Contacts of the strand formed by residues 202 - 208 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158G PHE* 3.4 34.3 - + + -
159G SER 5.0 0.4 - - - -
195G ILE* 4.1 13.2 - - + -
198G SER* 3.4 19.7 - - - -
200G PHE* 3.2 26.9 - - + -
201G PRO* 1.3 73.9 - - - +
203G TRP* 1.3 66.0 + - - +
204G MET* 3.5 0.5 + - - -
245G TYR* 3.6 3.1 - - - -
246G ILE* 2.8 57.0 + - + +
261G PHE* 3.4 14.6 - - + -
262G SER* 3.5 26.5 - - - -
263G ILE* 3.5 17.9 - - + -
197H TYR* 4.0 21.1 - + - -
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Residues in contact with TRP 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163G PHE 3.3 21.1 + - - -
164G ASN 3.4 5.9 - - - -
165G TRP* 3.2 38.8 - + + +
168G SER* 4.1 4.3 - - - -
179G LEU* 4.3 5.4 - - + +
180G LEU* 4.7 2.4 - - - +
201G PRO 4.1 0.8 + - - -
202G PHE* 1.3 73.2 - - - +
204G MET* 1.3 60.5 + - - +
243G CYS* 2.9 42.2 - - + -
244G ALA 2.8 25.1 - - - -
245G TYR* 3.3 15.6 - + + +
254G GLU* 4.2 12.8 - - + -
255G ASN 3.8 17.0 - - - -
256G CYS* 4.0 9.0 - - - -
258G LEU 3.5 22.3 + - - -
260G ALA* 3.7 19.3 - - + +
261G PHE 2.6 13.5 + - - +
262G SER* 3.5 24.1 - - - -
263G ILE* 3.7 7.3 + - - +
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Residues in contact with MET 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G TRP* 2.7 25.6 + - - -
179G LEU* 4.4 2.2 - - - -
180G LEU* 4.1 23.1 - - + +
182G ILE* 4.3 19.5 - - + -
202G PHE 3.5 2.7 + - - +
203G TRP* 1.3 74.8 - - - +
205G GLY* 1.3 54.5 + - - +
206G LEU* 2.9 25.1 + - - +
217G TRP* 4.1 13.7 - - - -
228G PHE* 4.4 8.5 - - + -
244G ALA* 3.0 38.2 + - + +
245G TYR 4.1 0.2 - - - +
246G ILE* 4.1 20.2 - - + +
251G VAL* 3.7 34.1 - - + -
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Residues in contact with GLY 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G TRP* 3.5 19.1 - - - -
179G LEU* 3.5 25.6 - - - +
180G LEU 3.0 17.8 + - - -
204G MET* 1.3 67.4 - - - +
206G LEU* 1.3 57.0 + - - +
207G SER* 4.7 0.2 + - - -
216G LEU 3.8 0.5 - - - +
217G TRP* 3.5 9.3 - - - -
218G GLU* 3.1 28.9 + - - -
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Residues in contact with LEU 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G TRP* 4.3 0.3 + - - -
204G MET* 2.9 12.4 + - - +
205G GLY* 1.3 73.9 - - - +
207G SER* 1.3 66.8 + - - +
215G TRP* 4.0 17.7 - - + +
216G LEU* 3.5 22.9 - - - +
217G TRP* 3.4 42.5 - - + +
223G LEU* 4.0 19.5 - - + -
228G PHE* 3.8 29.4 - - + -
230G VAL* 4.0 13.2 - - + -
243G CYS* 3.8 0.3 - - - -
244G ALA* 2.9 36.3 + - + +
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Residues in contact with SER 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G TRP* 3.5 24.2 - - - -
205G GLY 4.7 0.2 + - - -
206G LEU* 1.3 80.1 - - - +
208G ARG* 1.3 66.8 + - - +
214G PRO 3.9 0.2 - - - +
215G TRP* 3.7 10.7 - - - -
216G LEU* 3.3 29.3 + - - +
242G THR 3.2 15.0 - - - -
243G CYS* 3.5 19.5 - - - -
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Residues in contact with ARG 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G SER* 1.3 79.1 - - - +
209G ARG* 1.3 58.6 + - - +
210G ASN 3.8 7.2 - - - +
211G PRO* 3.5 26.8 + - - +
213G TYR* 2.9 33.7 + - + -
214G PRO* 3.2 16.4 - - - +
215G TRP* 3.3 39.1 - - + +
234G VAL* 2.6 48.7 + - - +
240G SER 4.5 1.1 - - - +
241G GLY* 3.3 3.1 - - - -
242G THR* 2.6 53.6 + - - +
256G CYS* 4.9 0.5 - - - -
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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