Contacts of the helix formed by residues 182 - 195 (chain E) in PDB entry 1RBO
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 ALA 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B GLN* 5.0 2.0 - - - +
157B VAL* 5.8 4.5 - - + -
181E SER* 1.3 72.9 - - - +
183E LYS* 1.3 63.2 + - - +
185E TYR* 3.3 4.9 + - - +
186E GLY 3.2 17.0 + - - -
211E PHE 4.6 0.6 + - - -
212E MET* 3.7 23.5 - - + +
216E ASP* 3.6 38.4 - - + -
217E ARG* 3.8 5.9 - - - +
220E PHE* 3.7 23.2 - - + +
221E CYS* 5.4 0.2 - - - -
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Residues in contact with LYS 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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160B ASP* 3.4 42.7 + - + +
163B ASN* 3.2 23.0 - - - +
165B TYR* 2.8 31.2 + - - +
65C ARG* 4.9 8.9 + - + +
66C TYR* 2.8 42.8 + - + +
100C ARG* 5.7 1.8 - - - +
111C GLN* 3.8 16.4 + - - +
181E SER* 3.3 2.3 + - - +
182E ALA* 1.3 80.7 - - - +
184E ASN* 1.3 61.2 + - - +
187E ARG* 3.1 25.7 + - - +
220E PHE* 3.8 15.5 - - + -
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Residues in contact with ASN 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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104C PHE* 4.0 14.3 - - - -
109C GLU* 2.8 37.5 - - - +
180E LEU* 4.2 16.5 - - + +
181E SER* 3.2 14.9 + - - +
183E LYS* 1.3 74.4 - - - +
185E TYR* 1.3 64.0 + - - +
187E ARG* 3.0 40.4 + - + +
188E ALA* 3.0 24.8 + - - +
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Residues in contact with TYR 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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174E ILE* 3.6 37.1 + - + +
176E PRO 5.1 2.0 - - - -
177E LYS 4.8 4.4 + - - -
180E LEU* 4.1 19.7 - - + +
181E SER 2.9 10.7 + - - +
182E ALA* 3.3 10.1 - - - +
183E LYS 3.2 0.2 - - - -
184E ASN* 1.3 76.4 - - - +
186E GLY* 1.3 56.4 + - - +
188E ALA* 3.3 5.8 + - - +
189E VAL* 2.9 33.2 + - + +
202E ASP* 3.3 39.6 - - - -
203E ASP 3.3 9.5 + - - -
206E VAL* 3.8 10.4 - - + +
212E MET* 3.6 30.1 - - + -
217E ARG* 3.8 15.3 - - + -
221E CYS* 3.9 17.0 - - - -
238E HIS* 3.9 11.7 - - - -
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Residues in contact with GLY 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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66C TYR* 3.2 21.5 - - - -
182E ALA 3.2 9.0 + - - -
183E LYS 3.4 0.4 + - - -
184E ASN 3.3 0.2 - - - -
185E TYR* 1.3 75.7 - - - +
187E ARG* 1.3 58.9 + - - +
189E VAL* 3.2 5.3 + - - -
190E TYR* 2.9 26.5 + - - +
220E PHE 4.1 9.6 - - - -
221E CYS* 4.5 3.2 - - - -
224E ALA* 3.1 18.5 - - - +
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Residues in contact with ARG 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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43C GLU* 2.8 32.2 + - - -
66C TYR* 3.4 20.0 + - + -
69C MET* 3.7 30.5 - - + -
102C ILE* 4.0 4.9 - - - +
104C PHE* 3.5 15.5 - - - -
111C GLN* 2.8 29.4 + - - +
183E LYS* 3.1 35.4 + - - +
184E ASN* 3.0 33.1 - - - +
185E TYR 3.3 0.2 - - - -
186E GLY* 1.3 75.6 - - - +
188E ALA* 1.3 64.8 + - - +
190E TYR* 3.4 4.9 + - - +
191E GLU* 3.3 30.9 + - + +
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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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174E ILE* 4.1 23.6 - - + -
180E LEU* 5.2 3.4 - - + -
184E ASN 3.0 13.6 + - - +
185E TYR 3.6 8.1 - - - +
187E ARG* 1.3 78.7 - - + +
189E VAL* 1.3 63.0 + - - +
191E GLU* 3.4 1.5 + - - -
192E CYS* 3.1 23.6 + - - -
407E LEU* 4.7 5.8 - - + -
413E ASN* 3.2 26.4 + - - +
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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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174E ILE* 4.0 13.2 - - + -
185E TYR* 2.9 22.3 + - + +
186E GLY* 3.5 10.5 - - - +
188E ALA* 1.3 73.4 - - - +
190E TYR* 1.3 67.4 + - - +
192E CYS* 3.3 2.1 + - - +
193E LEU* 3.0 38.0 + - + +
200E THR* 3.3 22.0 - - - +
221E CYS* 4.2 13.5 - - - +
224E ALA* 4.0 12.3 - - + -
238E HIS* 3.4 35.9 - - + +
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Residues in contact with TYR 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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66C TYR* 5.0 6.1 - + + -
67C TRP 3.8 13.0 - - - -
68C THR* 3.2 31.0 - - - +
186E GLY 2.9 16.8 + - - +
187E ARG* 3.9 5.2 - - - +
188E ALA 3.4 0.2 - - - -
189E VAL* 1.3 76.1 - - - +
191E GLU* 1.3 83.7 + - + +
193E LEU* 3.9 0.5 - - - +
194E ARG* 3.0 47.5 + - + +
224E ALA* 3.8 20.6 - - + +
227E LYS* 3.4 35.5 - - + -
228E ALA* 3.8 20.9 - - + -
231E GLU* 2.6 28.9 + - - -
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Residues in contact with GLU 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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67C TRP 4.3 1.0 - - - +
68C THR* 3.7 0.9 - - - -
69C MET* 2.9 48.1 + - + +
187E ARG* 3.3 22.8 + - + +
188E ALA* 3.8 1.6 - - - +
190E TYR* 1.3 92.3 - - + +
192E CYS* 1.3 62.9 + - - +
194E ARG* 3.0 36.4 + - - +
195E GLY 3.6 0.2 + - - -
413E ASN* 3.6 22.7 - - + +
414E ALA* 3.1 32.2 + - - +
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Residues in contact with CYS 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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172E CYS* 3.8 24.7 - - - -
174E ILE* 4.2 8.7 - - - -
188E ALA 3.1 19.1 + - - +
191E GLU* 1.3 74.7 - - - +
193E LEU* 1.3 66.2 + - - +
195E GLY 3.2 2.4 + - - -
197E LEU* 3.8 14.8 + - + +
200E THR* 3.5 20.0 - - + -
406E THR* 4.0 7.0 - - - -
407E LEU* 4.3 1.6 - - - -
413E ASN* 3.5 30.3 - - - -
417E ALA* 3.2 24.1 - - - +
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Residues in contact with LEU 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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189E VAL* 3.0 39.1 + - + +
192E CYS* 1.3 78.0 - - - +
194E ARG* 1.3 61.1 + - - +
195E GLY 3.1 1.4 + - - -
196E GLY 3.2 4.7 + - - -
197E LEU* 3.6 16.3 - - + +
198E ASP 3.8 10.1 - - - +
199E PHE* 3.8 29.2 - - - +
200E THR* 3.8 11.0 - - + +
225E LEU* 3.8 30.1 - - + -
228E ALA* 3.4 15.5 - - + -
236E LYS* 2.9 38.8 + - + -
237E GLY 3.9 4.0 - - - +
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Residues in contact with ARG 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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68C THR* 3.8 8.6 + - - -
69C MET 4.9 2.4 + - - -
190E TYR* 3.0 48.0 + - + +
191E GLU* 3.0 33.8 + - - +
193E LEU* 1.3 75.0 - - - +
195E GLY* 1.3 61.3 + - - +
196E GLY 3.3 0.9 + - - -
228E ALA* 3.8 5.1 - - + +
231E GLU* 2.9 34.7 + - - +
232E THR* 3.5 22.0 - - + +
414E ALA* 3.8 9.6 - - + +
3F VAL* 4.5 5.7 - - - +
4F TRP* 2.8 54.5 + - - +
5F PRO 3.3 6.9 + - - -
6F ILE* 2.9 21.9 - - - +
17F TYR* 4.3 2.4 + - - -
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Residues in contact with GLY 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 GLU 3.6 1.2 + - - -
192E CYS 3.2 4.0 + - - -
193E LEU 3.1 1.6 - - - -
194E ARG* 1.3 81.6 - - - +
196E GLY* 1.3 56.4 + - - +
414E ALA* 3.6 15.0 - - - -
417E ALA* 3.4 18.4 - - - +
418E VAL* 3.2 36.8 + - - +
421E ARG* 4.4 0.2 - - - +
4F TRP* 4.4 4.0 - - - -
17F TYR* 3.7 8.4 - - - -
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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