Contacts of the helix formed by residues 185 - 195 (chain E) in PDB entry 5K58
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 ASP 185 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183E THR 3.2 1.8 + - - -
184E ASP* 1.3 82.0 + - - +
186E PHE* 1.3 64.6 + - - +
187E ASP* 3.1 23.5 - - - +
188E ALA* 3.1 15.8 + - + +
189E ARG* 3.2 14.9 + - - +
157F LEU* 4.2 18.6 - - + +
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Residues in contact with PHE 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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89E ARG* 4.1 21.8 - - + -
92E VAL* 3.6 35.2 - - + -
93E LEU* 3.9 40.8 - - + -
96E LEU* 4.5 16.6 - - + -
165E PHE* 5.4 4.7 - + - -
182E PRO 4.9 2.0 - - - -
183E THR* 3.0 23.2 + - - +
184E ASP 2.9 4.8 + - - -
185E ASP* 1.3 75.7 - - - +
187E ASP* 1.3 59.5 + - - +
189E ARG* 3.3 10.2 + - + +
190E TRP* 2.9 68.5 + + + +
193E ILE* 6.3 0.4 - - + -
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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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185E ASP* 3.4 25.2 - - - +
186E PHE* 1.3 83.4 - - - +
188E ALA* 1.3 78.3 + - - +
190E TRP* 4.2 4.4 - - - +
191E PRO* 3.1 22.0 - - - +
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Residues in contact with ALA 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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185E ASP* 3.1 15.8 + - + +
187E ASP* 1.3 84.6 + - - +
189E ARG* 1.3 65.4 + - - +
190E TRP 3.2 1.3 - - - -
191E PRO* 3.2 13.3 - - - +
192E LEU* 4.1 11.1 - - - +
153F THR* 4.8 8.0 - - + +
157F LEU* 4.1 17.2 - - + +
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Residues in contact with ARG 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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165E PHE* 4.2 22.4 - - + -
169E MET* 4.1 19.4 - - - +
180E TYR* 2.6 35.0 + - - -
182E PRO 6.0 0.2 - - - -
184E ASP 4.7 6.5 + - - -
185E ASP 3.2 14.4 + - - +
186E PHE* 3.9 11.9 - - + +
188E ALA* 1.3 77.0 - - - +
190E TRP* 1.3 61.9 + - - +
192E LEU* 3.2 23.6 - - - +
193E ILE* 3.5 8.9 + - - +
157F LEU* 2.8 44.1 + - + +
160F SER* 2.5 29.7 + - - -
161F GLN* 3.1 33.8 - - - +
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Residues in contact with TRP 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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85E THR* 4.1 27.1 - - + -
86E ALA* 5.6 1.6 - - - -
88E LEU* 4.8 4.7 - - + +
89E ARG* 3.5 46.0 - - + +
92E VAL* 5.0 5.7 - - + +
186E PHE* 2.9 50.4 + + + +
187E ASP* 4.2 5.2 - - - +
189E ARG* 1.3 73.3 - - - +
191E PRO* 1.4 71.7 - - + +
192E LEU 2.9 5.2 - - - -
193E ILE* 2.7 33.8 + - + +
194E ALA* 2.9 39.2 + - + -
197E LEU* 5.8 1.1 - - + -
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Residues in contact with PRO 191 (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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187E ASP 3.1 22.0 - - - +
188E ALA* 3.2 13.5 - - - +
190E TRP* 1.4 100.9 - - + +
192E LEU* 1.3 58.8 + - + +
194E ALA* 4.0 3.8 - - + +
195E ALA* 3.2 23.4 + - - +
198F GLN* 4.4 16.3 + - - +
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Residues in contact with LEU 192 (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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188E ALA 4.1 7.4 - - - +
189E ARG* 3.2 17.3 - - - +
190E TRP 2.9 0.4 - - - -
191E PRO* 1.3 79.7 - - + +
193E ILE* 1.3 63.1 + - - +
195E ALA* 3.3 14.9 - - - +
196E GLN* 3.6 2.1 - - - +
153F THR* 4.5 16.8 - - + +
157F LEU* 4.4 10.1 - - + -
158F LEU* 4.4 17.9 - - + -
161F GLN* 3.2 33.0 - - + +
162F ILE* 6.4 0.2 - - + -
196F GLN* 3.0 67.4 - - + +
198F GLN* 4.7 7.6 - - + +
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Residues in contact with ILE 193 (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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88E LEU* 6.4 2.0 - - + -
92E VAL* 5.4 9.6 - - + -
162E ILE* 4.9 24.0 - - + +
165E PHE* 4.2 33.9 - - + -
186E PHE* 6.3 0.7 - - + -
189E ARG 3.7 13.0 - - - +
190E TRP* 2.7 23.7 + - + +
192E LEU* 1.3 73.4 - - - +
194E ALA* 1.3 57.7 + - - +
195E ALA 3.0 1.3 - - - -
196E GLN* 2.6 54.6 + - - +
197E LEU* 3.9 5.2 + - + +
161F GLN* 3.3 23.6 - - - +
196F GLN* 4.3 2.2 - - - +
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Residues in contact with ALA 194 (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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85E THR* 5.2 2.5 - - + -
190E TRP* 2.9 55.1 + - + +
191E PRO* 4.4 4.3 - - + +
193E ILE* 1.3 74.8 - - - +
195E ALA* 1.3 60.6 + - - +
196E GLN 3.0 1.1 + - - -
197E LEU* 3.2 33.5 + - + +
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Residues in contact with ALA 195 (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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191E PRO 3.2 21.4 + - - +
192E LEU* 3.3 11.0 - - - +
193E ILE 3.0 0.6 - - - -
194E ALA* 1.3 76.9 - - - +
196E GLN* 1.3 48.5 + - - +
197E LEU 3.3 1.6 - - - -
198E GLN* 2.7 32.2 + - - +
195F ALA* 4.1 22.6 - - + +
196F GLN* 5.0 0.2 - - - -
198F GLN* 5.3 7.0 - - + +
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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