Contacts of the strand formed by residues 186 - 192 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C SER 4.3 2.4 + - - -
117C ASN* 3.1 36.0 + - - +
118C CYS 3.9 9.1 + - - +
119C ASN* 3.2 22.6 + - - +
120C ILE 2.9 22.6 + - - +
184C GLY 3.9 5.1 + - - +
185C LEU* 1.3 70.7 - - - +
187C THR* 1.3 61.0 + - - +
256C VAL* 4.2 12.6 - - + +
260C ARG* 3.1 32.9 + - - +
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Residues in contact with THR 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 4.3 10.3 - - + -
120C ILE* 3.3 15.3 - - + -
176C MET* 2.8 52.8 + - - +
177C LEU* 4.4 1.8 - - - +
179C TYR* 5.0 0.2 - - + -
180C ALA* 3.3 11.4 - - - +
185C LEU* 3.1 23.6 + - + -
186C ASN* 1.3 76.0 - - - +
188C VAL* 1.3 68.4 + - - +
189C VAL* 5.7 0.4 - - - -
260C ARG* 3.4 0.5 - - - -
261C GLY* 2.7 35.6 + - - +
262C ASN 4.1 0.2 + - - -
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Residues in contact with VAL 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ILE 2.9 10.7 + - - +
121C ILE* 3.4 16.0 - - + -
122C TYR* 2.8 27.5 + - - +
187C THR* 1.3 81.4 - - - +
189C VAL* 1.3 65.9 + - - +
190C PHE* 3.8 31.0 - - + -
252C ALA 5.5 0.4 - - - +
256C VAL* 4.2 18.4 - - + -
259C ILE* 4.0 28.7 - - + +
260C ARG* 4.3 3.8 - - - -
262C ASN 3.7 9.6 - - - +
264C PHE* 4.1 13.2 - - + -
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Residues in contact with VAL 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C TYR* 3.5 8.5 - - + +
124C SER* 3.6 15.9 - - - -
173C ASP* 3.5 33.2 - - - +
176C MET* 3.6 34.8 - - + -
177C LEU* 3.9 13.5 - - + -
187C THR* 5.6 0.2 - - - +
188C VAL* 1.3 78.9 - - - +
190C PHE* 1.3 69.7 + - - +
191C ARG* 4.3 1.1 - - + -
262C ASN 3.0 8.2 + - - +
263C ALA* 3.2 17.6 - - + -
264C PHE* 2.9 26.3 + - - -
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE* 3.6 22.2 - - + -
122C TYR 2.9 11.6 + - - +
124C SER* 2.6 31.8 + - - +
188C VAL* 3.8 15.7 - - + -
189C VAL* 1.3 80.4 - - - +
191C ARG* 1.3 60.2 + - - +
192C HIS* 3.2 24.9 + + + +
248C LEU* 3.7 31.2 - - + -
249C TYR* 3.6 34.5 - + - -
252C ALA* 3.7 27.1 - - + -
264C PHE* 3.4 15.7 - + + -
266C ILE* 3.8 16.2 - - + -
313C ILE* 4.4 6.7 - - + -
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Residues in contact with ARG 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C SER* 4.0 5.8 - - - +
125C THR 3.9 18.6 - - - +
126C ASN* 4.7 2.4 + - - +
128C VAL* 3.8 9.9 - - - +
129C TYR* 3.0 34.3 + - + -
155C GLU* 4.2 14.6 + - - +
159C LEU* 4.0 19.6 - - - +
173C ASP* 2.9 43.8 + - - +
174C GLN* 3.4 15.2 - - - +
177C LEU* 3.8 4.4 - - - +
189C VAL* 4.0 2.7 + - + -
190C PHE* 1.3 70.3 - - - +
192C HIS* 1.3 62.3 + - - +
263C ALA* 3.6 26.5 - - + +
264C PHE 2.8 10.3 + - - +
265C ASN* 3.6 16.3 - - - +
266C ILE 3.0 22.8 + - - +
306C PHE* 5.2 2.8 - - - -
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Residues in contact with HIS 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 4.4 0.6 - - - +
123C SER* 3.6 23.3 - - - -
124C SER 3.3 6.2 + - - +
125C THR* 3.5 3.8 - - - -
126C ASN* 3.0 29.3 + - - -
190C PHE* 3.2 33.0 + + + +
191C ARG* 1.3 74.1 - - - +
193C SER* 1.3 65.3 + - - +
195C MET* 3.5 30.3 - - + +
245C MET* 5.0 0.2 - - + -
248C LEU* 4.4 2.2 - - + -
249C TYR* 2.7 39.8 + + - -
266C ILE* 3.7 24.8 + - + +
1400C NAD 3.5 21.4 - + + -
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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