Contacts of the helix formed by residues 182 - 193 (chain E) in PDB entry 5OF4
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 ILE 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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590B ASN* 5.0 11.0 - - - +
591B GLY 5.9 2.2 - - - +
145E LEU* 3.5 37.2 - - + +
146E TYR* 3.5 30.3 - - + +
149E LEU* 3.9 10.5 - - + -
176E THR* 5.1 1.6 - - + -
178E ASP* 3.5 17.5 + - - +
180E SER 3.1 5.5 + - - -
181E ASN* 1.3 66.7 - - - +
183E TYR* 1.3 61.2 + - - +
184E ASP 3.1 2.7 - - - -
185E LEU* 3.0 23.3 + - + +
186E ILE* 3.0 42.1 + - + +
207E VAL* 4.7 17.5 - - + -
211E LEU* 5.7 0.2 - - + -
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Residues in contact with TYR 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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589B GLU 5.6 3.6 - - - -
590B ASN* 4.3 18.1 - - - +
181E ASN* 3.1 6.5 - - + -
182E ILE* 1.3 82.9 - - - +
184E ASP* 1.3 58.5 + - - +
186E ILE* 3.3 17.4 + - + +
187E LYS* 2.9 58.1 + - + +
210E VAL* 4.2 23.8 - - + +
213E ARG* 5.9 0.3 + - - -
214E GLU* 4.2 22.4 + - - -
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Residues in contact with ASP 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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146E TYR* 6.3 0.2 - - + -
180E SER* 5.4 1.2 + - - -
181E ASN* 3.5 29.9 + - - +
182E ILE 3.1 0.4 - - - -
183E TYR* 1.3 77.7 - - - +
185E LEU* 1.3 62.2 + - + +
187E LYS* 3.2 34.3 + - + +
188E THR* 3.0 31.2 + - - -
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Residues in contact with LEU 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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146E TYR* 3.5 53.2 - - + +
149E LEU* 3.8 25.4 - - + +
150E SER* 4.6 8.5 - - - +
153E MET* 5.6 11.0 - - + -
181E ASN 4.3 0.2 + - - -
182E ILE* 3.0 22.6 + - + +
184E ASP* 1.3 77.7 - - + +
186E ILE* 1.3 59.1 + - + +
188E THR* 4.3 7.6 - - + +
189E LEU* 3.0 49.9 + - + +
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Residues in contact with ILE 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E LEU* 6.5 0.4 - - + -
182E ILE* 3.0 36.7 + - + +
183E TYR* 3.5 26.2 - - + +
184E ASP 3.2 0.2 - - - -
185E LEU* 1.3 76.0 - - + +
187E LYS* 1.3 64.5 + - - +
189E LEU* 5.1 2.6 - - + +
190E LYS* 3.7 16.8 + - - +
207E VAL* 4.9 7.2 - - + +
210E VAL* 4.5 11.0 - - + +
211E LEU* 3.8 41.5 - - + +
214E GLU* 3.3 38.2 - - + +
215E THR* 5.0 6.7 + - - +
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Residues in contact with LYS 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 TYR* 2.9 42.5 + - + +
184E ASP* 3.2 34.6 + - + +
186E ILE* 1.3 79.8 - - - +
188E THR* 1.3 64.2 + - - +
190E LYS* 3.4 15.1 - - - +
191E ALA* 4.0 4.3 + - - +
214E GLU* 5.1 4.0 - - - +
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Residues in contact with THR 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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153E MET* 5.0 13.0 - - + -
184E ASP 3.0 16.5 + - - -
185E LEU* 3.2 10.1 + - - +
187E LYS* 1.3 77.3 - - - +
189E LEU* 1.3 69.0 + - + +
191E ALA* 3.2 9.5 + - - +
192E ALA* 3.0 25.3 + - + +
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Residues in contact with LEU 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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149E LEU* 4.2 35.7 - - + +
153E MET* 4.0 30.3 - - + -
185E LEU* 3.0 36.7 + - + +
186E ILE* 5.1 2.5 - - - +
188E THR* 1.3 80.4 - - + +
190E LYS* 1.3 64.0 + - - +
192E ALA* 3.7 9.0 - - + -
193E LYS* 3.1 16.6 + - - -
194E ILE* 3.5 46.5 + - + +
196E VAL* 5.5 3.8 - - + -
211E LEU* 6.1 2.5 - - + -
215E THR* 5.0 8.1 - - + +
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Residues in contact with LYS 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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186E ILE 3.7 12.3 + - - +
187E LYS* 3.4 13.8 + - - +
188E THR 3.1 0.2 - - - -
189E LEU* 1.3 76.6 - - - +
191E ALA* 1.3 64.4 + - + +
193E LYS* 3.2 21.6 + - - +
214E GLU* 3.3 32.3 - - + +
215E THR* 5.1 9.0 + - - +
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Residues in contact with ALA 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 LYS 4.0 3.3 + - - +
188E THR* 3.2 9.6 + - - +
190E LYS* 1.3 79.8 - - - +
192E ALA* 1.4 63.0 + - - +
193E LYS* 3.3 9.0 + - - +
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Residues in contact with ALA 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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153E MET* 6.4 0.2 - - + -
165E ARG* 4.6 14.3 + - - +
188E THR* 3.0 19.9 + - + +
189E LEU* 3.8 8.3 - - + +
190E LYS 3.3 0.4 - - - -
191E ALA* 1.4 75.6 - - - +
193E LYS* 1.3 61.2 + - - +
194E ILE* 3.1 28.3 + - + +
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Residues in contact with LYS 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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161E GLY 6.0 1.8 - - - -
164E SER* 6.0 0.3 - - - -
165E ARG* 4.6 6.7 + - - +
189E LEU 3.1 6.5 + - - -
190E LYS* 3.2 16.3 + - - +
191E ALA 3.1 11.0 - - - +
192E ALA* 1.3 77.0 - - - +
194E ILE* 1.3 63.1 + - - +
195E ARG* 3.2 7.3 + - - +
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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