Contacts of the strand formed by residues 186 - 192 (chain B) in PDB entry 1ORR
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 ASN 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B SER 4.6 2.6 + - - -
117B ASN* 3.3 30.3 + - - +
118B CYS 4.3 5.2 + - - -
119B ASN* 3.3 25.8 + - - +
120B ILE 2.8 29.3 + - - +
184B GLY 3.9 5.4 + - - +
185B LEU* 1.3 71.6 - - - +
187B THR* 1.3 56.3 + - - +
256B VAL* 4.0 14.2 - - + +
257B SER* 6.4 0.7 - - - -
260B ARG* 2.9 33.4 + - + +
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Residues in contact with THR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.4 5.6 - - + -
120B ILE* 3.3 20.2 - - + -
176B MET* 2.8 53.9 + - - +
177B LEU* 4.3 3.0 - - - +
180B ALA* 3.4 12.7 - - - +
185B LEU* 3.3 22.3 + - + -
186B ASN* 1.3 73.9 - - - +
188B VAL* 1.3 68.3 + - - +
189B VAL* 5.7 0.2 - - - -
260B ARG* 3.3 1.3 - - - +
261B GLY* 2.7 32.4 + - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ILE 2.9 10.2 + - - +
121B ILE* 3.4 15.7 - - + +
122B TYR* 2.9 26.2 + - - +
176B MET* 5.2 0.3 - - - +
177B LEU* 5.4 0.2 - - - -
187B THR* 1.3 81.5 - - - +
189B VAL* 1.3 66.9 + - - +
190B PHE* 3.8 32.1 - - + -
252B ALA 5.7 0.4 - - - +
256B VAL* 4.2 16.8 - - + -
259B ILE* 3.9 33.7 - - + +
260B ARG* 4.3 0.4 - - - -
262B ASN 3.6 9.9 - - - +
264B PHE* 4.1 9.9 - - + -
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.7 6.1 - - + +
124B SER* 3.6 15.9 - - - -
173B ASP* 3.5 35.0 - - + +
176B MET* 3.5 35.0 - - + -
177B LEU* 3.6 23.6 - - + -
188B VAL* 1.3 77.0 - - - +
190B PHE* 1.3 70.8 + - - +
191B ARG* 4.3 4.3 - - + -
262B ASN 3.0 9.9 + - - +
263B ALA* 3.3 5.6 - - + -
264B PHE* 3.0 26.2 + - - -
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Residues in contact with PHE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.6 20.9 - - + -
122B TYR 2.9 10.2 + - - +
124B SER* 2.7 32.1 + - - +
188B VAL* 3.8 19.3 - - + -
189B VAL* 1.3 80.4 - - - +
191B ARG* 1.3 57.0 + - - +
192B HIS* 3.3 19.8 + - + +
248B LEU* 3.7 27.4 - - + -
249B TYR* 3.5 34.5 - + - -
252B ALA* 3.7 26.5 - - + -
264B PHE* 3.5 15.0 - + + -
266B ILE* 3.7 26.5 - - + -
313B ILE* 4.4 4.9 - - + -
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B SER* 4.0 4.0 - - - +
125B THR 3.9 18.2 - - - +
126B ASN* 4.4 2.3 - - - +
128B VAL* 3.8 12.5 - - - +
129B TYR* 3.0 34.3 + - + -
155B GLU* 4.4 14.5 + - - +
159B LEU* 4.4 15.2 - - - +
173B ASP* 2.8 43.7 + - - +
174B GLN* 3.4 16.6 - - - +
177B LEU* 3.9 4.4 - - - +
189B VAL* 4.3 3.4 - - + -
190B PHE* 1.3 69.5 - - - +
192B HIS* 1.3 62.4 + - - +
263B ALA* 3.5 27.4 - - + +
264B PHE 2.8 10.9 + - - +
265B ASN* 3.6 15.9 - - - +
266B ILE 2.9 24.9 + - - +
306B PHE* 5.5 2.8 - - + -
308B ALA* 5.5 0.3 - - - +
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Residues in contact with HIS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.6 0.4 - - - +
123B SER* 3.7 19.5 - - - -
124B SER 3.3 8.0 + - - -
126B ASN* 3.1 25.6 + - - +
190B PHE* 3.3 34.2 + + + +
191B ARG* 1.3 75.2 - - - +
193B SER* 1.3 65.3 + - - +
195B MET* 3.4 33.8 - - + +
245B MET* 4.8 0.7 - - + -
248B LEU* 4.5 2.0 - - + -
249B TYR* 2.7 38.6 + + - -
266B ILE* 3.5 24.4 + - + +
1300B NAD 3.5 25.8 - + + -
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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