Contacts of the helix formed by residues 179 - 190 (chain C) in PDB entry 3CQ6
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 SER 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C VAL* 3.7 11.3 + - - -
178C THR* 1.3 77.9 - - - +
180C LEU* 1.3 63.1 + - - +
181C ASP* 3.7 8.6 + - - +
182C ASP* 3.2 31.1 + - - +
183C VAL* 3.0 17.8 + - - +
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Residues in contact with LEU 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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169C THR* 6.2 2.0 - - + -
178C THR 5.2 2.0 - - - +
179C SER* 1.3 73.1 - - - +
181C ASP* 1.3 55.4 + - - +
183C VAL* 3.1 11.2 + - + +
184C GLU* 2.8 39.2 + - - +
198C GLU* 5.1 1.1 - - - +
207C PRO* 3.9 34.1 - - + +
208C SER 3.8 4.5 - - - +
209C ALA* 3.7 33.4 - - + +
211C THR* 3.2 26.7 - - - +
212C LEU* 4.0 20.3 - - + +
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Residues in contact with ASP 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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179C SER* 3.2 7.7 + - - +
180C LEU* 1.3 79.4 - - - +
182C ASP* 1.3 64.2 + - - +
184C GLU* 3.4 17.4 + - - +
185C ARG* 3.1 30.4 + - - +
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Residues in contact with ASP 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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150C MET* 3.5 30.3 - - - +
178C THR* 3.8 12.1 - - + +
179C SER* 3.2 25.3 + - - +
181C ASP* 1.3 75.6 - - - +
183C VAL* 1.3 61.7 + - - +
185C ARG* 2.9 33.9 + - - +
186C ILE* 3.0 32.5 + - - +
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Residues in contact with VAL 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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167C VAL* 4.6 13.0 - - + -
169C THR* 5.0 7.0 - - + -
178C THR* 3.9 22.4 - - + +
179C SER 3.0 21.2 + - - +
180C LEU* 3.1 18.1 + - + +
182C ASP* 1.3 73.0 - - - +
184C GLU* 1.3 55.8 + - - +
186C ILE* 3.2 9.5 + - - +
187C ILE* 2.8 53.0 + - + +
194C VAL* 5.3 2.5 - - + -
196C VAL* 4.1 22.2 - - + -
209C ALA* 5.2 1.8 - - + -
212C LEU* 3.9 9.0 - - + -
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Residues in contact with GLU 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 LEU* 2.8 23.2 + - - +
181C ASP* 3.6 19.7 - - - +
183C VAL* 1.3 72.0 - - - +
185C ARG* 1.3 64.1 + - + +
187C ILE* 3.2 9.7 + - - +
188C ASN* 2.9 31.7 + - - +
212C LEU* 3.7 32.5 - - + +
215C LYS* 2.7 32.8 + - - +
216C TYR* 2.7 21.2 + - + +
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Residues in contact with ARG 185 (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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150C MET* 3.8 31.4 - - + +
151C ASP* 4.5 10.5 + - - -
154C LEU* 3.5 31.3 - - + +
181C ASP* 3.1 21.9 + - - +
182C ASP* 2.9 32.4 + - - +
183C VAL 3.2 0.2 - - - -
184C GLU* 1.3 78.7 - - + +
186C ILE* 1.3 63.7 + - - +
188C ASN* 3.4 11.3 + - - +
189C VAL* 3.5 10.7 + - - +
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Residues in contact with ILE 186 (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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119C PHE* 4.4 14.4 - - + -
148C ILE* 4.4 13.5 - - + -
150C MET* 4.0 20.9 - - + -
153C ALA* 5.0 1.6 - - + -
154C LEU* 3.8 11.2 - - + -
157C ILE* 3.9 20.2 - - + -
165C VAL* 4.0 19.1 - - + -
167C VAL* 4.1 25.1 - - + -
178C THR* 4.8 2.5 - - + -
182C ASP 3.0 20.1 + - - +
183C VAL* 3.5 9.4 - - - +
185C ARG* 1.3 76.4 - - - +
187C ILE* 1.3 63.6 + - - +
189C VAL* 3.1 7.0 - - - +
190C ALA* 3.0 19.8 + - - +
194C VAL* 4.6 8.5 - - + -
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Residues in contact with ILE 187 (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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183C VAL* 2.8 41.3 + - + +
184C GLU* 3.6 5.8 - - - +
186C ILE* 1.3 72.1 - - - +
188C ASN* 1.3 52.0 + - - +
190C ALA* 3.4 6.4 + - - +
194C VAL* 4.0 27.1 - - + -
212C LEU* 4.1 14.8 - - + -
216C TYR* 3.4 44.9 - - + -
219C LYS* 2.6 48.9 + - + +
220C LEU* 4.0 22.7 - - + -
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Residues in contact with ASN 188 (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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184C GLU* 2.9 20.2 + - - +
185C ARG* 3.9 6.1 - - - +
186C ILE 3.2 0.6 - - - -
187C ILE* 1.3 78.4 - - - +
189C VAL* 1.3 62.0 + - + +
216C TYR* 3.0 38.4 + - - -
219C LYS* 3.4 13.1 + - - +
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Residues in contact with VAL 189 (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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154C LEU* 3.6 20.4 - - + -
157C ILE* 3.6 26.7 - - + +
158C ARG* 3.4 51.7 - - + +
161C GLN* 4.4 8.7 + - - +
185C ARG 3.5 11.4 + - - +
186C ILE* 3.1 15.3 - - - +
188C ASN* 1.3 78.0 - - + +
190C ALA* 1.3 64.8 + - - +
191C PRO* 3.2 8.3 - - - +
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Residues in contact with ALA 190 (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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157C ILE* 3.9 5.4 - - + -
162C PRO 5.6 0.2 - - - +
165C VAL* 4.4 13.7 - - + -
186C ILE 3.0 14.1 + - - +
187C ILE 3.4 5.3 + - - +
189C VAL* 1.3 74.4 - - - +
191C PRO* 1.3 67.2 - - + +
192C GLY 4.7 4.0 - - - +
193C ILE 4.9 2.7 - - - +
194C VAL* 3.5 31.6 - - + -
219C LYS* 2.6 35.0 + - + -
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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