Contacts of the helix formed by residues 175 - 184 (chain C) in PDB entry 3LOC
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 PHE 175 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115C CYS* 5.8 0.7 - - - -
171C HIS* 2.9 50.4 + + + +
174C ASP* 1.3 90.7 - - + +
176C ALA* 1.3 63.7 + - - +
177C PRO* 3.2 4.0 - - - -
178C GLN* 2.9 31.5 + - + +
179C VAL* 3.0 11.9 + - - +
76D TRP* 5.9 0.2 - + - -
114D PHE* 4.0 6.1 - + - -
115D CYS* 3.9 35.2 - - - -
118D MSE 3.6 26.5 - - + -
170D GLN* 3.7 17.3 - - + -
174D ASP* 4.2 7.9 - - - -
175D PHE* 6.5 0.7 - + - -
212D URA 3.5 17.5 - - - -
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Residues in contact with ALA 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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112C ARG* 4.7 8.7 - - - +
172C TYR 3.7 16.7 + - - +
173C ALA* 3.0 18.9 + - - +
175C PHE* 1.3 74.5 - - - +
177C PRO* 1.3 72.2 - - + +
179C VAL* 2.9 7.2 + - - +
180C GLU* 2.8 27.1 + - - +
186C THR* 6.0 8.0 - - + +
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Residues in contact with PRO 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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112C ARG* 6.0 1.1 - - - +
173C ALA 4.7 0.7 - - - +
174C ASP 4.4 1.6 - - - +
175C PHE* 3.3 1.1 - - - -
176C ALA* 1.3 93.4 - - + +
178C GLN* 1.3 55.5 + - - +
180C GLU* 3.5 7.5 + - + +
181C ALA* 2.9 29.5 + - - +
118D MSE 3.2 31.2 - - + +
121D GLY* 3.7 31.0 - - - +
122D ALA* 3.9 15.9 - - + -
126D MSE 3.7 17.0 - - + +
129D LEU* 4.5 0.4 - - - -
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Residues in contact with GLN 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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171C HIS* 4.4 2.6 + - - -
175C PHE* 2.9 21.2 + - + +
177C PRO* 1.3 77.9 - - - +
179C VAL* 1.3 66.4 + - + +
181C ALA* 3.2 7.8 + - - +
182C VAL* 3.0 25.0 - - + +
114D PHE* 3.4 23.7 - - - -
118D MSE 3.1 13.8 - - + +
129D LEU* 4.1 11.0 - - + +
133D LEU* 3.4 26.0 - - + +
163D PHE* 5.4 1.1 - - + -
166D TRP* 3.3 21.8 - - + -
212D URA 2.7 43.3 + - - +
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Residues in contact with VAL 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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171C HIS* 4.2 22.4 - - + +
172C TYR* 4.1 20.2 - - + +
175C PHE 3.0 14.2 + - - +
176C ALA* 2.9 10.5 + - - +
178C GLN* 1.3 76.5 - - - +
180C GLU* 1.3 55.0 + - - +
182C VAL* 3.3 1.4 + - - +
183C THR* 2.7 37.5 + - - -
185C ALA 4.1 5.8 - - - +
186C THR* 5.6 1.1 - - - -
192C PHE* 3.6 35.2 - - + -
163D PHE* 4.0 26.9 - - + -
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Residues in contact with GLU 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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176C ALA* 2.8 16.9 + - - +
177C PRO* 3.8 7.3 - - + +
179C VAL* 1.3 77.9 - - - +
181C ALA* 1.3 59.6 + - - +
184C GLY* 2.6 36.5 + - - +
185C ALA 3.3 27.1 + - - +
186C THR* 3.6 21.8 - - + +
188C ARG* 5.5 0.7 + - - -
126D MSE 4.7 14.3 - - + +
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Residues in contact with ALA 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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177C PRO 2.9 18.4 + - - +
178C GLN 3.2 5.1 + - - +
180C GLU* 1.3 77.3 - - - +
182C VAL* 1.3 59.4 + - + +
184C GLY* 4.6 0.7 + - - -
126D MSE 4.2 6.0 - - + +
129D LEU* 3.7 34.3 - - + +
130D THR* 3.8 25.0 - - + +
134D LYS* 3.5 23.9 - - - +
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Residues in contact with VAL 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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178C GLN* 3.0 26.9 - - + +
179C VAL 4.2 0.2 - - - +
180C GLU 3.2 0.4 - - - -
181C ALA* 1.3 79.0 - - + +
183C THR* 1.3 62.0 + - - +
129D LEU 5.3 0.2 - - - +
133D LEU* 4.8 12.1 - - + -
134D LYS* 4.1 30.3 + - + -
137D ILE* 4.5 22.0 - - + -
138D ASP* 4.3 6.6 - - - +
159D GLN* 3.3 25.8 + - - +
163D PHE* 3.6 34.3 - - + -
166D TRP* 5.3 0.9 - - + -
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Residues in contact with THR 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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179C VAL* 2.7 15.3 + - + +
182C VAL* 1.3 85.2 - - - +
184C GLY* 1.3 57.4 + - - +
185C ALA* 2.9 42.9 - - + +
192C PHE* 3.4 28.2 - - + -
134D LYS* 6.0 0.4 - - - -
159D GLN* 3.9 19.4 + - - +
160D HIS* 5.6 0.2 - - - -
163D PHE* 4.1 7.8 - - - -
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Residues in contact with GLY 184 (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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180C GLU* 2.6 31.4 + - - +
181C ALA 4.5 0.6 + - - -
182C VAL 3.7 1.2 - - - -
183C THR* 1.3 73.5 - - - +
185C ALA* 1.3 56.7 + - - +
189C ASP* 4.6 0.9 - - - +
134D LYS* 5.8 1.7 - - - +
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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