Contacts of the strand formed by residues 182 - 190 (chain B) in PDB entry 1SBB
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 TYR 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B SER* 2.7 23.6 + - - -
138B GLU* 3.5 21.7 + - + -
172B LYS* 3.5 41.0 + - + +
174B LEU* 4.0 25.1 - - + -
180B SER* 3.1 20.0 + - - +
181B PRO* 1.3 96.0 - - + +
183B GLU* 1.3 55.9 + - - +
184B THR 4.0 11.4 - - - +
201B MET* 4.0 7.7 - - + +
234B LEU* 4.0 32.4 - - + +
235B THR 3.0 17.3 - - - +
236B THR* 3.8 23.8 - - + -
237B LYS* 3.6 4.4 - - - -
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Residues in contact with GLU 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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12B HIS 3.5 0.7 - - - +
13B LYS* 2.9 30.2 - - + +
14B SER* 2.8 35.0 + - - -
15B SER* 2.8 29.6 + - - -
182B TYR* 1.3 74.3 - - - +
184B THR* 1.3 70.2 + - + +
201B MET* 4.0 1.5 - - - +
235B THR* 2.6 20.9 + - + +
236B THR 4.3 8.3 - - - +
237B LYS* 3.4 26.6 - - + +
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Residues in contact with THR 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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11B LEU* 4.0 21.1 - - + +
12B HIS 3.5 11.4 - - - +
13B LYS* 3.4 39.9 - - + +
182B TYR* 4.0 6.9 - - - +
183B GLU* 1.3 88.9 - - + +
185B GLY* 1.3 59.7 + - - +
201B MET* 4.2 8.5 - - - -
233B TYR 5.4 0.3 + - - -
234B LEU* 3.5 2.8 - - - +
235B THR* 2.6 51.6 + - - +
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Residues in contact with GLY 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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11B LEU* 4.3 3.0 - - - +
12B HIS 5.0 0.4 + - - -
184B THR* 1.3 79.8 - - - +
186B TYR* 1.3 66.3 + - - +
199B ASP* 3.3 10.8 + - - +
200B MET* 3.0 25.5 + - - +
201B MET* 4.2 9.9 + - - +
233B TYR 3.0 13.9 - - - -
234B LEU* 4.0 10.8 - - - -
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Residues in contact with TYR 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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5B ASP* 4.1 9.8 + - - -
6B PRO* 3.4 38.1 - - + +
11B LEU* 3.8 31.0 - - + -
185B GLY* 1.3 73.9 - - - +
187B ILE* 1.3 59.5 + - - +
188B LYS* 4.3 14.1 - - + -
197B TRP* 3.8 18.2 - - + -
198B TYR 2.9 20.2 - - - +
200B MET* 3.8 8.0 - - - -
231B GLU 4.0 0.2 - - - +
232B VAL* 3.6 2.6 - - - +
233B TYR* 3.0 81.3 + + + -
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Residues in contact with ILE 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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161B ASP* 3.3 29.2 - - - +
164B THR* 3.8 22.9 - - + -
186B TYR* 1.3 72.6 - - - +
188B LYS* 1.3 61.3 + - - +
189B PHE* 3.4 32.7 + - + -
197B TRP* 3.0 5.2 - - - -
198B TYR* 2.8 49.1 + - + +
200B MET* 3.9 12.7 - - + -
230B ILE* 3.7 25.8 - - + -
231B GLU 3.6 2.0 - - - -
232B VAL* 3.9 11.2 - - + +
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Residues in contact with LYS 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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1B GLU* 3.0 22.0 + - - +
5B ASP* 3.0 37.7 + - - +
186B TYR* 4.1 12.8 + - + -
187B ILE* 1.3 73.2 - - - +
189B PHE* 1.3 62.2 + - - +
190B ILE* 3.7 31.8 - - + +
195B SER* 4.1 15.9 - - - -
196B PHE 3.5 9.2 - - - +
197B TRP* 4.0 7.4 - - + -
229B LYS 3.5 5.7 - - - +
230B ILE* 3.6 1.9 - - - -
231B GLU* 2.7 50.0 + - + +
233B TYR* 4.4 12.2 + - + -
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Residues in contact with PHE 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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157B ALA* 3.9 9.0 - - + -
160B LEU* 4.0 31.2 - - + -
161B ASP* 3.6 19.3 - - + -
187B ILE* 3.4 40.4 - - + -
188B LYS* 1.3 70.1 - - - +
190B ILE* 1.3 60.6 + - - +
191B GLU* 4.1 0.7 - - - -
195B SER* 3.2 3.1 - - - -
196B PHE* 2.6 83.3 + + + +
198B TYR* 3.3 29.6 - + - -
223B VAL* 5.3 4.7 - - + -
228B VAL* 6.2 2.9 - - + -
229B LYS 4.2 2.2 - - - -
230B ILE* 4.1 17.0 - - + +
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Residues in contact with ILE 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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1B GLU* 6.1 1.3 - - + +
188B LYS* 3.7 31.2 - - + +
189B PHE* 1.3 76.3 - - - +
191B GLU* 1.3 62.3 + - - +
192B ASN 4.2 13.7 - - - +
193B GLU 5.2 1.6 - - - +
194B ASN 3.8 6.5 - - - +
195B SER* 3.8 16.6 - - - -
228B VAL* 3.5 3.1 - - - +
229B LYS* 2.9 77.3 + - + +
231B GLU* 3.2 28.9 - - - +
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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