Contacts of the strand formed by residues 130 - 137 (chain J) in PDB entry 3EOA
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 VAL 130 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J GLY 4.0 7.2 + - - +
129J ASN* 1.3 77.9 - - - +
131J ASP* 1.3 65.4 + - - +
132J LEU* 3.7 3.8 + - + +
165J SER* 4.0 4.4 + - - -
166J TYR* 3.4 49.2 - - + +
167J GLN 3.0 25.1 + - - -
227J ARG* 3.3 6.6 + - - +
231J THR* 3.2 24.0 - - + +
233J VAL* 3.9 23.3 - - + -
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Residues in contact with ASP 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J VAL* 1.3 70.5 - - - +
132J LEU* 1.3 60.1 + - - +
167J GLN* 3.6 14.1 + - - +
183J PHE* 3.7 20.2 - - + -
220J PHE* 3.7 14.0 - - + -
226J ALA* 3.7 9.2 - - - +
227J ARG* 3.0 61.1 + - - +
230J ALA* 3.6 9.2 - - + +
231J THR 2.9 10.0 + - - +
232J LYS* 3.6 4.7 - - - +
233J VAL 2.8 27.2 + - - +
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Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J VAL* 3.7 6.9 + - + -
131J ASP* 1.3 72.6 - - - +
133J VAL* 1.3 76.4 + - - +
134J PHE* 3.8 33.4 - - + -
157J VAL* 5.7 3.1 - - + -
161J LEU* 5.5 2.2 - - + -
166J TYR* 3.8 25.8 - - + -
167J GLN 2.8 14.6 + - - +
168J PHE* 3.3 21.4 - - + -
169J ALA 3.0 23.9 + - - +
183J PHE* 3.7 2.3 - - - -
233J VAL* 3.3 21.8 - - + +
235J ILE* 3.8 22.9 - - + -
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Residues in contact with VAL 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J LEU* 1.3 80.4 - - - +
134J PHE* 1.3 64.3 + - - +
169J ALA* 3.2 12.3 - - + +
171J VAL* 3.8 26.5 - - + -
183J PHE* 3.7 18.4 - - + -
215J VAL* 4.0 8.3 - - + -
219J VAL* 3.7 11.7 - - + -
220J PHE* 3.4 27.4 - - + -
233J VAL 2.8 9.8 + - - +
234J LEU* 3.3 23.7 - - + +
235J ILE* 2.8 28.9 + - - -
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Residues in contact with PHE 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J LEU* 3.8 16.4 - - + -
133J VAL* 1.3 71.6 - - - +
135J LEU* 1.3 56.2 + - - +
136J PHE* 3.7 2.1 + - - -
153J PHE* 4.7 4.3 - + - -
154J MET* 3.6 53.6 - - + -
157J VAL* 3.8 36.8 - - + -
158J MET* 3.7 18.8 - - + -
168J PHE* 3.6 26.2 - + + -
169J ALA 2.9 14.9 + - - +
170J ALA* 3.5 0.8 - - + -
171J VAL 2.7 33.3 + - - +
235J ILE* 3.5 28.9 - - + -
237J ILE* 4.4 3.8 - - + -
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Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133J VAL 3.6 1.2 + - - -
134J PHE* 1.3 70.3 - - - +
136J PHE* 1.3 59.2 + - - +
171J VAL* 3.2 29.8 - - + +
173J PHE* 3.5 28.9 - - + -
208J THR* 5.0 0.7 - - + +
211J ALA* 3.8 35.7 - - + +
212J ILE* 3.9 18.6 - - + +
215J VAL* 3.8 14.4 - - + -
234J LEU* 3.7 17.7 - - + -
235J ILE 2.8 11.2 + - - +
236J ILE* 3.5 15.4 - - + -
237J ILE* 3.0 26.4 + - - +
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Residues in contact with PHE 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J PHE 4.2 2.2 - - - -
135J LEU* 1.3 73.0 - - - +
137J ASP* 1.3 62.8 + - - +
147J PHE* 3.8 31.9 - + - -
150J ILE* 3.9 27.6 - - + -
151J LEU* 4.1 15.0 - - + -
154J MET* 3.7 33.4 - - + -
170J ALA* 4.3 3.8 - - + -
171J VAL 2.7 20.0 + - - -
172J GLN* 3.3 43.0 - - + +
173J PHE* 2.9 30.0 + - - -
180J GLU* 3.8 20.0 - - + -
196J LEU* 4.5 1.1 - - + -
199J VAL* 4.1 8.5 - - + -
237J ILE* 3.7 8.5 - - + -
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Residues in contact with ASP 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J PHE* 1.3 76.1 - - - +
138J GLY* 1.3 75.5 + - - +
139J SER* 2.4 30.5 + - - -
142J LEU* 3.4 18.2 - - + +
147J PHE* 3.8 10.4 - - - -
150J ILE* 4.3 5.7 - - + +
173J PHE* 3.5 16.9 - - + +
205J LEU 4.2 0.3 - - - +
206J THR* 4.0 7.3 + - - +
237J ILE* 2.9 20.2 + - - +
238J THR* 3.2 15.6 + - - -
239J ASP* 2.6 36.7 + - - +
240J GLY 3.9 1.7 + - - -
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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