Contacts of the helix formed by residues 171 - 181 (chain C) in PDB entry 5FFO
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 VAL 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124C ALA 3.1 12.9 + - - +
126C LEU* 3.9 18.8 - - + -
141C LEU* 4.3 22.4 - - + -
153C LEU* 4.7 7.0 - - + -
154C SER* 6.0 0.4 - - - +
169C PHE* 3.1 13.6 + - + +
170C ASP* 1.3 74.9 - - - +
172C THR* 1.3 63.8 + - - +
173C GLY 3.3 2.2 - - - -
174C VAL* 3.1 17.4 + - + +
175C VAL* 3.0 26.2 + - + +
188C PHE* 4.0 23.3 - - + -
229C LEU* 4.0 12.1 - - + -
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Residues in contact with THR 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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121C LEU* 3.8 13.1 - - + +
122C SER 3.5 22.7 - - - +
123C ARG* 3.5 4.2 - - - +
124C ALA* 2.7 29.9 + - - -
170C ASP* 2.7 23.9 + - - -
171C VAL* 1.3 76.4 - - - +
173C GLY* 1.3 62.5 + - - +
174C VAL 3.1 0.3 + - - -
175C VAL* 3.2 2.1 + - - +
176C ARG* 3.0 43.1 + - - +
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Residues in contact with GLY 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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171C VAL 3.3 0.6 - - - -
172C THR* 1.3 78.6 - - - +
174C VAL* 1.3 61.0 + - - +
176C ARG* 4.1 12.4 - - - +
177C GLN* 3.4 31.4 + - - +
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLN* 3.5 41.7 - - - +
153C LEU* 4.3 18.6 - - + -
171C VAL* 3.1 21.9 + - + +
172C THR 3.1 0.6 - - - -
173C GLY* 1.3 77.2 - - - +
175C VAL* 1.3 66.0 + - - +
177C GLN* 3.3 7.2 + - - +
178C TRP* 3.2 41.5 + - + -
188C PHE* 3.9 13.9 - - + -
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Residues in contact with VAL 175 (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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111C LEU* 5.5 5.8 - - + -
121C LEU* 4.6 9.9 - - + -
124C ALA* 3.7 28.0 - - + -
171C VAL* 3.0 25.6 + - + +
172C THR 3.9 1.1 - - - +
174C VAL* 1.3 77.2 - - + +
176C ARG* 1.3 62.7 + - - +
178C TRP* 3.1 19.9 + - + +
179C LEU* 3.2 30.4 + - + +
188C PHE* 5.0 5.6 - - + -
229C LEU* 3.9 22.7 - - + -
231C LEU* 4.2 13.5 - - + -
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Residues in contact with ARG 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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118C PRO* 3.7 40.7 + - + +
119C VAL* 5.2 2.8 + - - +
121C LEU* 2.7 39.7 + - + +
122C SER* 4.1 5.1 + - - +
172C THR* 3.0 39.1 + - - +
173C GLY* 4.2 10.5 - - - +
174C VAL 3.2 0.2 - - - -
175C VAL* 1.3 79.2 - - - +
177C GLN* 1.3 65.0 + - + +
178C TRP 3.5 0.2 + - - -
179C LEU* 3.5 7.8 + - - -
180C SER* 3.8 3.5 + - - -
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Residues in contact with GLN 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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143C GLN* 5.1 5.5 + - - -
145C TYR* 4.8 8.8 + - - -
173C GLY* 3.4 17.8 + - - +
174C VAL* 3.3 8.1 + - - +
175C VAL 3.3 0.4 - - - -
176C ARG* 1.3 80.4 - - + +
178C TRP* 1.3 65.2 + - + +
180C SER* 2.7 23.7 + - - +
181C ARG* 3.2 38.0 + - - +
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Residues in contact with TRP 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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106C PHE* 5.4 4.9 - + + -
108C THR* 4.1 13.6 - - + +
111C LEU* 4.8 17.5 - - + -
143C GLN* 3.2 29.5 - - + +
144C LYS 4.8 1.7 + - - -
174C VAL* 3.2 27.5 + - + +
175C VAL* 3.1 17.5 + - + +
177C GLN* 1.3 84.1 - - + +
179C LEU* 1.3 67.0 + - + +
181C ARG* 3.4 32.7 + - - +
183C GLY 5.2 1.0 - - - +
186C GLU* 3.6 48.3 + - + +
187C GLY* 3.2 33.4 - - - -
188C PHE* 3.5 32.3 - + - -
229C LEU* 6.1 1.3 - - + -
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Residues in contact with LEU 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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108C THR* 5.6 0.7 - - + -
111C LEU* 4.1 26.7 - - + +
112C ARG* 3.2 39.3 + - + -
115C VAL* 3.4 45.3 - - + +
116C PRO 5.1 1.4 - - - +
118C PRO* 3.8 28.4 - - + +
121C LEU* 4.9 10.1 - - + -
175C VAL* 3.2 29.9 + - + +
176C ARG* 3.5 3.6 + - - +
177C GLN 3.3 0.6 - - - -
178C TRP* 1.3 80.6 - - + +
180C SER* 1.3 59.5 + - - +
181C ARG 3.4 0.4 - - - -
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Residues in contact with SER 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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112C ARG* 5.0 2.4 + - - -
118C PRO* 3.8 16.1 - - - +
176C ARG 3.8 4.1 + - - -
177C GLN* 2.7 26.4 + - - +
179C LEU* 1.3 79.3 - - - +
181C ARG* 1.3 62.9 + - - +
182C GLY 4.0 0.5 + - - -
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Residues in contact with ARG 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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108C THR* 4.5 1.6 - - - +
112C ARG* 3.2 18.4 + - - -
145C TYR* 6.1 3.4 - - - -
177C GLN* 3.2 49.8 + - - +
178C TRP* 3.4 30.5 + - - +
179C LEU 3.4 0.8 - - - +
180C SER* 1.3 84.5 - - - +
182C GLY* 1.3 60.4 + - - +
183C GLY* 3.2 11.9 + - - +
186C GLU* 4.7 10.5 - - - +
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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