Contacts of the strand formed by residues 238 - 250 (chain F) in PDB entry 1DU3
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 GLY 238 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228E ASN* 3.7 3.1 - - - -
191F ARG* 3.2 3.3 - - - -
192F PHE* 3.0 41.2 + - - -
237F TYR* 1.3 79.7 - - - +
239F LEU* 1.3 70.0 + - - +
240F TYR* 3.4 24.0 - - - -
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Residues in contact with LEU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU* 4.1 15.7 - - + -
99C MET* 3.3 30.3 - - + -
205E GLN* 4.2 24.9 - - + -
226E ALA* 3.4 16.8 - - + +
227E ARG* 3.3 29.4 - - - +
228E ASN* 3.0 28.1 + - + +
189F TYR* 3.9 18.6 - - - +
190F PHE 3.5 2.9 - - - -
191F ARG* 4.2 6.7 - - + -
237F TYR* 3.6 8.7 - - + -
238F GLY* 1.3 84.1 - - - +
240F TYR* 1.3 65.5 + - - +
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Residues in contact with TYR 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ALA 3.5 1.1 + - - -
227E ARG* 4.8 8.1 - - + +
228E ASN* 3.6 17.4 + - - -
188F THR 3.5 3.1 - - - +
189F TYR* 4.0 1.4 - - - -
190F PHE* 2.8 35.4 + - + +
192F PHE* 3.8 13.3 - + - -
206F MET* 3.6 29.6 - - + -
227F ARG* 4.2 24.5 - - + -
228F ASN 3.9 15.3 - - - -
229F SER* 3.5 6.0 - - - -
230F CYS* 3.0 30.0 + - - +
237F TYR 4.9 1.2 + - - -
238F GLY* 3.4 26.6 - - - -
239F LEU* 1.3 78.2 - - - +
241F SER* 1.3 66.3 + - - +
242F ILE* 4.1 1.7 - - + +
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Residues in contact with SER 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LYS 4.1 2.3 + - - -
225E SER* 3.2 31.2 - - - -
226E ALA 2.8 27.5 + - - -
227E ARG* 3.7 21.0 + - - +
187F GLN* 4.5 10.9 + - - -
188F THR 3.4 5.8 - - - -
189F TYR* 3.2 22.1 - - - +
227F ARG* 4.4 4.3 + - - -
240F TYR* 1.3 76.1 - - - +
242F ILE* 1.3 62.5 + - - +
243F TYR 4.2 0.2 - - - -
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Residues in contact with ILE 242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F GLN* 3.0 3.9 - - - +
188F THR* 2.7 44.4 + - - +
190F PHE* 3.7 25.6 - - + -
206F MET* 3.7 21.5 - - + +
207F VAL* 4.7 0.9 - - - +
208F GLN* 3.3 24.1 - - + +
225F SER* 3.2 32.8 - - - +
227F ARG* 3.6 39.5 - - + +
240F TYR* 4.1 2.9 - - + +
241F SER* 1.3 78.8 - - - +
243F TYR* 1.3 62.2 + - - +
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Residues in contact with TYR 243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLN* 4.3 1.0 - - - +
243D TYR* 3.5 28.2 - + - +
183E TYR* 2.3 26.2 + - - -
225E SER* 5.8 0.7 - - - +
227E ARG* 5.7 2.6 - - - +
243E TYR* 3.4 39.9 - + - +
244E GLN* 4.4 0.2 - - - -
245E GLY 3.4 34.1 - - - -
183F TYR* 2.6 16.3 + - - -
185F TYR* 3.3 26.6 - + + +
186F SER 3.3 9.4 - - - -
187F GLN* 3.6 24.5 - - + +
225F SER* 4.7 2.6 + - - -
227F ARG* 4.6 6.9 + - - +
241F SER 4.2 1.0 + - - -
242F ILE* 1.3 79.2 - - - +
244F GLN* 1.3 75.7 + - - +
274F PHE* 4.5 0.2 - + - -
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Residues in contact with GLN 244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLN* 2.9 24.0 + - - +
243D TYR* 4.3 2.0 - - - -
185F TYR* 3.0 25.1 - - - +
186F SER 3.1 10.8 + - - -
208F GLN* 2.9 45.5 + - - +
210F ILE* 3.5 14.5 - - + +
223F MET* 3.5 21.5 - - + -
224F LYS 2.7 37.7 + - - +
225F SER* 3.0 7.9 + - - -
243F TYR* 1.3 86.1 - - - +
245F GLY* 1.3 61.4 + - - +
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Residues in contact with GLY 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D TYR* 4.0 1.4 - - - -
243D TYR* 3.1 17.6 - - - -
274D PHE* 3.0 20.8 - - - -
183F TYR* 3.7 21.1 - - - -
184F ILE 3.0 13.7 - - - -
185F TYR* 4.0 0.2 - - - -
223F MET* 3.3 8.1 - - - -
244F GLN* 1.3 80.2 - - - +
246F GLY* 1.3 58.0 + - - -
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Residues in contact with GLY 246 (chain F).
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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125D HIS* 3.9 7.0 - - - -
185D TYR* 3.8 15.7 - - - -
182F TYR 3.2 1.9 - - - +
183F TYR* 3.6 8.3 - - - -
184F ILE 2.8 28.4 + - - +
223F MET* 3.3 11.4 - - - -
245F GLY* 1.3 73.3 - - - -
247F ILE* 1.3 63.9 + - - -
248F PHE* 3.5 7.8 - - - -
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Residues in contact with ILE 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ALA* 3.9 9.2 - - + -
124D ALA 3.8 14.1 - - - +
125D HIS* 3.3 19.3 + - + +
163D PHE* 3.8 12.1 - - + -
185D TYR* 2.9 26.2 + - + +
277D ALA 4.2 0.4 - - - +
278D PHE* 3.4 40.8 - - + -
181F PHE* 3.5 29.6 - - + -
182F TYR 3.2 14.6 - - - +
183F TYR* 4.1 6.3 - - + +
246F GLY* 1.3 70.2 - - - -
248F PHE* 1.3 76.2 + - - +
280F VAL* 4.2 6.1 - - + -
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Residues in contact with PHE 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D HIS* 3.7 18.8 - + - -
160D GLY 5.2 2.0 - - - -
161D HIS* 4.3 28.7 - - + -
163D PHE* 4.7 4.0 - - - -
274D PHE* 6.0 0.2 - + - -
180F GLY 3.6 0.7 - - - +
181F PHE* 3.4 3.0 - - - -
182F TYR* 2.7 33.3 + - - +
184F ILE* 4.2 13.2 - - + -
212F LYS* 6.1 1.1 - - + -
222F LEU* 3.4 56.8 - - + -
223F MET* 3.2 38.4 - - + -
246F GLY* 3.5 13.2 - - - -
247F ILE* 1.3 93.2 - - - +
249F GLU* 1.3 66.4 + - - +
250F LEU* 3.6 2.8 + - + +
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Residues in contact with GLU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D ARG* 4.8 4.4 + - - +
158D ARG* 3.6 37.3 + - - -
163D PHE* 4.6 12.9 - - + +
179F LYS* 5.9 1.9 + - - +
180F GLY* 3.5 8.7 - - - +
181F PHE* 3.5 34.0 - - + +
212F LYS* 4.3 10.0 + - - +
248F PHE* 1.3 73.4 - - - +
250F LEU* 1.3 70.3 + - - +
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F ILE* 3.8 31.9 - - + -
178F GLU 4.4 0.3 - - - +
179F LYS* 3.1 5.2 - - - +
180F GLY 2.9 30.6 + - - -
182F TYR* 4.0 16.6 - - + -
184F ILE* 3.8 24.5 - - + -
212F LYS* 3.8 27.6 - - + -
222F LEU* 4.7 5.8 - - + -
248F PHE* 4.0 8.7 - - + +
249F GLU* 1.3 84.9 - - - +
251F LYS* 1.3 63.1 + - - +
254F ASP* 3.5 13.7 - - + +
256F ILE* 3.8 19.1 - - + -
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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