Contacts of the strand formed by residues 229 - 238 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F TYR* 5.0 6.0 - - - -
11G THR* 3.5 1.3 - - - -
12G LEU* 2.9 33.9 + - - +
193G THR* 4.4 6.5 - - - -
195G HIS* 3.4 17.5 - - - -
228G ALA* 1.3 75.8 - - - +
230G THR* 1.3 62.8 + - - -
231G PHE* 3.5 14.5 + - - -
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Residues in contact with THR 230 (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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30F TYR* 6.2 0.2 - - + -
301F GLU* 4.4 12.3 - - + +
9G ILE* 4.7 11.0 - - - -
11G THR* 3.5 32.8 - - + +
193G THR* 4.7 0.4 - - - +
194G VAL* 3.1 39.8 + - - +
195G HIS* 3.3 18.9 + - + -
229G GLY* 1.3 70.0 - - - -
231G PHE* 1.3 65.5 + - - +
310G TYR* 4.2 19.4 - - + +
311G THR* 4.5 6.7 - - + +
314G ALA* 5.0 1.9 - - - +
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Residues in contact with PHE 231 (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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8G ALA 3.9 0.3 - - - +
9G ILE* 3.5 4.7 - - - +
10G GLN* 2.9 38.3 + - + +
12G LEU* 3.3 37.0 - - + -
15G SER* 4.4 12.8 - - - -
17G ILE* 4.9 0.4 - - + -
36G THR* 3.8 18.4 - - - -
37G ARG 5.1 0.2 - - - -
38G VAL* 3.5 29.2 - - + -
43G TRP* 5.7 4.0 - + - -
191G ALA* 4.4 18.4 - - + -
192G PHE 3.4 4.5 - - - +
193G THR* 3.1 39.0 - - + -
194G VAL* 4.9 0.9 - - - -
227G SER* 5.7 1.6 - - - -
228G ALA 5.6 1.1 - - - -
229G GLY* 4.1 11.0 - - - -
230G THR* 1.3 73.9 - - - +
232G TYR* 1.3 59.8 + - - +
233G ARG* 4.4 6.6 - - + +
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Residues in contact with TYR 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G HIS* 3.0 29.0 + - + -
8G ALA 3.6 3.4 - - - -
9G ILE* 3.6 18.2 - - + -
190G HIS 4.5 0.9 - - - +
191G ALA* 3.1 23.6 - - - -
192G PHE* 2.9 39.4 + + + +
194G VAL* 4.4 5.8 - - + +
230G THR 3.7 1.6 + - - -
231G PHE* 1.3 73.0 - - - +
233G ARG* 1.3 73.9 + - - +
234G TYR* 3.9 17.9 - - + +
295G SER* 5.5 0.7 - - - -
296G PHE* 3.0 23.2 + - + +
297G ALA* 3.9 19.7 - - + -
300G PHE* 3.6 31.4 - + + -
318G LEU* 4.0 14.8 - - + -
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Residues in contact with ARG 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE 4.5 0.2 - - - -
7G HIS* 3.4 4.2 - - - -
8G ALA* 2.9 43.1 + - + +
10G GLN* 2.8 38.1 + - - -
43G TRP* 3.0 37.4 - - - -
188G PHE* 5.3 3.4 - - + -
189G ALA 5.7 0.4 - - - -
191G ALA* 3.7 20.8 - - + +
231G PHE* 4.4 7.4 - - + +
232G TYR* 1.3 85.8 - - - +
234G TYR* 1.3 61.6 + - - +
263G PHE* 2.7 64.3 + - + -
264G LEU* 4.6 1.4 + - - +
281G PRO* 3.7 15.4 - - - +
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Residues in contact with TYR 234 (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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5G ASP* 3.5 16.2 - - + +
6G ILE 3.3 7.4 - - - -
7G HIS* 3.5 37.0 - + - -
188G PHE* 4.1 3.9 - - - -
189G ALA* 3.1 41.9 + - + +
232G TYR* 3.9 16.6 - - + +
233G ARG* 1.3 76.7 - - - +
235G ALA* 1.3 68.7 + - - +
236G ASN* 2.3 42.9 + - - -
263G PHE* 4.5 1.7 - - - -
293G PRO* 3.4 10.7 - - - +
294G ILE 3.7 7.7 + - - -
295G SER* 3.7 27.9 + - - -
276H ALA* 3.9 23.1 - - + -
278H MET* 4.9 1.6 - - + +
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Residues in contact with ALA 235 (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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5G ASP* 3.2 3.8 - - - +
6G ILE* 2.9 41.8 + - + +
186G VAL* 5.2 0.4 - - + -
187G GLN 3.2 12.6 - - - +
188G PHE* 4.0 8.7 - - + -
234G TYR* 1.3 82.2 - - - +
236G ASN* 1.3 65.6 + - - +
237G VAL* 5.6 0.2 - - - -
259G PHE* 4.8 9.4 - - + -
263G PHE* 3.7 25.8 - - + -
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Residues in contact with ASN 236 (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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3G PHE* 5.3 4.3 - - + -
4G VAL 3.4 4.3 - - - +
5G ASP* 3.0 13.7 - - - +
186G VAL* 3.3 9.2 - - - +
187G GLN* 2.8 61.5 + - + +
234G TYR* 2.3 41.8 + - - -
235G ALA* 1.3 71.1 - - - +
237G VAL* 1.3 70.2 + - - +
238G ASN 4.2 0.9 - - - +
293G PRO* 3.2 24.8 - - + +
276H ALA* 4.7 0.6 - - - +
278H MET* 4.2 4.6 - - - +
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Residues in contact with VAL 237 (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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3G PHE* 3.4 3.3 - - - -
4G VAL* 2.8 42.4 + - + +
6G ILE* 6.3 1.6 - - + -
169G LEU* 5.1 0.7 - - + -
185G ALA 3.5 9.4 - - - +
186G VAL* 3.7 17.0 - - + -
235G ALA 5.6 0.4 - - - -
236G ASN* 1.3 80.8 - - - +
238G ASN* 1.3 62.2 + - - +
239G LEU* 3.2 16.6 + - + +
242G LEU* 4.3 11.4 - - + -
256G VAL* 4.1 25.4 - - + -
259G PHE* 3.7 25.8 - - + -
260G LEU* 4.6 8.1 - - + -
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Residues in contact with ASN 238 (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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2G THR* 3.8 4.7 + - - +
3G PHE* 3.3 39.6 - - + -
185G ALA* 3.0 18.2 + - - +
187G GLN* 6.0 3.4 - - + +
236G ASN* 4.2 2.0 - - + +
237G VAL* 1.3 68.9 - - - +
239G LEU* 1.3 64.4 + - - +
240G ASP* 2.5 30.2 + - - +
241G ARG* 3.2 35.0 + - + +
242G LEU* 3.1 19.4 + - - +
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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