Contacts of the helix formed by residues 176 - 184 (chain B) in PDB entry 1G8I
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 ASP 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B ARG* 5.4 5.2 + - - -
152B ILE* 5.6 0.5 - - - +
155B MET* 3.2 32.9 - - + +
172B GLY 3.6 3.7 + - - +
173B SER 3.3 6.4 + - - +
174B LYS 3.3 0.6 - - - -
175B ALA* 1.3 75.5 - - - +
177B PRO* 1.3 72.1 - - - +
178B SER* 2.8 31.1 + - - -
179B ILE* 3.1 27.5 + - + +
180B VAL* 3.0 22.5 + - - +
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Residues in contact with PRO 177 (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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175B ALA 3.3 10.5 - - - +
176B ASP* 1.3 89.7 - - - +
178B SER* 1.3 56.1 + - - +
180B VAL* 3.7 8.0 - - + +
181B GLN* 2.9 31.5 + - - +
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Residues in contact with SER 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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148B ARG* 5.7 2.3 + - - -
176B ASP* 2.8 22.5 + - - -
177B PRO* 1.3 78.1 - - - +
179B ILE* 1.3 61.1 + - - +
181B GLN* 3.4 7.7 + - - +
182B ALA* 3.0 27.5 + - - +
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Residues in contact with ILE 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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148B ARG* 4.6 11.9 - - - +
152B ILE* 4.5 13.5 - - + -
155B MET* 5.6 0.2 - - + -
156B MET* 3.9 25.1 - - + -
173B SER* 3.5 22.9 - - - +
176B ASP* 3.1 29.2 + - + +
178B SER* 1.3 76.1 + - - +
180B VAL* 1.3 66.8 + - - +
182B ALA* 3.1 7.0 + - - +
183B LEU* 3.0 43.5 + - + +
953B 1PE 3.7 27.6 - - - +
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Residues in contact with VAL 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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97B LEU* 4.3 26.9 - - + +
173B SER 4.6 0.2 - - - -
174B LYS* 3.3 39.5 - - + +
176B ASP 3.0 16.9 + - - +
177B PRO* 3.7 10.3 - - + +
179B ILE* 1.3 76.8 - - - +
181B GLN* 1.3 57.5 + - - +
183B LEU* 3.4 1.4 + - - +
184B SER* 2.5 41.2 + - - +
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Residues in contact with GLN 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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177B PRO 2.9 18.1 + - - +
178B SER* 3.5 8.7 - - - +
179B ILE 3.1 0.2 - - - -
180B VAL* 1.3 81.7 - - - +
182B ALA* 1.3 61.2 + - - +
183B LEU 3.4 0.3 + - - -
184B SER* 3.6 15.3 + - - -
185B LEU* 3.7 18.5 - - + +
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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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100B LYS* 5.6 0.2 + - - -
178B SER 3.0 16.7 + - - +
179B ILE* 3.1 6.9 + - - +
181B GLN* 1.3 77.1 - - - +
183B LEU* 1.3 60.1 - - - +
184B SER 3.6 0.2 - - - -
185B LEU* 3.9 20.3 + - - +
953B 1PE 4.2 19.3 - - - -
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Residues in contact with LEU 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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97B LEU* 3.2 27.4 + - + +
100B LYS* 2.9 57.0 + - + +
101B LEU* 3.1 38.1 - - + -
104B ALA* 5.3 3.8 - - + -
173B SER* 4.8 0.2 - - - -
179B ILE* 3.0 23.6 + - + +
180B VAL* 3.4 0.4 + - - -
181B GLN 3.2 0.2 - - - -
182B ALA* 1.3 76.4 - - - +
184B SER* 1.3 55.7 + - - +
185B LEU 3.3 5.4 - - - -
953B 1PE 3.4 37.0 - - - -
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Residues in contact with SER 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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97B LEU* 5.0 11.2 - - - +
100B LYS* 4.1 1.6 - - - +
180B VAL* 2.5 32.8 + - - +
181B GLN* 3.6 14.1 + - - -
182B ALA 3.6 0.8 - - - -
183B LEU* 1.3 76.7 - - - +
185B LEU* 1.3 64.9 + - - +
186B TYR* 4.0 1.6 + - - +
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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