Contacts of the strand formed by residues 142 - 147 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LYS 3.1 4.9 + - - +
119A ASN* 2.9 30.1 + - + +
120A VAL 3.1 23.7 + - - -
140A VAL* 3.6 2.5 - - - +
141A GLU* 1.3 82.9 + - + +
143A ILE* 1.3 65.6 - - - +
144A ASP* 2.8 24.5 + - - +
171A ARG* 3.3 6.8 + - - +
173A ASN* 2.7 33.9 - - - +
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Residues in contact with ILE 143 (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 VAL* 3.4 8.7 - - + +
122A VAL* 4.5 1.6 - - + -
131A ILE* 4.1 20.2 - - + +
134A LEU* 3.8 45.1 - - + -
135A CYS* 4.0 27.4 - - - +
140A VAL* 3.6 21.1 - - + -
142A ASN* 1.3 77.6 - - - +
144A ASP* 1.3 69.0 + - - +
171A ARG* 2.9 17.1 + - + -
172A VAL* 3.1 18.7 - - + +
173A ASN 2.8 30.1 + - - +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 4.8 1.7 + - - -
120A VAL 3.0 5.6 + - - +
121A LEU* 3.3 11.6 - - + -
122A VAL* 2.8 26.2 + - - +
142A ASN* 2.8 25.1 + - - +
143A ILE* 1.3 76.2 - - - +
145A ILE* 1.3 62.2 + - - +
173A ASN* 3.4 22.0 - - - +
175A PHE* 3.7 21.9 - - + -
182A PHE* 4.6 0.3 - - - -
188A ASN* 5.5 3.1 - - - +
190A TYR* 2.5 36.9 + - + +
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Residues in contact with ILE 145 (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 LEU* 4.5 0.7 - - - -
122A VAL* 3.3 15.5 - - + +
124A GLY 3.1 26.9 - - - +
125A GLY 3.4 21.1 - - - +
126A GLY* 4.0 2.7 - - - +
131A ILE* 3.7 28.7 - - + -
144A ASP* 1.3 77.0 - - - +
146A CYS* 1.3 65.1 + - - +
147A GLU* 4.2 5.8 - - + +
153A ILE* 5.3 0.2 - - + -
167A TYR* 3.7 14.8 - - + +
172A VAL* 4.5 3.1 - - + -
173A ASN 2.9 17.3 + - - +
174A VAL* 3.9 24.1 - - + +
175A PHE* 2.8 32.9 + - - +
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Residues in contact with CYS 146 (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 LEU* 4.1 3.0 - - + +
122A VAL 2.9 10.9 + - - +
123A VAL* 3.8 2.8 - - + -
124A GLY 2.9 25.0 + - - -
145A ILE* 1.3 73.5 - - - +
147A GLU* 1.3 56.8 + - - +
175A PHE* 3.3 3.6 - - - -
177A GLU* 3.2 31.0 - - - -
179A ALA* 3.7 14.1 - - + +
182A PHE* 3.3 53.2 - - + -
401A MTA 3.4 7.3 - - - -
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Residues in contact with GLU 147 (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 GLY 3.7 9.5 - - - +
126A GLY* 2.8 31.0 + - - -
145A ILE* 3.9 6.0 - - + -
146A CYS* 1.3 74.5 - - - +
148A ILE* 1.3 66.0 + - - +
149A ASP* 2.7 40.2 + - - +
152A VAL* 4.4 0.7 - - - -
153A ILE* 4.0 22.0 - - + -
174A VAL* 5.7 0.2 - - + -
175A PHE 3.0 6.4 + - - +
176A ILE* 3.2 24.9 - - - +
177A GLU 3.7 1.8 - - - -
401A MTA 2.7 51.2 + - - +
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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