 2.9 27.9 + - + +
214E PRO* 3.2 22.1 - - - +
215E TRP* 3.4 53.3 - - + +
234E VAL* 3.5 27.3 + - - +
241E GLY* 4.8 0.4 - - - -
242E THR* 2.9 29.3 + - - +
256E CYS* 6.1 0.2 - - - -
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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