Contacts of the strand formed by residues 184 - 193 (chain B) in PDB entry 3WOO
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 THR 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B ASP* 4.1 6.1 - - - +
134B THR* 3.5 16.2 + - - +
178B SER* 3.5 4.7 + - - -
179B PHE* 2.7 44.0 + - - +
180B SER* 5.2 2.9 + - - -
182B GLY 3.3 0.2 - - - -
183B ASN* 1.3 84.7 + - - +
185B TYR* 1.3 71.5 + - - +
186B ARG* 3.9 34.7 + - - +
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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
----------------------------------------------------------
132B ASP* 3.4 0.3 - - - +
133B VAL* 3.2 30.6 + - + -
134B THR* 3.2 27.4 + - + -
137B ALA* 3.5 24.9 - - + -
138B LYS* 4.9 5.2 - - + -
141B ILE* 3.3 26.6 - - + +
155B LEU* 4.2 18.1 - - + +
176B LEU* 4.1 16.8 - - + -
177B TYR 3.2 6.5 - - - +
178B SER* 3.8 25.8 + - - -
182B GLY* 3.4 36.6 + - - -
184B THR* 1.3 75.9 - - - +
186B ARG* 1.3 68.1 + - - +
550B LEU* 4.1 15.1 + - - +
554B PRO* 6.0 0.5 - - - +
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Residues in contact with ARG 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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30B VAL* 4.4 10.1 - - - +
32B GLN* 3.5 54.4 + - - +
130B ILE* 3.8 15.7 - - + -
131B THR 3.4 11.0 - - - +
132B ASP* 4.3 16.3 + - - +
133B VAL* 4.5 0.9 - - - -
175B ARG 3.9 0.3 - - - +
176B LEU* 3.5 5.4 - - - +
177B TYR* 2.8 40.3 + - - +
179B PHE* 3.4 51.8 - - + +
184B THR* 3.9 19.0 - - + +
185B TYR* 1.3 79.2 - - - +
187B LEU* 1.3 60.7 + - - +
188B PHE* 4.5 6.1 - - + -
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Residues in contact with LEU 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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129B GLU 3.8 0.9 - - - +
130B ILE* 3.5 3.8 - - - -
131B THR* 3.0 48.2 + - - +
133B VAL* 4.2 10.7 - - + +
162B LEU* 4.0 33.7 - - + +
163B ILE* 4.4 9.6 - - + -
166B CYS* 4.0 26.9 - - + -
174B CYS* 4.3 7.6 - - + -
175B ARG 3.5 26.7 - - - +
176B LEU* 4.3 4.0 - - - +
186B ARG* 1.3 72.6 - - - +
188B PHE* 1.3 66.8 + - - +
189B LYS* 5.2 0.4 - - + +
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Residues in contact with PHE 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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31B PRO* 5.7 2.9 - - + -
32B GLN* 5.8 0.4 - - - -
127B LEU* 3.6 20.0 - - + -
129B GLU 3.5 3.6 - - - -
130B ILE* 3.6 40.4 - - + -
173B ARG 4.1 0.5 - - - +
174B CYS* 3.1 8.1 - - - +
175B ARG* 2.9 33.7 + - + +
177B TYR* 3.4 37.2 - + + -
179B PHE* 4.5 6.5 - + - -
186B ARG* 4.5 10.5 - - + -
187B LEU* 1.3 78.5 - - - +
189B LYS* 1.3 59.0 + - - +
190B ASN* 4.3 13.5 - - - +
272B TYR* 4.6 7.2 - + - -
578B SER* 3.9 17.3 - - - -
579B LEU* 3.9 30.3 - - + -
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Residues in contact with LYS 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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127B LEU* 4.0 0.9 - - - +
128B ASP* 2.8 50.8 + - + +
129B GLU* 2.9 39.0 + - + +
166B CYS* 3.6 33.0 + - - +
169B GLU* 3.1 28.8 + - - +
172B PHE* 3.4 36.2 - - + -
174B CYS* 3.8 7.4 - - - -
187B LEU* 5.8 1.1 - - + -
188B PHE* 1.3 72.3 - - - +
190B ASN* 1.3 60.1 + - - +
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Residues in contact with ASN 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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66B ALA* 6.0 1.2 - - - +
125B PHE* 4.0 30.0 + - + +
126B VAL 3.3 5.6 + - - +
127B LEU* 3.4 35.5 - - - +
172B PHE* 3.1 10.3 - - - -
173B ARG 2.7 44.0 + - - +
177B TYR* 5.5 0.3 + - - -
188B PHE* 4.3 13.7 - - - +
189B LYS* 1.3 77.9 + - - +
191B LEU* 1.3 60.7 + - - +
272B TYR* 5.0 6.1 + - - -
804B GOL 3.4 24.9 + - - -
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Residues in contact with LEU 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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124B VAL 3.3 3.1 - - - +
125B PHE* 3.2 8.7 - - - -
126B VAL* 2.9 41.3 + - + +
128B ASP* 4.7 0.2 - - - +
171B GLY 3.3 17.7 - - - +
172B PHE* 3.6 23.8 - - + -
190B ASN* 1.3 70.0 - - - +
192B GLU* 1.3 59.9 + - - +
193B ILE* 3.5 15.0 + - + -
232B VAL* 5.5 2.0 - - + -
237B LYS* 6.3 0.7 - - + -
238B PRO* 3.7 21.8 - - + -
248B TYR* 3.7 39.3 - - + +
802B GOL 3.7 19.3 - - - +
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Residues in contact with GLU 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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123B ARG* 3.0 36.4 + - - +
124B VAL 4.0 2.0 - - - -
125B PHE* 3.7 17.8 - - + -
171B GLY 2.9 16.0 + - - +
172B PHE 4.6 3.3 - - - +
173B ARG* 3.6 49.7 + - + +
190B ASN 3.5 0.8 + - - -
191B LEU* 1.3 72.4 - - - +
193B ILE* 1.3 58.1 - - - +
194B LYS* 3.5 17.5 + - + +
238B PRO* 3.1 24.6 - - - +
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Residues in contact with ILE 193 (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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123B ARG* 3.4 11.8 - - - -
124B VAL* 2.9 45.9 + - + +
126B VAL* 4.5 8.1 - - + -
191B LEU* 4.2 16.2 - - + +
192B GLU* 1.3 70.8 - - - +
194B LYS* 1.3 61.3 + - - +
195B ASP 3.9 12.6 - - - +
196B VAL* 4.0 7.2 - - + +
230B ALA* 3.7 18.6 - - + -
231B TYR 3.5 23.1 - - - +
232B VAL* 4.4 8.1 - - + -
238B PRO* 4.7 2.9 - - + -
248B TYR* 3.7 43.5 - - + -
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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