Contacts of the strand formed by residues 202 - 208 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197G TYR* 3.9 23.1 - + + -
158H PHE* 3.5 29.6 - + + -
159H SER 5.5 0.2 - - - -
195H ILE* 4.1 19.7 - - + -
198H SER* 3.4 22.4 - - - -
200H PHE* 3.1 25.4 - - + -
201H PRO* 1.3 75.1 - - - +
203H TRP* 1.3 62.6 + - - +
245H TYR* 3.2 3.7 - - - +
246H ILE* 2.9 45.2 + - + +
261H PHE* 3.0 20.6 - - + +
262H SER 3.7 9.4 - - - -
263H ILE* 3.5 37.7 - - + -
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Residues in contact with TRP 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H PHE 3.4 16.2 + - - -
165H TRP* 3.5 29.9 - + + +
168H SER* 3.5 25.1 - - - -
179H LEU* 4.3 4.3 - - + +
180H LEU* 4.6 1.2 - - - +
201H PRO 4.3 0.4 - - - -
202H PHE* 1.3 76.9 - - - +
204H MET* 1.3 59.9 + - - +
243H CYS* 3.5 33.7 - - + -
244H ALA 3.4 17.5 - - - -
245H TYR* 3.7 19.9 - + + +
254H GLU* 4.0 12.6 - - + -
255H ASN 3.4 22.4 - - - -
256H CYS* 4.1 7.9 - - - -
258H LEU* 3.2 22.8 + - + -
260H ALA* 3.8 24.1 - - + +
261H PHE 2.8 11.6 + - - +
262H SER* 4.1 9.6 - - - -
263H ILE* 3.5 23.7 + - - +
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Residues in contact with MET 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H TRP* 2.7 28.4 + - - -
179H LEU* 3.8 6.6 - - - +
180H LEU* 3.4 28.3 - - + +
182H ILE* 3.4 28.3 - - + -
203H TRP* 1.3 75.0 - - - +
205H GLY* 1.3 56.8 + - - +
206H LEU* 3.2 9.1 + - - +
217H TRP* 4.2 17.9 - - + -
228H PHE* 4.7 2.9 - - - -
244H ALA* 3.1 35.7 + - + +
245H TYR* 4.0 1.3 - - - -
246H ILE* 3.4 33.4 - - + -
251H VAL* 4.2 19.3 - - + -
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Residues in contact with GLY 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H TRP* 3.8 11.2 - - - -
179H LEU* 3.5 20.7 - - - +
180H LEU 2.9 18.2 + - - -
204H MET* 1.3 70.5 - - - +
206H LEU* 1.3 58.1 + - - +
207H SER 4.1 0.3 + - - -
217H TRP* 2.9 38.8 - - - -
218H GLU* 3.1 9.8 + - - +
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Residues in contact with LEU 206 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H TRP* 4.4 0.4 + - - -
204H MET* 3.2 8.6 + - + +
205H GLY* 1.3 77.5 - - - +
207H SER* 1.3 65.4 + - - +
215H TRP* 3.9 27.1 - - + -
216H LEU* 3.4 25.1 - - - +
217H TRP* 3.5 39.2 - - + +
223H LEU* 4.0 12.3 - - + -
228H PHE* 4.2 25.8 - - + -
230H VAL* 4.4 3.1 - - + -
243H CYS* 3.9 0.7 - - - +
244H ALA* 3.0 45.7 + - + +
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Residues in contact with SER 207 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H TRP* 3.8 20.0 - - - -
205H GLY 5.0 0.7 + - - -
206H LEU* 1.3 78.4 - - - +
208H ARG* 1.3 67.8 + - - +
214H PRO 4.3 0.7 - - - +
215H TRP* 3.6 9.3 - - - -
216H LEU* 3.0 29.8 + - - +
217H TRP 5.1 2.3 + - - -
242H THR 3.5 14.4 - - - -
243H CYS* 3.8 18.6 - - - -
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Residues in contact with ARG 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207H SER* 1.3 80.6 + - - +
209H ARG* 1.3 64.0 + - - +
210H ASN 3.3 14.4 + - - +
211H PRO* 3.8 22.8 + - - +
213H TYR* 2.9 37.0 + - + +
214H PRO* 4.0 7.4 - - - +
215H TRP* 3.5 56.9 - - + +
234H VAL* 2.8 37.2 + - - +
241H GLY* 4.1 0.4 - - - -
242H THR* 3.0 29.5 + - - +
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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