Contacts of the helix formed by residues 176 - 188 (chain W) in PDB entry 5IY8
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 ASN 176 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77W VAL 5.3 0.5 - - - +
80W ILE* 4.4 1.9 - - - +
81W GLU* 2.8 63.1 + - + +
84W ILE* 4.1 9.5 - - + +
88W ARG* 3.5 21.2 - - - +
108W ALA* 3.8 3.6 - - - -
175W TYR* 1.4 72.9 - - - +
177W LEU* 1.3 71.7 + - - +
178W ASP* 3.9 14.9 + - - +
179W ASP* 3.4 15.1 + - + +
180W LEU* 3.0 25.2 + - - +
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Residues in contact with LEU 177 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77W VAL* 4.2 20.9 - - + -
80W ILE* 4.9 9.4 - - + -
108W ALA* 3.3 18.3 - - + +
109W LEU* 3.9 8.3 - - - +
110W SER* 3.8 38.4 - - - +
114W ASN* 3.4 25.1 - - - +
115W LEU* 3.7 33.0 - - + -
176W ASN* 1.3 78.3 + - - +
178W ASP* 1.3 65.4 + - - +
180W LEU* 3.3 8.6 + - + +
181W LYS* 3.1 20.2 + - - +
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Residues in contact with ASP 178 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77W VAL* 4.9 9.2 - - + +
81W GLU* 4.2 7.6 - - - +
176W ASN* 3.5 14.7 - - - +
177W LEU* 1.3 81.5 - - - +
179W ASP* 1.4 58.0 + - - +
181W LYS* 3.3 22.8 + - - +
182W ALA* 3.0 26.3 + - - +
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Residues in contact with ASP 179 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88W ARG* 5.7 3.5 + - - +
175W TYR* 5.9 1.9 - - - +
176W ASN* 3.4 24.6 + - + +
177W LEU 3.3 0.6 - - - -
178W ASP* 1.4 77.2 - - - +
180W LEU* 1.3 58.4 + - - +
182W ALA* 3.3 11.0 + - - +
183W LEU* 2.9 33.5 + - - +
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Residues in contact with LEU 180 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108W ALA 4.7 4.3 - - - +
115W LEU* 4.1 16.6 - - + -
170W LEU* 4.8 16.2 - - + -
175W TYR* 3.8 33.1 - - + +
176W ASN 3.0 17.9 + - - +
177W LEU* 3.3 8.9 + - + +
179W ASP* 1.3 74.1 + - - +
181W LYS* 1.4 56.1 + - - +
183W LEU* 3.4 22.5 + - + +
184W GLY* 2.8 27.5 + - - +
191W PRO* 4.0 25.4 - - + +
194W LEU* 5.4 5.8 - - + -
195W ALA* 4.2 16.4 - - + -
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Residues in contact with LYS 181 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77W VAL* 5.7 3.2 - - - +
114W ASN* 2.9 52.7 + - - +
115W LEU* 3.7 26.5 - - + +
177W LEU* 3.1 16.0 + - - +
178W ASP* 3.3 23.2 + - - +
180W LEU* 1.4 74.5 - - - +
182W ALA* 1.3 56.7 + - - +
184W GLY* 3.7 0.8 - - - +
185W ARG* 2.9 42.0 + - + +
191W PRO* 5.1 0.7 - - - -
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Residues in contact with ALA 182 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178W ASP* 3.0 17.5 + - - +
179W ASP* 3.3 17.7 + - - +
181W LYS* 1.3 74.5 - - - +
183W LEU* 1.3 62.5 + - - +
185W ARG* 3.2 18.2 + - - +
186W ARG* 4.9 2.4 - - - +
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Residues in contact with LEU 183 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169W PRO* 5.0 20.0 - - + -
170W LEU* 5.0 7.2 - - + -
179W ASP* 2.9 24.1 + - - +
180W LEU* 3.4 22.7 - - + +
182W ALA* 1.3 76.5 - - - +
184W GLY* 1.3 57.3 + - - +
185W ARG 2.8 13.7 - - - +
186W ARG* 5.1 9.5 + - - +
187W GLN* 3.4 40.3 + - + +
194W LEU* 6.1 2.5 - - + -
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Residues in contact with GLY 184 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180W LEU* 2.8 16.8 + - - -
181W LYS 3.2 1.8 + - - -
183W LEU* 1.3 74.1 - - - +
185W ARG* 1.3 64.9 + - - +
187W GLN* 3.9 3.3 - - - -
188W GLY* 3.0 23.7 + - - -
189W TRP 3.9 12.2 + - - +
191W PRO* 4.3 22.0 - - - -
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Residues in contact with ARG 185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115W LEU 5.9 2.5 - - - +
117W ILE* 3.7 37.8 - - + +
156W ARG* 6.4 0.2 - - - +
181W LYS* 2.9 28.3 + - + +
182W ALA* 3.2 11.0 - - - +
183W LEU 2.8 10.6 - - - +
184W GLY* 1.3 76.3 - - - +
186W ARG* 1.3 65.0 + - + +
187W GLN 2.7 8.8 + - - -
188W GLY* 4.7 0.9 - - - +
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Residues in contact with ARG 186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182W ALA 4.9 2.9 - - - +
183W LEU* 5.2 8.1 + - - +
185W ARG* 1.3 74.6 - - + +
187W GLN* 1.3 82.6 + - - +
188W GLY* 3.2 3.8 + - - +
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Residues in contact with GLN 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158W TYR* 3.2 10.8 + - - +
160W GLU* 5.8 3.1 - - + +
166W ARG* 2.9 45.0 - - - +
183W LEU* 3.4 40.2 + - - +
184W GLY* 4.1 3.2 - - - +
185W ARG 2.7 10.1 + - - -
186W ARG* 1.3 93.5 - - - +
188W GLY* 1.4 59.3 + - - +
189W TRP* 3.6 29.5 - - + +
194W LEU* 5.5 1.2 - - - +
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Residues in contact with GLY 188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155W CYS 3.3 11.6 - - - +
156W ARG* 3.6 31.7 - - - -
158W TYR* 2.5 30.6 + - - -
184W GLY 3.0 11.5 + - - -
185W ARG* 5.2 0.9 - - - -
186W ARG 3.2 6.4 - - - +
187W GLN* 1.4 71.6 - - - +
189W TRP* 1.3 54.5 + - - +
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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