Contacts of the strand formed by residues 176 - 184 (chain B) in PDB entry 3MH5
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 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B ALA 3.5 1.7 - - - +
167B ILE* 3.4 4.0 - - - -
168B GLY 2.7 31.1 + - - -
170B PRO* 3.4 19.6 - - + +
171B PHE* 5.0 4.6 - - + -
173B LEU* 4.6 10.7 - - - +
175B GLU* 1.3 76.4 + - - +
177B VAL* 1.3 70.4 + - - +
178B THR* 4.5 7.2 - - + -
500B DFP 3.5 33.7 - - + +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 5.6 4.3 - - + -
19B LEU* 3.8 30.3 - - + -
23B MET* 4.8 8.1 - - + -
165B VAL* 3.2 30.3 - - + -
166B ALA 3.3 3.4 - - - +
167B ILE* 4.2 18.8 - - + -
175B GLU* 5.3 2.9 - - + +
176B THR* 1.3 83.0 - - - +
178B THR* 1.3 70.9 + - - +
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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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165B VAL* 3.3 5.9 - - - +
166B ALA* 2.8 39.8 + - - +
176B THR* 4.5 10.5 - - + -
177B VAL* 1.3 81.8 - - - +
179B SER* 1.3 61.6 + - - +
203B ALA 2.3 28.8 + - - +
204B ALA* 5.3 1.1 - - - -
500B DFP 3.5 25.0 + - + +
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 4.3 22.6 - - - +
164B THR 3.5 9.2 - - - -
165B VAL* 4.4 2.5 - - - -
178B THR* 1.3 76.0 - - - +
180B GLY* 1.3 59.8 + - - +
202B ASP* 3.9 4.3 - - - +
203B ALA* 3.4 15.8 - - - -
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Residues in contact with GLY 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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163B TYR* 3.4 10.1 - - - +
164B THR* 3.0 27.0 + - - +
179B SER* 1.3 78.1 - - - +
181B ILE* 1.3 69.9 + - - +
202B ASP* 3.1 16.6 - - - -
203B ALA* 3.4 6.1 - - - +
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Residues in contact with ILE 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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160B VAL* 4.6 4.7 - - + +
161B GLY* 4.2 17.0 - - - +
162B ASP 3.0 11.4 - - - +
163B TYR* 4.1 20.9 - - + -
164B THR* 3.7 4.2 + - - -
180B GLY* 1.3 81.2 - - - +
182B VAL* 1.3 75.7 + - - +
183B SER* 3.3 12.0 + - - +
201B THR* 2.8 21.3 + - - -
202B ASP* 2.7 21.9 + - - +
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Residues in contact with VAL 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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158B LEU* 4.3 16.4 - - + -
159B ARG 3.4 12.6 - - - +
160B VAL* 2.4 41.9 - - - +
162B ASP* 2.7 26.2 + - + +
164B THR* 3.4 20.9 - - + -
181B ILE* 1.3 75.6 - - - +
183B SER* 1.3 60.0 + - - +
184B ALA 3.9 7.4 - - - +
185B LEU* 3.6 42.0 - - + -
199B ILE* 4.2 7.2 - - + -
200B GLN 3.8 6.3 - - - +
201B THR* 4.7 1.1 - - - -
222B ILE* 5.1 0.2 - - + -
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Residues in contact with SER 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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160B VAL* 4.0 12.9 - - - +
181B ILE* 3.5 12.5 + - - +
182B VAL* 1.3 73.2 - - - +
184B ALA* 1.3 63.5 + - - +
200B GLN* 2.8 14.0 + - - -
202B ASP* 3.3 27.0 + - - +
238B ILE* 3.7 25.4 - - - +
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Residues in contact with ALA 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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160B VAL* 3.9 7.5 - - - +
182B VAL* 3.5 2.7 - - - +
183B SER* 1.3 83.3 - - - +
185B LEU* 1.3 68.0 + - - +
186B GLY 3.4 6.3 - - - +
199B ILE* 3.7 2.6 - - - -
200B GLN* 2.9 59.3 + - + +
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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