Contacts of the strand formed by residues 186 - 192 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A SER 4.8 2.4 + - - +
117A ASN* 4.4 7.8 + - - +
118A CYS 4.1 8.3 + - - +
119A ASN* 3.0 33.2 + - - +
120A ILE 2.9 23.2 + - - +
184A GLY 3.7 3.8 + - - +
185A LEU* 1.3 73.9 - - - +
187A THR* 1.3 60.2 + - - +
256A VAL* 4.1 19.7 + - + +
257A SER* 5.0 3.4 - - - +
260A ARG* 2.8 39.3 + - - +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 4.4 9.2 - - + -
120A ILE* 3.2 17.3 - - + -
176A MET* 2.8 52.3 + - - +
177A LEU* 4.4 3.3 - - - +
180A ALA* 3.5 10.5 - - - +
185A LEU* 3.3 24.6 + - + -
186A ASN* 1.3 76.4 - - - +
188A VAL* 1.3 66.6 + - - +
260A ARG* 3.4 1.5 - - - +
261A GLY* 2.7 33.3 + - - -
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Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ILE 2.9 9.6 + - - +
121A ILE* 3.5 16.5 - - + +
122A TYR* 2.8 26.3 + - - +
176A MET* 5.3 0.2 - - - +
187A THR* 1.3 80.2 - - - +
189A VAL* 1.3 67.1 + - - +
190A PHE* 3.7 32.8 - - + -
252A ALA 5.7 0.4 - - - +
256A VAL* 4.1 17.0 - - + -
259A ILE* 3.9 34.1 - - + +
260A ARG* 4.2 0.7 - - - -
262A ASN 3.7 10.3 - - - +
264A PHE* 4.1 10.8 - - + -
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 3.7 7.2 - - + +
124A SER* 3.6 15.7 - - - -
173A ASP* 3.5 34.1 - - + +
176A MET* 3.6 34.8 - - + -
177A LEU* 3.8 14.8 - - + -
188A VAL* 1.3 77.0 - - - +
190A PHE* 1.3 69.7 + - - +
191A ARG* 4.3 1.3 - - + -
262A ASN 3.0 9.0 + - - +
263A ALA* 3.2 17.7 - - + -
264A PHE* 2.8 27.0 + - - -
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Residues in contact with PHE 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ILE* 3.7 17.7 - - + -
122A TYR 2.9 10.8 + - - +
124A SER* 2.7 31.3 + - - +
188A VAL* 3.7 18.6 - - + -
189A VAL* 1.3 80.0 - - - +
191A ARG* 1.3 58.3 + - - +
192A HIS* 3.2 18.0 + - - +
248A LEU* 3.7 27.8 - - + -
249A TYR* 3.7 33.4 - + - -
252A ALA* 3.7 26.9 - - + -
264A PHE* 3.4 15.3 - + + -
266A ILE* 3.7 22.4 - - + -
313A ILE* 4.2 11.2 - - + -
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Residues in contact with ARG 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A SER* 3.9 5.8 - - - +
125A THR 3.8 17.7 - - - +
126A ASN* 4.4 2.3 - - - +
128A VAL* 3.7 12.8 - - - +
129A TYR* 3.0 33.5 + - + -
155A GLU* 4.5 13.3 + - - +
159A LEU* 4.0 18.3 - - - +
173A ASP* 2.8 45.1 + - - +
174A GLN* 3.5 14.6 - - - +
177A LEU* 3.8 4.2 - - - +
189A VAL* 4.0 3.3 + - + -
190A PHE* 1.3 68.4 - - - +
192A HIS* 1.3 62.6 + - - +
263A ALA* 3.5 27.8 - - + +
264A PHE 2.8 10.3 + - - +
265A ASN* 3.4 16.2 - - - +
266A ILE 2.8 24.8 + - - +
306A PHE* 5.4 2.8 - - + -
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Residues in contact with HIS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A SER* 3.8 15.9 - - - -
124A SER 3.3 6.4 + - - +
125A THR* 3.5 3.5 - - - +
126A ASN* 2.9 30.5 + - - +
190A PHE* 3.2 32.8 + + + +
191A ARG* 1.3 75.0 - - - +
193A SER* 1.3 64.3 + - - +
195A MET* 3.7 32.7 - - + +
240A LEU* 5.4 0.2 - - + -
245A MET* 5.0 0.7 - - + -
248A LEU* 4.5 2.0 - - + -
249A TYR* 2.8 39.0 + + - -
266A ILE* 3.6 26.7 + - + +
306A PHE* 5.5 0.2 - - - -
1200A NAD 3.5 22.1 - + + -
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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