Contacts of the helix formed by residues 179 - 190 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E VAL* 3.7 9.4 + - - -
178E THR* 1.3 73.5 - - - +
180E LEU* 1.3 59.6 + - - +
181E ASP* 3.7 10.3 + - - +
182E ASP* 2.7 39.7 + - - -
183E VAL* 2.9 27.4 + - - +
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Residues in contact with LEU 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E THR* 6.2 1.8 - - + -
178E THR 3.7 3.0 + - - +
179E SER* 1.3 72.7 - - - +
181E ASP* 1.3 59.3 + - - +
183E VAL* 3.4 12.1 - - + +
184E GLU* 2.8 35.5 + - - +
198E GLU* 5.1 0.9 - - - +
207E PRO* 3.6 34.8 - - + +
208E SER 3.6 6.1 - - - +
209E ALA* 3.8 31.4 - - + +
211E THR* 3.3 26.7 - - - +
212E LEU* 3.9 19.3 - - + +
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Residues in contact with ASP 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E SER* 3.1 10.2 - - - +
180E LEU* 1.3 80.4 - - - +
182E ASP* 1.3 63.2 + - - +
184E GLU* 3.4 15.1 + - - +
185E ARG* 3.2 31.0 + - - +
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Residues in contact with ASP 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E MET* 3.3 38.9 - - - +
178E THR* 4.0 12.2 - - + +
179E SER* 2.7 27.9 + - - +
181E ASP* 1.3 76.2 - - - +
183E VAL* 1.3 64.9 + - - +
185E ARG* 2.8 33.4 + - - +
186E ILE* 3.1 22.1 + - - +
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Residues in contact with VAL 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E VAL* 4.6 13.9 - - + -
169E THR* 5.0 6.5 - - + -
178E THR* 3.8 24.9 - - + +
179E SER 2.9 20.0 + - - +
180E LEU* 3.4 19.5 - - + +
181E ASP 3.3 0.2 - - - -
182E ASP* 1.3 75.2 - - - +
184E GLU* 1.3 65.7 + - - +
186E ILE* 3.0 11.5 + - + +
187E ILE* 2.9 33.1 + - + +
194E VAL* 5.5 0.4 - - + -
196E VAL* 4.1 24.7 - - + -
209E ALA* 5.0 1.6 - - + -
212E LEU* 3.8 17.0 - - + -
220E LEU* 5.2 0.2 - - + -
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Residues in contact with GLU 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E LEU 2.8 21.5 + - - +
181E ASP* 3.4 16.8 - - - +
182E ASP 3.4 0.2 - - - -
183E VAL* 1.3 74.5 - - - +
185E ARG* 1.3 57.3 - - + +
187E ILE* 3.1 13.7 + - - +
188E ASN* 2.9 35.6 + - - +
212E LEU* 3.7 29.4 - - + +
215E LYS* 3.4 23.0 + - - +
216E TYR* 2.7 31.6 + - + +
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Residues in contact with ARG 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E MET* 3.6 28.5 - - + +
151E ASP* 4.4 9.9 + - - -
154E LEU* 3.2 43.0 - - + +
181E ASP* 3.2 18.0 + - - +
182E ASP* 2.8 35.5 + - - +
183E VAL 3.2 0.2 - - - -
184E GLU* 1.3 79.4 - - + +
186E ILE* 1.3 62.7 + - - +
188E ASN* 3.4 12.3 + - - +
189E VAL* 3.3 10.9 + - - +
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Residues in contact with ILE 186 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119E PHE* 3.9 25.1 - - + -
148E ILE* 4.3 15.0 - - + -
150E MET* 4.0 19.1 - - + -
153E ALA* 4.9 3.1 - - + -
154E LEU* 4.0 2.5 - - + -
157E ILE* 3.6 21.3 - - + -
165E VAL* 3.8 22.7 - - + -
167E VAL* 4.1 16.4 - - + -
178E THR* 5.2 1.8 - - + -
182E ASP 3.1 16.2 + - - +
183E VAL* 3.0 10.2 + - - +
185E ARG* 1.3 74.1 - - - +
187E ILE* 1.3 66.7 + - - +
189E VAL* 3.1 9.9 - - - +
190E ALA* 3.0 21.5 + - - +
194E VAL* 4.8 5.2 - - + -
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Residues in contact with ILE 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E VAL* 2.9 32.8 + - + +
184E GLU* 3.4 8.5 - - - +
186E ILE* 1.3 75.0 - - - +
188E ASN* 1.3 59.6 + - - +
190E ALA* 3.3 8.5 + - - +
194E VAL* 3.9 24.7 - - + -
212E LEU* 4.2 10.8 - - + -
216E TYR* 3.5 45.8 - - + -
219E LYS* 2.8 45.5 + - + +
220E LEU* 4.0 24.0 - - + -
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Residues in contact with ASN 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E GLU* 2.9 17.8 + - - +
185E ARG* 3.9 8.0 - - - +
186E ILE 3.2 0.8 - - - -
187E ILE* 1.3 77.8 - - - +
189E VAL* 1.3 62.6 + - + +
216E TYR* 2.7 37.0 + - - -
219E LYS* 3.6 13.4 + - - +
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Residues in contact with VAL 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E LEU* 3.3 26.2 - - + +
157E ILE* 3.6 28.9 - - + +
158E ARG* 3.7 47.7 + - + +
161E GLN* 4.7 7.4 + - - -
185E ARG 3.3 10.9 + - - +
186E ILE 3.1 17.3 - - - +
188E ASN* 1.3 79.4 - - + +
190E ALA* 1.3 65.0 + - - +
191E PRO* 3.3 7.6 - - - +
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Residues in contact with ALA 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ILE* 3.7 5.8 - - + -
162E PRO 5.5 0.2 - - - +
165E VAL* 4.2 15.9 - - + -
186E ILE 3.0 18.2 + - - +
187E ILE 3.4 3.3 + - - +
189E VAL* 1.3 77.5 - - - +
191E PRO* 1.3 65.8 - - + +
192E GLY 4.8 1.8 - - - +
193E ILE 4.8 4.0 - - - +
194E VAL* 3.5 27.8 - - + -
219E LYS* 2.8 32.3 + - - -
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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