Contacts of the helix formed by residues 177 - 184 (chain B) in PDB entry 4M83
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 HIS 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B ARG* 4.7 5.5 + - - -
162B TYR* 3.4 26.0 - + - -
166B GLU* 3.6 22.0 + - - -
169B LEU* 4.4 0.2 - - - -
175B THR 3.6 0.8 + - - -
176B GLU* 1.3 73.9 - - - +
178B PRO* 1.3 76.4 - - + +
179B ASP* 3.0 42.9 + - + +
180B THR* 3.0 16.4 + - - +
181B PHE* 2.9 19.8 + - - +
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Residues in contact with PRO 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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162B TYR* 4.4 14.4 - - + -
165B PHE* 3.5 49.9 - - + -
166B GLU* 4.0 24.9 - - + +
169B LEU* 4.1 6.1 - - + -
176B GLU 3.6 4.0 - - - +
177B HIS* 1.3 101.3 - - + +
179B ASP* 1.3 56.1 + - - +
181B PHE* 3.8 8.5 - - + +
182B ALA* 2.9 33.3 + - - +
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Residues in contact with ASP 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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141B GLU* 4.8 12.1 - - - +
145B ALA* 5.6 8.0 - - + +
146B GLU* 6.2 0.3 - - - +
149B TRP* 4.5 8.0 + - - -
153B ARG* 4.4 4.2 + - - -
162B TYR* 2.8 33.0 + - - -
177B HIS* 3.0 26.2 + - + -
178B PRO* 1.3 77.0 - - - +
180B THR* 1.3 58.1 + - - +
182B ALA* 5.1 1.3 - - - -
183B SER* 3.0 36.4 + - - +
184B HIS* 3.3 5.3 - - + -
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Residues in contact with THR 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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121B ARG* 6.1 0.7 - - - +
141B GLU* 5.2 4.2 + - - -
176B GLU* 4.3 13.7 - - + -
177B HIS* 3.0 22.7 + - - +
179B ASP* 1.3 77.1 - - - +
181B PHE* 1.3 61.4 + - - +
184B HIS* 3.0 54.3 + - + +
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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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114B TYR* 3.8 20.4 - + + -
117B ARG* 3.0 56.7 + - + -
118B VAL* 3.6 26.9 - - + -
121B ARG* 3.3 35.8 + - - +
165B PHE* 3.6 31.2 - + - -
168B TRP* 4.1 2.2 - + - -
169B LEU* 3.8 24.7 - - + -
174B ILE* 4.2 3.6 - - + -
176B GLU* 3.9 10.5 - - + -
177B HIS 2.9 14.1 + - - +
178B PRO 3.8 2.5 - - - +
180B THR* 1.3 79.7 - - - +
182B ALA* 1.3 63.6 + - - +
184B HIS 4.6 2.9 + - - -
185B PRO* 5.3 1.9 - - - +
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Residues in contact with ALA 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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114B TYR* 3.9 17.0 - - + +
117B ARG* 2.9 26.6 + - - +
165B PHE* 4.5 9.4 - - + -
178B PRO 2.9 17.7 + - - +
179B ASP* 4.5 1.1 - - - +
181B PHE* 1.3 82.1 - - - +
183B SER* 1.3 63.3 + - - +
184B HIS 3.6 0.6 + - - -
185B PRO* 5.0 2.1 - - - +
501B ERY 3.3 27.9 + - + +
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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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136B ALA* 3.9 8.5 + - - +
140B TYR* 4.9 11.0 - - - -
179B ASP* 3.0 19.9 + - - +
182B ALA* 1.3 78.9 - - - +
184B HIS* 1.3 77.4 + - - +
185B PRO* 3.5 11.0 - - - +
208B TYR* 3.8 6.4 + - - -
501B ERY 2.9 40.5 + - - +
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Residues in contact with HIS 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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136B ALA* 3.7 27.6 - - + +
137B TRP 5.2 2.7 - - - -
140B TYR* 4.6 10.4 - + + -
141B GLU* 2.4 33.2 + - - -
179B ASP* 3.3 25.2 + - - +
180B THR* 3.0 37.2 + - + +
181B PHE 5.1 0.9 - - - -
182B ALA 3.6 0.8 - - - -
183B SER* 1.3 88.5 + - - +
185B PRO* 1.3 69.0 - - - +
186B PRO* 4.4 0.7 - - - +
208B TYR* 4.3 5.3 + - - -
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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