Contacts of the helix formed by residues 170 - 183 (chain C) in PDB entry 4RQI
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 GLU 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C LEU* 4.0 21.3 - - + -
165C CYS* 2.7 24.7 + - + +
168C ASN* 3.8 12.3 - - + +
169C LYS* 1.3 71.7 - - - +
171C PHE* 1.3 58.5 + - - +
172C GLU* 3.4 14.0 - - - +
173C LYS* 3.3 17.6 + - + +
174C ALA* 3.0 27.0 + - - +
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Residues in contact with PHE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C ILE* 4.3 17.7 - - + -
169C LYS* 3.3 36.7 + - + -
170C GLU* 1.3 69.8 - - - +
172C GLU* 1.3 72.6 + - + +
174C ALA* 3.7 6.0 - - - +
175C SER* 3.0 25.5 + - - -
198C ILE 4.7 0.4 - - - -
199C ILE* 3.8 38.5 - - + +
202C LYS* 3.1 65.3 - - + +
204C LEU* 3.8 23.6 - - + -
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Residues in contact with GLU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LYS 5.0 1.5 - - - +
170C GLU* 4.0 12.8 - - - +
171C PHE* 1.3 89.4 + - + +
173C LYS* 1.3 58.7 + - - +
175C SER* 3.4 5.6 + - - -
176C LYS* 3.0 29.3 + - - +
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Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C THR* 5.7 4.7 - - + -
165C CYS* 4.0 15.3 - - - -
170C GLU* 3.3 21.6 + - + +
171C PHE 3.3 0.2 - - - -
172C GLU* 1.3 78.4 + - - +
174C ALA* 1.3 60.9 + - - +
176C LYS* 3.3 6.5 + - - +
177C ILE* 2.9 38.5 + - + +
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Residues in contact with ALA 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C VAL* 3.9 11.0 - - + +
165C CYS* 3.7 20.5 - - + +
166C ILE* 3.8 26.2 - - + -
170C GLU 3.0 16.9 + - - +
171C PHE* 3.7 7.2 - - - +
173C LYS* 1.3 76.7 - - - +
175C SER* 1.3 57.5 + - - +
177C ILE* 3.8 4.1 - - - +
178C LEU* 2.9 30.5 + - - +
199C ILE* 4.1 9.2 - - + -
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Residues in contact with SER 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C PHE 3.0 17.9 + - - -
172C GLU* 3.7 5.6 - - - -
174C ALA* 1.3 75.6 - - - +
176C LYS* 1.3 57.5 + - - +
178C LEU* 3.2 2.6 + - - +
179C LYS* 2.9 63.5 + - - +
196C LEU* 4.6 1.3 - - - +
199C ILE* 3.9 20.3 - - - +
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Residues in contact with LYS 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C GLU 3.0 17.9 + - - +
173C LYS* 3.6 7.6 - - - +
175C SER* 1.3 78.3 - - - +
177C ILE* 1.3 62.3 + - + +
179C LYS* 3.5 6.7 + - - +
180C LYS* 3.3 27.2 + - - +
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Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C THR* 4.1 5.6 - - + +
130C GLU* 3.6 39.3 - - + +
133C ILE* 5.5 1.6 - - + -
158C LYS* 4.9 1.6 - - - +
161C ALA* 4.1 22.0 - - + +
162C VAL* 3.9 16.6 - - + -
165C CYS* 3.6 31.4 - - - -
173C LYS* 2.9 17.2 + - + +
174C ALA* 3.8 4.0 - - - +
176C LYS* 1.3 73.2 - - + +
178C LEU* 1.3 66.7 + - - +
180C LYS* 3.3 2.4 + - - +
181C HIS* 3.0 44.6 + - + +
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Residues in contact with LEU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C VAL* 4.1 13.7 - - + +
174C ALA 2.9 17.9 + - - +
175C SER* 3.6 6.3 - - - +
177C ILE* 1.3 77.1 - - - +
179C LYS* 1.3 65.1 + - + +
182C MET* 2.7 48.5 + - + +
183C SER* 3.8 2.1 + - - +
192C ARG* 3.6 33.4 - - + +
195C LEU* 3.5 42.8 - - + -
196C LEU* 4.0 26.9 - - + +
199C ILE* 4.6 3.6 - - + -
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Residues in contact with LYS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C SER* 2.9 49.0 + - - +
176C LYS* 3.8 6.5 - - - +
177C ILE 3.3 0.2 - - - -
178C LEU* 1.3 84.5 - - + +
180C LYS* 1.3 60.6 + - - +
183C SER* 2.6 31.0 + - - +
196C LEU* 3.1 35.8 - - + +
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Residues in contact with LYS 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C LEU* 5.9 4.2 - - - +
130C GLU* 4.7 12.7 + - - -
176C LYS* 3.3 16.6 + - - +
177C ILE* 5.4 0.9 - - - +
178C LEU 3.3 0.2 - - - -
179C LYS* 1.3 79.1 - - + +
181C HIS* 1.3 85.8 + - + +
183C SER* 5.0 2.0 - - - -
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Residues in contact with HIS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLU* 5.0 10.4 + - + +
133C ILE* 4.0 34.5 - - + +
134C ASN* 5.4 4.7 - - - -
158C LYS* 2.9 59.8 + - + +
177C ILE* 3.0 37.3 + - + +
178C LEU* 5.3 0.4 - - - -
180C LYS* 1.3 110.0 + - + +
182C MET* 1.3 63.8 + - - +
183C SER 3.5 2.2 - - - -
184C LYS* 3.4 6.3 - - - -
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Residues in contact with MET 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C LYS 5.3 0.7 - - - +
158C LYS* 4.4 16.8 - - + -
159C GLU* 4.1 21.8 - - + +
162C VAL* 4.2 21.5 - - + -
178C LEU* 2.7 36.8 + - + +
181C HIS* 1.3 72.2 - - - +
183C SER* 1.3 53.2 + - - +
184C LYS* 2.7 26.7 + - - +
188C THR* 4.0 13.6 + - + +
191C LEU* 4.2 17.3 - - + -
192C ARG* 3.2 37.7 + - + +
195C LEU* 3.6 25.8 - - + -
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Residues in contact with SER 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C LEU* 3.8 0.9 + - - +
179C LYS* 2.6 31.1 + - - +
180C LYS 5.5 1.3 - - - -
181C HIS 3.5 2.0 - - - +
182C MET* 1.3 75.2 - - - +
184C LYS* 1.3 58.8 + - - +
185C ASP* 4.1 2.3 + - - +
192C ARG* 3.8 14.4 - - - +
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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