Contacts of the strand formed by residues 119 - 125 (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 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C ASP* 3.0 12.3 + - - +
76C SER* 3.3 22.3 + - - +
77C CYS 2.7 32.7 + - - +
117C ASN 3.7 3.2 + - - +
118C CYS* 1.3 70.1 - - - +
120C ILE* 1.3 54.7 + - - +
121C ILE* 5.7 0.2 - - - -
186C ASN* 3.2 30.8 + - - +
253C LEU* 3.7 17.9 - - + +
256C VAL* 3.6 30.8 - - + +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C CYS* 3.3 18.8 - - + +
79C HIS* 4.2 12.3 - - + -
107C LEU* 4.3 11.0 - - + -
108C LEU* 4.3 19.7 - - + -
111C VAL* 3.9 35.7 - - + -
118C CYS* 3.9 11.2 - - - +
119C ASN* 1.3 78.9 - - - +
121C ILE* 1.3 71.5 + - - +
122C TYR 4.1 0.2 + - - -
176C MET* 4.1 21.1 - - + -
185C LEU* 4.9 1.1 - - + -
186C ASN 2.9 12.6 + - - +
187C THR* 3.3 13.9 - - + -
188C VAL* 2.9 28.3 + - - +
256C VAL* 5.5 0.4 - - - +
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Residues in contact with ILE 121 (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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77C CYS 2.9 8.3 + - - +
78C PHE* 3.7 26.7 - - + -
79C HIS* 3.0 25.8 + - - +
119C ASN 5.7 0.2 - - - -
120C ILE* 1.3 76.3 - - - +
122C TYR* 1.3 61.6 + - - +
123C SER 4.2 0.3 + - - -
188C VAL* 3.4 20.9 - - + +
190C PHE* 3.6 32.5 - - + -
249C TYR* 3.6 41.1 - - + +
252C ALA* 4.0 12.3 - - + -
253C LEU* 4.0 21.5 - - + +
256C VAL* 6.3 0.9 - - + -
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Residues in contact with TYR 122 (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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79C HIS* 3.4 43.3 - + - -
81C ALA 5.5 3.1 - - - -
100C ASN* 4.3 4.5 + - - +
104C THR* 3.7 8.1 + - - -
120C ILE 4.1 0.4 - - - -
121C ILE* 1.3 77.2 - - - +
123C SER* 1.3 70.1 + - - +
124C SER* 3.3 27.3 + - - -
169C LYS* 3.3 29.8 + - - +
172C ALA* 3.2 30.2 - - + +
173C ASP* 3.9 10.8 - - - -
176C MET* 3.8 35.7 - - + -
188C VAL 2.8 13.8 + - - +
189C VAL* 3.5 5.4 - - + -
190C PHE* 2.9 28.1 + - - +
249C TYR* 4.6 0.2 - - - -
1400C NAD 5.4 0.4 - - - -
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Residues in contact with SER 123 (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* 4.5 0.7 - - - -
79C HIS 3.4 8.2 + - - -
80C LEU* 3.3 12.8 - - - +
121C ILE 4.2 0.6 + - - -
122C TYR* 1.3 75.7 - - - +
124C SER* 1.3 62.6 + - - +
169C LYS* 2.9 23.7 + - - -
192C HIS* 3.6 15.5 - - - -
249C TYR* 3.4 20.3 + - - -
1400C NAD 3.3 36.7 + - - -
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Residues in contact with SER 124 (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* 3.3 14.9 + - - -
123C SER* 1.3 77.5 - - - +
125C THR* 1.3 77.8 + - - +
128C VAL* 3.8 10.2 - - - +
169C LYS* 4.0 7.7 + - - +
173C ASP* 2.8 33.4 + - - +
189C VAL* 3.6 12.8 - - - -
190C PHE 2.6 20.0 + - - +
191C ARG* 4.0 3.2 - - - +
192C HIS* 3.3 10.4 + - - +
1400C NAD 3.2 9.2 - - - -
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Residues in contact with THR 125 (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* 1.3 75.9 + - - +
126C ASN* 1.3 66.1 + - - +
127C LYS* 3.0 12.7 + - + +
128C VAL* 3.3 26.2 + - - +
165C TYR* 2.8 38.0 - - + +
166C GLY* 5.5 0.3 - - - -
169C LYS* 3.4 25.5 - - - +
191C ARG* 3.9 5.0 - - - +
192C HIS 3.5 9.2 - - - +
1400C NAD 3.0 30.7 - - + -
1401C CDP 5.7 1.3 - - - +
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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