Contacts of the strand formed by residues 190 - 196 (chain C) in PDB entry 3RIE
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 TYR 190 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ASN* 3.5 28.9 - - - -
120C VAL 3.8 1.3 - - - -
121C LEU* 3.6 45.5 - - + -
144C ASP* 2.6 32.6 + - + +
182C PHE* 3.5 21.6 - + - -
183C LEU* 4.4 2.2 - - + -
186C VAL* 3.9 16.4 - - + +
189C THR* 1.3 88.5 - - + +
191C ASP* 1.3 62.2 + - - +
192C VAL 3.8 5.4 - - - +
193C ILE* 3.7 27.8 - - + -
219C ALA* 3.1 15.7 + - + +
220C LEU* 3.3 5.2 - - + +
221C LYS* 3.0 25.4 + - - -
224C GLY* 4.4 0.2 - - - -
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Residues in contact with ASP 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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114C SER* 4.3 6.5 + - - +
116C GLU 4.5 4.9 - - - +
117C PRO* 3.8 21.8 - - + -
118C LYS* 2.7 30.4 + - - +
119C ASN* 3.0 20.2 + - - +
189C THR 4.0 0.2 + - - -
190C TYR* 1.3 71.9 - - - +
192C VAL* 1.4 64.7 + - - +
220C LEU* 4.0 0.9 - - - -
221C LYS* 3.6 24.6 - - - +
223C ASN 4.7 0.2 - - - +
224C GLY* 3.2 9.7 - - - -
225C TYR* 3.1 24.3 + - - -
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Residues in contact with VAL 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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110C PRO* 4.0 24.7 - - + -
111C MET* 3.9 19.3 - - - -
114C SER* 4.1 22.4 - - - +
117C PRO* 4.4 4.3 - - + -
119C ASN 3.7 2.2 + - - -
120C VAL* 3.4 13.5 - - + -
121C LEU 3.0 23.2 + - - -
190C TYR* 3.8 1.6 - - - +
191C ASP* 1.4 84.2 - - - +
193C ILE* 1.3 71.4 - - - +
194C ILE* 3.7 31.2 - - + -
220C LEU* 4.1 0.2 - - - -
225C TYR* 3.2 10.8 - - + +
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Residues in contact with ILE 193 (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 LEU* 3.3 29.4 - - + +
123C VAL* 4.2 6.5 - - + -
183C LEU* 4.6 2.2 - - + -
190C TYR* 3.7 27.4 - - + -
192C VAL* 1.3 78.3 - - - +
194C ILE* 1.3 65.9 + - - +
195C VAL* 4.1 20.0 - - + -
216C ILE* 4.0 27.1 - - + +
219C ALA* 4.1 10.5 - - + -
220C LEU* 3.8 23.1 - - + -
225C TYR 2.9 9.0 + - - +
226C CYS* 3.2 8.6 - - + -
227C VAL 3.1 24.4 + - - +
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Residues in contact with ILE 194 (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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106C MET* 3.9 33.7 - - + +
107C THR* 4.2 8.1 - - + +
110C PRO* 4.2 2.5 - - + -
111C MET* 5.0 0.2 - - + -
120C VAL* 4.3 4.9 - - + -
121C LEU 2.7 13.1 + - - +
122C VAL* 3.4 3.3 - - - +
123C VAL 2.9 23.4 + - - +
130C ILE* 3.7 44.9 - - + -
134C LEU* 4.1 19.3 - - + -
192C VAL* 3.7 21.3 - - + -
193C ILE* 1.3 78.8 - - - +
195C VAL* 1.3 62.4 + - - +
196C ASP* 3.4 5.1 + - + +
227C VAL* 3.5 18.2 - - + -
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Residues in contact with VAL 195 (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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106C MET* 3.6 2.6 - - - +
123C VAL* 3.9 25.4 - - + -
193C ILE* 4.1 10.1 - - + -
194C ILE* 1.3 71.6 - - - +
196C ASP* 1.3 58.9 + - - +
197C SER* 3.5 20.3 + - - +
207C LEU* 4.4 7.0 - - + +
212C PHE* 4.3 10.3 - - + -
213C TYR* 4.9 2.5 - - - +
216C ILE* 4.0 26.2 - - + -
226C CYS* 4.1 9.0 - - - -
227C VAL 2.8 15.6 + - - +
228C ALA* 3.5 16.9 - - + -
229C GLN* 3.0 26.2 + - - +
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Residues in contact with ASP 196 (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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102C TYR* 2.5 40.5 + - - +
106C MET* 4.1 4.9 - - + -
122C VAL* 4.6 1.8 - - + -
123C VAL 2.9 15.3 + - - +
124C GLY* 3.6 0.2 - - - -
125C GLY* 2.9 36.3 + - - -
127C ASP* 4.6 0.5 - - - +
130C ILE* 3.5 26.6 - - + +
194C ILE* 3.4 3.0 + - + -
195C VAL* 1.3 71.7 - - - +
197C SER* 1.3 56.0 + - - +
401C MTA 3.2 5.0 - - - +
501C JFQ 2.8 31.0 + - - -
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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