Contacts of the strand formed by residues 229 - 238 (chain F) in PDB entry 5U07
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 229 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30E TYR* 4.9 6.4 - - - -
11F THR* 3.5 1.3 - - - -
12F LEU* 2.8 33.9 + - - +
193F THR* 4.2 10.3 - - - -
195F HIS* 3.4 17.0 - - - -
228F ALA* 1.3 75.6 - - - +
230F THR* 1.3 64.0 + - - -
231F PHE* 3.6 8.9 + - - -
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Residues in contact with THR 230 (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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30E TYR* 6.1 0.7 - - + -
31E GLY* 6.2 0.4 - - - -
301E GLU* 4.2 13.2 - - + +
9F ILE* 4.8 9.4 - - - -
10F GLN 3.8 0.2 - - - -
11F THR* 3.5 32.8 - - + +
193F THR* 4.2 0.6 - - - +
194F VAL* 3.0 34.5 + - - +
195F HIS* 3.2 25.4 + - + -
229F GLY* 1.3 69.2 - - - -
231F PHE* 1.3 64.7 + - - +
310F TYR* 4.2 20.4 - - + +
311F THR* 4.6 3.8 - - + +
314F ALA* 5.1 2.5 - - - +
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Residues in contact with PHE 231 (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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8F ALA 4.0 0.2 - - - +
9F ILE* 3.6 5.2 - - - +
10F GLN 2.9 37.7 + - - +
12F LEU* 3.4 35.2 - - + -
15F SER* 4.8 10.1 - - - -
17F ILE* 4.4 0.9 - - + -
36F THR* 3.9 17.3 - - - -
37F ARG 5.1 0.2 - - - -
38F VAL* 3.3 35.0 - - + -
43F TRP* 5.7 4.5 - + - -
191F ALA* 4.4 17.9 - - + -
192F PHE 3.4 4.9 - - - +
193F THR* 3.1 38.4 - - + -
194F VAL* 4.8 1.3 - - - -
227F SER 6.6 0.2 - - - -
228F ALA* 5.5 1.3 - - - -
229F GLY* 3.6 10.9 + - - -
230F THR* 1.3 74.7 - - - +
232F TYR* 1.3 59.5 + - - +
233F ARG* 4.3 7.5 - - + +
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Residues in contact with TYR 232 (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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7F HIS* 3.0 20.3 + - + -
8F ALA 3.7 2.5 - - - -
9F ILE* 3.6 24.7 - - + -
190F HIS 4.5 0.7 - - - +
191F ALA* 3.1 24.1 - - - -
192F PHE* 2.8 39.1 + + + +
194F VAL* 4.3 7.9 - - + -
230F THR 3.7 1.4 + - - -
231F PHE* 1.3 70.1 - - - +
233F ARG* 1.3 76.7 + - - +
234F TYR* 3.9 18.6 - - + +
295F SER* 5.5 0.7 - - - -
296F PHE* 3.0 31.6 + - + +
297F ALA* 3.8 21.5 - - + -
300F PHE* 3.7 18.6 - + + -
318F LEU* 3.9 20.0 - - + -
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Residues in contact with ARG 233 (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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6F ILE 4.6 0.4 - - - -
7F HIS* 3.4 3.3 - - - -
8F ALA* 2.9 41.5 + - + +
10F GLN* 2.4 48.1 + - - -
43F TRP* 3.1 34.6 - - - -
188F PHE* 5.4 2.9 - - + -
189F ALA 5.7 0.4 - - - -
190F HIS 6.1 0.2 - - - -
191F ALA* 3.7 20.6 - - + +
231F PHE* 4.3 7.9 - - + +
232F TYR* 1.3 87.0 - - - +
234F TYR* 1.3 62.5 + - - +
263F PHE* 2.6 63.6 + - + -
264F LEU* 4.7 1.0 + - - +
281F PRO* 3.7 15.6 - - - +
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Residues in contact with TYR 234 (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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5F ASP* 3.7 9.0 - - + +
6F ILE 3.4 7.6 - - - -
7F HIS* 3.4 39.3 - + - -
188F PHE* 4.1 1.4 - - - -
189F ALA* 3.1 40.8 + - + +
232F TYR* 3.9 15.0 - - + +
233F ARG* 1.3 76.2 - - - +
235F ALA* 1.3 67.5 + - - +
236F ASN* 2.4 37.9 + - - -
263F PHE* 4.5 6.0 - - - -
293F PRO* 3.5 10.6 - - - +
294F ILE 3.5 12.1 + - - -
295F SER* 3.5 29.1 + - - -
276G ALA* 3.6 30.3 - - + -
278G MET* 4.7 2.0 - - + +
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Residues in contact with ALA 235 (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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5F ASP* 3.2 4.5 - - - +
6F ILE* 2.9 44.5 + - + +
187F GLN 3.2 11.7 - - - +
188F PHE* 4.2 8.1 - - + -
234F TYR* 1.3 81.0 - - - +
236F ASN* 1.3 65.8 + - - +
259F PHE* 4.7 9.9 - - + -
263F PHE* 3.8 24.7 - - + -
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Residues in contact with ASN 236 (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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3F PHE* 5.3 3.8 - - + -
4F VAL 3.5 3.4 - - - +
5F ASP* 3.0 16.3 - - - +
186F VAL* 3.3 7.1 - - - +
187F GLN* 2.7 63.0 + - + +
234F TYR* 2.4 40.0 + - - -
235F ALA* 1.3 72.8 - - - +
237F VAL* 1.3 71.4 + - - +
238F ASN 4.2 1.6 - - - +
293F PRO* 3.2 22.9 - - + +
276G ALA* 4.4 0.6 - - - +
278G MET* 4.1 4.0 - - - +
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Residues in contact with VAL 237 (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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3F PHE* 3.5 2.8 - - - -
4F VAL* 2.8 42.7 + - + +
6F ILE* 6.2 0.9 - - + -
169F LEU* 4.9 0.9 - - + -
185F ALA 3.7 4.5 - - - +
186F VAL* 3.9 12.1 - - + -
235F ALA 5.6 0.7 - - - -
236F ASN* 1.3 82.0 - - - +
238F ASN* 1.3 60.6 + - - +
239F LEU* 3.1 13.9 + - + +
242F LEU* 4.2 14.4 - - + -
256F VAL* 4.0 26.5 - - + -
259F PHE* 3.6 34.1 - - + -
260F LEU* 4.3 9.4 - - + -
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Residues in contact with ASN 238 (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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2F THR* 3.7 6.4 + - - +
3F PHE* 3.3 38.4 - - + -
185F ALA* 2.9 21.0 + - - +
187F GLN* 6.0 3.4 - - + +
236F ASN* 4.2 1.8 - - + +
237F VAL* 1.3 69.1 - - - +
239F LEU* 1.3 64.9 + - - +
240F ASP* 2.5 28.3 + - - +
241F ARG* 3.3 33.2 + - + +
242F LEU* 3.1 19.8 + - - +
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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