Contacts of the strand formed by residues 142 - 147 (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 ASN 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C LYS 2.9 5.1 + - - +
119C ASN* 2.7 35.3 + - + +
120C VAL 3.0 23.9 + - - -
140C VAL* 3.6 5.8 - - - +
141C GLU* 1.3 83.0 - - + +
143C ILE* 1.3 63.8 + - - +
144C ASP* 3.0 28.3 + - - +
171C ARG* 3.4 7.7 - - - +
173C ASN* 3.0 25.3 - - - +
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Residues in contact with ILE 143 (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 VAL* 3.4 7.0 - - + +
122C VAL* 4.6 1.1 - - + -
131C ILE* 4.2 21.3 - - + +
134C LEU* 3.8 45.3 - - + -
135C CYS* 4.0 27.8 - - - +
140C VAL* 3.7 18.2 - - + -
142C ASN* 1.3 79.6 - - - +
144C ASP* 1.3 71.5 + - - +
171C ARG* 2.8 21.1 + - + +
172C VAL* 4.2 12.5 - - + +
173C ASN 2.9 24.9 + - - -
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Residues in contact with ASP 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN* 4.6 1.4 + - - -
120C VAL 3.0 7.2 + - - +
121C LEU* 3.4 10.9 - - + -
122C VAL* 2.9 24.9 + - - +
142C ASN* 3.0 23.1 + - - +
143C ILE* 1.3 77.3 - - - +
145C ILE* 1.3 61.1 + - - +
173C ASN* 3.4 22.4 - - - +
175C PHE* 3.7 20.8 - - + -
182C PHE* 4.7 0.5 - - - -
189C THR* 5.5 0.3 - - - +
190C TYR* 2.6 38.7 + - + +
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Residues in contact with ILE 145 (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* 4.4 0.7 - - - -
122C VAL* 3.3 16.2 - - + +
124C GLY 3.3 25.1 - - - +
125C GLY 3.3 20.9 - - - +
126C GLY* 4.3 1.8 - - - +
131C ILE* 3.4 34.3 - - + -
144C ASP* 1.3 76.7 - - - +
146C CYS* 1.3 61.9 + - - +
147C GLU* 3.9 6.1 - - + -
167C TYR* 3.7 10.3 - - + +
172C VAL* 4.4 2.2 - - + -
173C ASN 2.9 17.6 + - - +
174C VAL* 3.8 24.5 - - + -
175C PHE* 2.8 35.1 + - - +
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Residues in contact with CYS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LEU* 4.0 6.2 - - + +
122C VAL 2.9 12.3 + - - +
123C VAL* 3.7 1.7 - - + -
124C GLY 2.8 28.1 + - - -
145C ILE* 1.3 71.2 - - - +
147C GLU* 1.3 55.2 + - - +
175C PHE* 3.4 5.8 - - + -
177C GLU* 3.2 35.7 - - - -
179C ALA* 3.6 14.1 - - + +
182C PHE* 3.4 49.8 - - + -
401C MTA 3.4 7.6 - - - -
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Residues in contact with GLU 147 (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 GLY 3.7 11.0 - - - +
126C GLY* 3.0 30.1 + - - -
145C ILE* 3.9 5.5 - - + -
146C CYS* 1.3 75.2 - - - +
148C ILE* 1.3 64.3 + - - +
149C ASP* 2.7 38.4 + - - +
152C VAL* 4.5 0.4 - - - -
153C ILE* 4.0 22.2 - - + -
175C PHE 3.0 7.2 + - - +
176C ILE* 3.3 11.8 - - + +
177C GLU 3.2 15.0 + - - -
401C MTA 2.6 55.0 + - - +
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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