Contacts of the strand formed by residues 164 - 180 (chain B) in PDB entry 5O67
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 TRP 164 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B PHE* 4.2 2.5 - - - -
159B ASN* 3.6 3.5 - - - +
160B LEU* 2.8 54.6 + - + +
163B ARG* 1.3 89.5 - - + +
165B GLN* 1.3 60.0 + - - +
166B PHE* 3.9 27.4 - + + -
210B ILE* 4.0 25.1 - - + -
211B ALA 3.4 17.0 - - - -
212B TYR* 3.5 41.8 - + + -
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 3.5 22.0 + - - -
102B PHE* 3.7 18.8 - - + +
103B ALA* 2.9 33.0 + - - +
157B ARG* 3.6 25.0 + - - +
158B TYR 3.4 16.4 - - - +
159B ASN* 3.1 18.0 + - - +
164B TRP* 1.3 75.7 - - - +
166B PHE* 1.3 69.7 + - - +
167B ASP* 5.2 6.3 - - - +
209B GLY 3.7 1.0 - - - +
210B ILE* 3.5 6.4 - - - +
211B ALA* 3.0 36.9 + - + +
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ARG* 3.2 5.1 - - - +
158B TYR* 2.8 60.1 + + + +
160B LEU* 4.8 10.8 - - + -
164B TRP* 3.9 36.6 - + + -
165B GLN* 1.3 79.4 - - - +
167B ASP* 1.3 61.0 + - - +
209B GLY 3.5 4.7 - - - +
210B ILE* 4.1 30.3 - - + -
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Residues in contact with ASP 167 (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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155B THR* 3.1 29.2 - - - +
156B GLY 3.3 10.5 - - - +
157B ARG* 3.8 25.4 + - + +
165B GLN* 5.2 6.1 - - - +
166B PHE* 1.3 75.1 - - - +
168B VAL* 1.3 66.6 + - - +
169B ASN* 4.5 1.9 + - - +
208B PHE* 3.3 8.9 - - - +
209B GLY* 3.1 32.5 + - - +
229B ARG* 2.4 32.7 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU 4.0 0.6 - - - +
155B THR* 3.3 6.4 - - - +
156B GLY* 2.8 37.5 + - - +
167B ASP* 1.3 78.8 - - - +
169B ASN* 1.3 66.1 - - - +
170B VAL* 5.0 8.5 - - + -
206B VAL* 5.4 6.1 - - + -
207B ASN 3.7 4.0 - - - +
208B PHE* 3.6 17.9 - - + -
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASP* 2.8 28.1 + - - +
154B LEU 3.3 11.6 + - - +
155B THR* 3.6 21.9 + - + +
167B ASP* 4.5 3.6 - - - +
168B VAL* 1.3 75.6 - - - +
170B VAL* 1.3 69.0 + - - +
171B PRO* 3.2 14.0 - - - +
206B VAL* 3.6 6.9 - - - +
207B ASN* 3.0 63.7 + - - +
229B ARG* 5.2 0.4 - - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU 3.8 1.0 - - - +
153B ASP* 3.7 0.7 - - - -
154B LEU* 2.8 49.5 + - + +
168B VAL* 5.0 9.0 - - + -
169B ASN* 1.3 80.8 - - - +
171B PRO* 1.3 75.0 - - - +
172B VAL* 3.8 5.1 + - + -
203B ILE* 4.2 20.2 - - + -
206B VAL* 4.2 25.8 - - + -
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Residues in contact with PRO 171 (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 THR* 4.2 17.0 - - + -
152B LEU 3.4 5.6 - - - +
153B ASP* 4.2 8.3 - - - +
169B ASN* 3.2 18.8 - - - +
170B VAL* 1.3 85.9 - - + +
172B VAL* 1.3 58.3 + - - +
173B VAL* 4.8 5.4 - - + -
203B ILE* 3.4 6.6 - - - +
204B GLY* 2.8 32.7 + - - -
205B ASP 3.8 38.1 - - - +
206B VAL 4.5 0.2 - - - +
207B ASN* 5.0 0.7 - - - +
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP 4.2 0.2 - - - +
151B THR* 3.4 6.2 - - - +
152B LEU* 2.8 56.4 + - + +
154B LEU* 4.3 23.3 - - + -
170B VAL* 4.5 6.1 - - + +
171B PRO* 1.3 77.0 - - - +
173B VAL* 1.3 62.2 + - - +
201B PRO* 4.0 24.7 - - + -
202B THR 3.6 14.4 - - - +
203B ILE* 4.4 7.0 - - + +
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP 3.9 3.1 - - - +
151B THR* 4.3 16.8 - - + +
171B PRO* 4.8 5.2 - - + -
172B VAL* 1.3 77.3 - - - +
174B TYR* 1.3 63.6 + - - +
175B ARG* 3.8 29.2 - - + +
199B ARG* 4.1 6.9 - - + +
200B ASP 4.1 0.3 - - - +
201B PRO* 3.4 4.7 - - - +
202B THR 2.8 34.8 + - - +
204B GLY* 4.5 10.3 - - - -
260B THR* 3.7 39.0 - - + +
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASP* 5.3 0.4 - - + -
150B TRP* 3.0 66.2 + + + +
172B VAL 4.3 0.2 + - - -
173B VAL* 1.3 73.4 - - - +
175B ARG* 1.3 75.7 + - - +
176B GLU* 3.5 28.0 + - + +
198B SER* 5.4 5.3 - - - -
199B ARG 3.4 18.2 - - - -
200B ASP* 4.2 15.4 + - - -
201B PRO* 3.8 24.9 - - + -
502B LDA 5.2 8.1 + - - -
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASP 3.5 6.7 - - - +
149B ASN* 3.5 33.4 + - + +
173B VAL* 3.8 22.2 - - + -
174B TYR* 1.3 84.9 - - - +
176B GLU* 1.3 62.6 + - - +
177B SER* 4.5 7.2 + - - +
198B SER* 3.4 4.5 - - - -
199B ARG* 2.9 39.3 + - + +
258B LEU* 3.7 36.5 - - + +
259B PRO* 2.6 49.8 + - - +
260B THR* 4.8 1.4 - - - +
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Residues in contact with GLU 176 (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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147B ALA* 3.4 0.5 - - - +
148B ASP* 3.0 49.1 + - + +
174B TYR* 3.5 27.0 + - + +
175B ARG* 1.3 75.7 - - - +
177B SER* 1.3 67.4 + - - +
178B THR* 6.0 1.3 - - - +
196B SER* 5.7 6.3 - - - -
197B VAL 3.7 6.5 - - - +
198B SER* 4.6 8.1 - - - +
502B LDA 4.6 17.2 - - - +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 5.1 2.6 - - - +
146B LYS 3.4 9.0 - - - -
147B ALA* 3.7 15.0 - - - +
175B ARG* 4.5 8.3 + - - +
176B GLU* 1.3 80.5 + - - +
178B THR* 1.3 63.4 + - - +
179B TYR* 3.8 19.2 - - - -
196B SER* 3.2 5.4 - - - -
197B VAL* 3.0 36.7 + - - +
258B LEU* 3.9 22.0 - - - +
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Residues in contact with THR 178 (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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361A ASP* 5.4 4.9 + - - +
144B ARG 4.0 0.5 - - - +
145B ILE* 3.3 6.8 - - - +
146B LYS* 2.9 58.2 + - + +
176B GLU* 6.0 1.4 - - - +
177B SER* 1.3 73.0 - - - +
179B TYR* 1.3 65.3 + - - +
180B GLN* 4.1 3.3 + - + +
194B GLU* 3.5 36.1 - - + +
195B GLU 3.6 6.5 - - - +
196B SER* 4.0 9.8 - - - -
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Residues in contact with TYR 179 (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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142B LEU* 3.8 28.3 - - + -
144B ARG 4.0 3.8 - - - -
145B ILE* 3.9 30.4 - - + +
177B SER* 3.8 16.6 - - - -
178B THR* 1.3 75.2 - - - +
180B GLN* 1.3 61.5 + - - +
194B GLU* 3.5 2.5 - - - -
195B GLU 2.8 32.1 + - - +
197B VAL* 3.6 26.0 - - + -
252B LEU* 3.8 9.9 - - + +
253B TYR 4.7 3.4 - - - -
254B VAL* 4.4 12.8 - - + -
255B PRO* 3.1 42.1 - - + +
258B LEU* 4.1 11.2 - - + +
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Residues in contact with GLN 180 (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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358A VAL* 5.2 7.9 - - + -
359A SER* 6.0 4.9 - - - -
142B LEU* 3.5 10.4 - - - +
143B ASP* 3.3 19.6 + - + -
144B ARG* 3.2 24.5 + - + +
146B LYS* 6.0 6.5 - - - +
178B THR* 4.0 5.0 - - + +
179B TYR* 1.3 75.2 - - - +
181B SER* 1.3 60.9 + - - +
192B THR* 6.5 0.2 - - - -
193B SER 3.5 8.3 - - - +
194B GLU* 4.2 12.8 - - + +
252B LEU* 4.4 1.5 - - - +
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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
------------------------------------------------------------
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