Contacts of the helix formed by residues 182 - 188 (chain E) in PDB entry 3TJK
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 HIS 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D LEU* 3.2 19.3 + - - +
181D THR 4.6 0.8 + - - -
182D HIS* 3.2 34.5 + + - -
150E VAL* 3.4 28.0 + - + +
179E ASP* 2.9 29.5 + - - -
180E LEU 3.5 5.9 + - - -
181E THR* 1.3 75.7 + - - +
183E GLN* 1.3 63.0 + - - +
185E SER* 3.5 1.6 + - - -
186E LYS* 3.1 39.1 + - - +
191E TYR* 3.0 44.0 + + + -
196E GLY 3.8 7.2 + - - -
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Residues in contact with GLN 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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78E LYS* 4.2 7.2 - - - +
179E ASP* 3.3 0.6 + - - +
181E THR* 3.1 20.7 + - - +
182E HIS* 1.3 78.7 - - - +
184E ILE* 1.3 65.9 + - + +
186E LYS* 3.5 13.7 + - - +
187E ASP* 3.0 55.8 + - - +
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Residues in contact with ILE 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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87E TYR 5.8 0.4 - - - +
88E TRP* 3.8 32.3 - - + -
89E GLU 4.0 19.5 - - - +
113E PHE* 4.0 11.0 - - + -
115E PHE* 4.0 19.7 - - + -
148E CYS* 4.8 1.3 - - - -
177E LEU* 3.9 22.4 - - + -
178E SER 4.5 7.9 - - - +
179E ASP* 3.1 23.6 + - + +
183E GLN* 1.3 79.1 - - + +
185E SER* 1.3 57.8 + - - +
187E ASP* 3.3 7.6 + - - +
188E TYR* 3.0 34.6 + - + +
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Residues in contact with SER 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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115E PHE* 3.9 7.0 - - - -
148E CYS* 5.4 0.2 - - - -
150E VAL* 4.0 5.5 + - - +
179E ASP* 2.7 25.1 + - - +
182E HIS 3.6 5.6 - - - -
184E ILE* 1.3 76.7 - - - +
186E LYS* 1.3 57.4 + - - +
188E TYR 3.3 0.9 + - - -
189E GLY 2.9 22.5 + - - -
190E VAL* 3.0 22.4 + - - +
191E TYR* 3.8 19.3 - - - -
198E THR* 3.1 31.5 - - - +
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Residues in contact with LYS 186 (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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186D LYS* 5.3 8.7 - - - +
76E LEU 4.0 9.9 - - - +
77E SER* 4.1 3.3 - - - -
181E THR 4.8 4.0 + - - -
182E HIS* 3.1 31.3 + - - +
183E GLN* 3.8 15.9 - - - +
185E SER* 1.3 77.4 - - - +
187E ASP* 1.3 59.0 + - - +
189E GLY* 3.0 19.4 + - - -
191E TYR* 3.8 40.5 - - + -
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Residues in contact with ASP 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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78E LYS* 2.9 67.9 + - + +
79E ALA 3.4 6.4 + - - -
86E PRO* 3.9 11.6 - - + +
87E TYR 4.2 13.0 - - - +
183E GLN* 3.0 42.5 + - - +
184E ILE* 3.3 8.0 + - - +
186E LYS* 1.3 74.5 - - - +
188E TYR* 1.3 67.2 + - + +
189E GLY 3.2 0.2 - - - -
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Residues in contact with TYR 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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77E SER* 3.7 7.2 + - - -
79E ALA* 4.1 7.8 - - + +
85E ALA* 3.5 19.5 - - + +
86E PRO* 2.6 48.9 + - + -
87E TYR 4.9 0.2 - - - -
88E TRP* 3.4 28.2 + + + -
103E LEU* 4.0 1.4 - - - +
113E PHE* 3.8 12.8 - + - -
115E PHE* 3.6 31.0 - + + -
184E ILE* 3.0 21.7 + - + +
185E SER 4.1 2.2 - - - +
187E ASP* 1.3 80.2 - - + +
189E GLY* 1.3 63.1 + - - +
190E VAL* 3.3 2.7 + - + +
203E PHE* 3.4 54.1 - + + -
205E ILE* 4.0 4.9 - - + +
211E LEU* 5.4 1.3 - - + -
216E LEU* 5.5 1.0 - - - +
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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