Contacts of the strand formed by residues 182 - 188 (chain E) in PDB entry 1RFU
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 THR 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145E ASP 3.4 2.6 + - - +
146E ILE* 3.2 39.9 - - + +
147E ILE 3.2 22.3 + - - -
180E PRO* 3.8 1.2 - - - +
181E ASP* 1.3 83.3 + - - +
183E VAL* 1.3 65.6 + - - +
184E VAL* 4.9 4.5 - - + -
204E SER 3.4 5.6 - - - +
205E GLN* 3.6 22.1 + - + +
241E LEU* 5.9 0.4 - - + -
245E THR* 5.4 4.3 - - + -
252E LEU* 3.7 30.3 - - + -
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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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147E ILE* 3.5 25.1 - - + -
172E MET* 3.4 27.8 - - + -
175E LEU* 3.6 27.1 - - + -
176E HIS* 3.8 24.0 - - + +
180E PRO* 3.7 14.8 - - + -
182E THR* 1.3 80.7 - - - +
184E VAL* 1.3 67.4 + - - +
185E ILE* 4.6 3.8 - - + -
202E LEU 4.0 0.5 - - - +
203E GLY* 3.3 1.7 - - - -
204E SER 2.6 41.1 + - - +
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Residues in contact with VAL 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 ILE* 5.7 0.4 - - + -
147E ILE 3.1 11.0 + - - +
148E THR* 3.4 4.2 - - - -
149E PRO* 2.9 29.3 - - - +
182E THR* 4.9 2.5 - - + -
183E VAL* 1.3 83.5 - - - +
185E ILE* 1.3 75.9 + - - +
186E THR* 3.4 2.5 + - - +
201E ALA* 5.4 3.1 - - + -
202E LEU 3.4 11.4 - - - +
203E GLY* 4.1 9.9 - - - -
221E MET* 5.6 2.5 - - + -
237E PHE* 3.9 30.5 - - + -
241E LEU* 4.4 16.6 - - + -
252E LEU* 4.5 9.4 - - + -
256E CYS* 4.4 18.2 - - - -
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Residues in contact with ILE 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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149E PRO* 3.3 28.7 - - + +
151E GLN* 3.8 20.0 - - + +
154E ALA* 3.5 17.9 - - + -
168E ALA* 5.7 4.5 - - + +
171E VAL* 5.5 2.5 - - + -
172E MET* 4.3 19.3 - - + -
175E LEU* 4.3 12.1 - - + -
183E VAL* 4.6 1.8 - - + -
184E VAL* 1.3 72.1 - - - +
186E THR* 1.3 61.3 + - - +
187E SER 2.8 35.5 + - - +
188E SER* 4.6 4.9 - - - -
201E ALA* 3.3 3.7 - - - +
202E LEU* 2.8 42.0 + - + +
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Residues in contact with THR 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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148E THR* 4.1 20.4 - - - +
149E PRO 3.2 12.9 + - - +
150E ASN* 4.3 4.0 + - - -
184E VAL* 4.3 5.6 - - - +
185E ILE* 1.3 72.8 - - - +
187E SER* 1.3 63.3 + - - +
201E ALA* 3.4 14.4 - - - +
223E MET* 3.5 2.9 - - - +
234E GLY* 5.5 2.7 - - - -
237E PHE* 3.3 40.2 - - + -
4402E ADP 2.7 57.5 + - - +
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Residues in contact with SER 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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119E GLN* 2.9 23.8 + - - -
151E GLN* 3.1 8.3 + - - +
185E ILE* 2.8 11.5 + - - +
186E THR* 1.3 83.6 + - - +
188E SER* 1.3 66.4 + - - +
199E LEU* 4.1 27.6 - - - +
200E MET 2.9 14.6 - - - -
223E MET* 4.2 1.1 - - - -
4402E ADP 2.4 28.4 + - - -
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Residues in contact with SER 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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119E GLN* 3.8 8.5 + - - -
151E GLN* 2.8 30.5 - - - -
162E ILE* 6.1 0.9 - - - -
185E ILE* 4.6 5.6 - - - -
187E SER* 1.3 79.6 - - - +
189E ASN* 1.3 61.2 + - - +
190E LEU* 3.3 31.5 + - - +
198E TYR 5.2 1.0 - - - +
199E LEU* 4.2 12.2 - - - +
200E MET* 3.0 26.5 + - - +
202E LEU* 5.9 0.5 - - - +
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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