Contacts of the strand formed by residues 182 - 188 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145H ASP 3.4 2.8 + - - -
146H ILE* 3.2 41.3 - - + +
147H ILE 3.2 21.9 + - - -
180H PRO* 3.7 1.7 - - - +
181H ASP* 1.3 83.7 - - - +
183H VAL* 1.3 65.4 + - - +
184H VAL* 4.8 4.0 - - + -
204H SER 3.4 4.7 - - - +
205H GLN* 3.5 22.8 + - + +
241H LEU* 5.9 0.7 - - + -
245H THR* 5.3 4.0 - - + -
252H LEU* 3.6 31.0 - - + -
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Residues in contact with VAL 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ILE* 3.5 25.6 - - + -
172H MET* 3.3 30.7 - - + +
175H LEU* 3.6 27.4 - - + -
176H HIS* 3.8 24.2 - - - +
180H PRO* 3.8 10.8 - - + -
182H THR* 1.3 79.6 - - - +
184H VAL* 1.3 69.2 + - - +
185H ILE* 4.5 4.3 - - + -
202H LEU 4.1 0.2 - - - +
203H GLY* 3.3 0.2 - - - -
204H SER 2.7 42.7 + - - +
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Residues in contact with VAL 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146H ILE* 5.6 0.2 - - + -
147H ILE 3.0 12.8 + - - +
148H THR* 3.5 3.0 - - - -
149H PRO* 2.9 30.1 - - - +
182H THR* 4.8 3.1 - - + -
183H VAL* 1.3 84.5 - - - +
185H ILE* 1.3 75.6 + - - +
186H THR* 3.4 2.1 + - - -
201H ALA* 5.4 2.9 - - + -
202H LEU 3.4 10.1 - - - +
203H GLY* 4.0 9.9 - - - -
221H MET* 5.7 3.6 - - + -
237H PHE* 3.9 33.2 - - + -
241H LEU* 4.4 17.3 - - + -
252H LEU* 4.5 17.0 - - + -
256H CYS* 4.6 7.6 - - - -
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Residues in contact with ILE 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149H PRO* 3.4 28.9 - - + +
151H GLN* 3.8 21.3 - - + +
154H ALA* 3.5 17.3 - - + -
168H ALA* 5.8 5.2 - - + +
171H VAL* 5.4 2.0 - - + -
172H MET* 4.1 22.4 - - + -
175H LEU* 4.3 12.3 - - + -
183H VAL* 4.5 0.2 - - + -
184H VAL* 1.3 73.9 - - - +
186H THR* 1.3 58.6 + - - +
187H SER 2.8 35.1 + - - +
188H SER* 4.7 4.7 - - - -
200H MET 5.7 0.2 - - - +
201H ALA* 3.2 3.1 - - - +
202H LEU* 2.7 43.3 + - + +
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Residues in contact with THR 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H THR* 4.1 13.7 - - - +
149H PRO 3.2 18.5 + - - +
150H ASN* 4.3 3.5 - - - -
184H VAL* 3.5 4.2 - - - +
185H ILE* 1.3 71.5 - - - +
187H SER* 1.3 62.6 + - - +
201H ALA* 3.4 15.5 - - - +
223H MET* 3.4 2.6 - - - +
234H GLY* 5.5 2.9 - - - -
237H PHE* 3.3 40.4 - - + -
7402H ADP 2.7 63.3 + - - +
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Residues in contact with SER 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H GLN* 3.0 22.5 + - - -
151H GLN* 3.2 8.5 + - - +
185H ILE* 2.8 11.8 + - - +
186H THR* 1.3 83.1 + - - +
188H SER* 1.3 65.8 + - - +
199H LEU* 4.2 18.2 - - - +
200H MET 2.9 16.2 - - - -
223H MET* 3.9 10.8 - - - -
7402H ADP 2.3 30.8 + - - -
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Residues in contact with SER 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H GLN* 3.9 8.0 - - - +
151H GLN* 2.9 30.1 - - - -
162H ILE* 6.1 0.7 - - - -
185H ILE* 4.7 5.2 - - - -
187H SER* 1.3 80.1 - - - +
189H ASN* 1.3 61.2 + - - +
190H LEU* 3.3 31.5 + - - +
198H TYR 5.1 1.4 - - - +
199H LEU* 4.1 12.2 - - - +
200H MET* 3.1 26.1 + - - +
202H LEU* 5.7 1.6 - - - +
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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