Contacts of the strand formed by residues 180 - 192 (chain B) in PDB entry 1D0G
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 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B GLU 3.7 1.4 + - - -
179B LYS* 1.3 77.7 - - - +
181B PHE* 1.3 66.5 + - - -
182B TYR* 3.5 6.3 - - - -
249B GLU* 3.3 5.4 - - - +
250B LEU 2.7 33.8 + - - +
279B LEU* 4.1 6.7 - - - -
281B GLY* 4.0 4.5 - - - -
121D ARG* 3.9 15.5 - - - -
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Residues in contact with PHE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLY* 1.3 71.0 - - - -
182B TYR* 1.3 60.3 - - - +
247B ILE* 3.8 14.6 - - + -
248B PHE 3.6 2.0 - - - -
249B GLU* 3.7 40.6 - - + -
279B LEU* 3.4 8.1 - - - +
280B VAL* 2.9 30.6 + - + -
281B GLY* 2.7 28.6 + - - +
121D ARG* 3.4 36.1 - - + -
123D ALA* 4.4 7.4 - - + -
163D PHE* 3.6 47.3 - + + -
165D SER* 4.0 19.1 - - - -
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 3.5 26.5 - - + +
167B LEU* 4.6 8.1 - - + +
176B ILE* 3.6 26.8 - - + +
177B HIS 4.7 0.7 + - - -
178B GLU* 2.5 35.0 + - - +
180B GLY 3.5 16.4 - - - -
181B PHE* 1.3 74.9 - - - +
183B TYR* 1.3 62.0 + - - +
184B ILE* 3.4 10.8 + - + +
246B GLY 3.3 1.4 - - - +
247B ILE* 3.1 4.8 - - - +
248B PHE 2.8 41.4 + - - +
250B LEU* 3.9 25.4 - - + -
277B ALA* 4.4 7.6 - - + -
278B PHE* 3.4 23.3 - - - +
279B LEU* 3.5 26.3 - - + +
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 4.0 9.9 - + - -
182B TYR* 1.3 71.4 - - - +
184B ILE* 1.3 57.8 + - - +
185B TYR* 3.7 19.7 - + + -
243B TYR* 2.7 29.1 + - - -
245B GLY* 3.5 8.7 - - - -
246B GLY* 3.2 29.2 - - - -
247B ILE* 4.1 5.8 - - + +
277B ALA* 3.2 4.2 - - - -
278B PHE* 3.0 52.1 + + + -
280B VAL* 3.5 25.8 - - + +
183D TYR* 3.8 16.4 + + - -
185D TYR* 4.4 3.8 - + - -
243D TYR* 2.8 30.4 + - - -
278D PHE* 3.8 15.5 - + + -
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B TYR* 3.9 15.0 - - + +
183B TYR* 1.3 75.9 - - - +
185B TYR* 1.3 67.3 + - - +
210B ILE* 3.8 24.9 - - + -
222B LEU* 3.7 28.5 - - + -
223B MET* 3.6 9.1 - - + +
245B GLY* 3.0 23.2 - - - -
246B GLY 2.8 13.5 + - - +
248B PHE* 4.1 14.8 - - + -
250B LEU* 4.0 21.1 - - + -
256B ILE* 4.1 13.2 - - + -
275B PHE* 4.1 13.2 - - + -
276B GLY 3.6 10.5 - - - +
277B ALA* 4.2 6.5 - - + -
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Residues in contact with TYR 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 4.5 3.8 - + - -
245A GLY 4.2 0.4 - - - -
246A GLY* 3.8 13.0 - - - -
247A ILE* 3.0 33.7 + - + +
125B HIS* 2.7 24.6 + - - -
183B TYR* 3.7 21.1 - + + -
184B ILE* 1.3 76.2 - - - +
186B SER* 1.3 67.2 + - - +
210B ILE* 4.1 4.9 - - - -
243B TYR* 3.3 34.8 - + + +
244B GLN 3.4 8.5 - - - +
274B PHE* 3.7 27.6 - + - -
275B PHE* 3.3 5.7 - - - -
276B GLY* 2.9 61.4 + - - -
277B ALA* 3.7 3.8 - - - -
278B PHE* 4.5 3.8 - + - -
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B TRP* 4.6 1.0 - - - -
185B TYR* 1.3 81.7 - - - +
187B GLN* 1.3 61.0 + - - +
188B THR* 4.0 2.6 - - - +
208B GLN* 3.1 32.7 + - - +
210B ILE* 3.8 8.2 - - - +
243B TYR* 3.2 6.3 - - - -
244B GLN 3.1 26.7 + - - +
258B VAL* 3.5 30.0 - - - +
274B PHE 2.8 19.2 + - - -
275B PHE* 4.2 0.4 - - - +
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Residues in contact with GLN 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LYS 3.1 27.1 + - - -
225A SER* 3.8 11.6 + - - -
243A TYR 4.1 0.3 - - - +
244A GLN* 3.2 34.7 + - - +
186B SER* 1.3 75.0 - - - +
188B THR* 1.3 66.8 + - - +
241B SER* 4.6 6.2 - - - -
242B ILE 3.1 11.9 - - - +
243B TYR* 3.5 15.8 - - + +
272B ALA 3.4 14.8 + - - +
273B SER* 3.1 5.0 - - - -
274B PHE* 2.9 64.6 + - + +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 4.1 16.4 - - + -
154B TRP* 5.3 1.6 - - + -
186B SER* 4.0 9.2 - - - +
187B GLN* 1.3 76.6 - - - +
189B TYR* 1.3 62.2 + - - +
190B PHE* 3.6 14.6 + - - -
208B GLN* 3.1 31.5 + - + +
240B TYR 3.6 1.0 - - - +
241B SER* 4.7 0.7 - - - -
242B ILE* 2.9 30.1 + - - +
258B VAL* 4.1 2.0 - - + -
260B VAL* 3.9 21.3 - - + +
266B ILE* 4.3 15.0 - - + -
272B ALA 4.6 0.7 - - - -
273B SER* 3.8 6.3 - - - +
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LYS* 4.0 10.3 - - + +
225A SER* 6.3 0.2 - - - -
226A ALA* 3.6 15.4 - - + +
188B THR* 1.3 68.7 - - - +
190B PHE* 1.3 76.8 + - - +
191B ARG* 3.4 26.4 + - + -
239B LEU* 3.7 6.8 - - - +
240B TYR 4.1 7.0 - - - -
241B SER* 3.2 27.1 - - - +
266B ILE* 3.3 4.7 - - - +
267B ASP* 2.8 51.0 + - + +
272B ALA* 3.5 30.4 + - + +
273B SER* 3.0 18.4 + - - +
98S GLU* 3.0 41.0 + - - +
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Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B THR* 3.9 20.0 - - - -
189B TYR* 1.3 75.5 - - - +
191B ARG* 1.3 61.7 + - - +
192B PHE* 5.1 2.0 - - + -
206B MET* 3.6 52.9 - - + -
207B VAL 4.0 17.0 - - - -
238B GLY 4.0 0.6 - - - +
239B LEU* 3.7 0.2 - - - -
240B TYR* 2.8 47.7 + - + +
242B ILE* 3.8 19.5 - - + -
260B VAL* 4.2 3.1 - - + -
261B THR 3.3 26.0 - - - -
262B ASN* 3.9 13.0 - - + -
265B LEU* 3.5 12.8 - - + -
266B ILE* 3.4 22.2 - - + -
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B TYR* 3.4 22.6 + - + -
190B PHE* 1.3 75.9 - - - +
192B PHE* 1.3 65.7 + - - +
193B GLN* 5.3 1.6 + - - -
238B GLY 3.4 5.6 - - - -
239B LEU* 4.2 5.6 - - + +
265B LEU* 2.9 26.0 + - - +
267B ASP* 3.4 31.9 + - + -
67S ASP* 2.6 45.4 + - - +
68S SER* 5.4 3.6 + - - -
98S GLU* 2.9 34.3 + - - +
99S MET* 3.3 29.7 - - + +
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ARG* 1.3 83.5 - - - +
193B GLN* 1.3 58.7 + - - +
194B GLU* 3.3 48.5 - - + +
204B LYS* 3.6 31.9 - - + -
206B MET* 3.9 11.0 - - - -
229B SER* 4.1 8.3 - - - -
237B TYR* 3.2 6.2 - - - +
238B GLY* 2.9 53.4 + - - +
240B TYR* 3.8 24.7 - + - -
265B LEU* 3.6 27.6 - - + -
99S MET* 3.8 5.5 - - - +
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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