Contacts of the strand formed by residues 150 - 160 (chain A) in PDB entry 2JQY
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 ARG 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A SER 4.2 1.1 - - - +
134A MET* 3.3 10.4 - - - +
135A TYR* 3.3 54.6 + - + +
136A LYS* 5.2 0.2 + - - -
137A PHE* 3.3 31.7 - - + -
147A ALA* 3.3 29.2 - - - +
148A ASP 4.3 0.4 - - - -
149A THR* 1.3 77.7 - - - +
151A VAL* 1.3 61.4 + - - +
152A GLU* 3.6 25.5 + - - +
175A ARG 5.5 5.6 - - - +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 4.0 17.3 - - + -
133A SER 3.5 2.5 - - - -
134A MET* 4.0 26.2 - - + -
149A THR* 5.0 9.0 - - + +
150A ARG* 1.3 77.6 - - - +
152A GLU* 1.3 68.6 + - - +
153A THR* 5.3 1.3 - - - +
173A LEU 3.7 8.3 - - - +
175A ARG* 4.0 28.9 + - + +
177A PHE* 6.0 7.4 - - + -
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A LEU* 3.1 5.6 - - - -
133A SER* 2.6 50.0 + - - +
135A TYR* 5.2 6.1 - - - -
150A ARG* 3.6 28.2 + - - +
151A VAL* 1.3 73.4 - - - +
153A THR* 1.3 60.2 + - - +
154A GLU* 3.3 6.2 - - - +
172A TYR* 3.4 34.5 + - + -
173A LEU 3.5 2.7 - - - +
174A GLU* 3.2 44.1 - - + +
175A ARG 5.3 0.2 + - - -
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Residues in contact with THR 153 (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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132A LEU* 3.4 26.4 - - - +
151A VAL* 4.3 1.7 - - - +
152A GLU* 1.3 72.5 - - - +
154A GLU* 1.3 65.6 + - - +
155A THR* 4.5 9.8 + - - +
171A TYR 3.0 14.3 - - - +
173A LEU* 3.1 48.0 + - + +
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Residues in contact with GLU 154 (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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130A GLY* 3.2 6.1 - - - -
131A TRP* 2.8 76.7 + - + +
133A SER* 3.2 22.6 + - - -
152A GLU 3.3 5.9 - - - +
153A THR* 1.3 80.2 + - - +
155A THR* 1.3 63.2 + - - +
156A GLY 3.8 1.5 + - - -
170A ASN* 3.2 20.9 + - - +
171A TYR 3.3 3.8 - - - -
172A TYR* 3.1 49.0 + - + -
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Residues in contact with THR 155 (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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128A PHE* 3.0 46.8 - - + -
129A ASN 3.5 3.4 - - - -
130A GLY* 5.6 0.5 - - - -
153A THR* 4.5 8.1 + - - +
154A GLU* 1.3 72.5 - - - +
156A GLY* 1.3 52.7 + - - +
157A LEU* 5.2 2.2 - - + +
169A VAL 2.7 24.1 - - - +
170A ASN* 3.9 2.2 - - - -
171A TYR* 3.2 30.6 + - - +
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Residues in contact with GLY 156 (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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127A ARG 3.9 0.5 - - - +
128A PHE* 3.6 1.6 - - - -
129A ASN* 2.7 47.5 + - - +
154A GLU 3.8 1.8 + - - -
155A THR* 1.3 74.2 - - - +
157A LEU* 1.3 61.5 + - - +
158A GLN 4.2 0.4 - - - -
168A ARG* 4.1 15.0 - - - -
169A VAL 3.4 4.9 - - - -
170A ASN* 3.7 15.8 - - - +
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Residues in contact with LEU 157 (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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122A LEU* 5.0 6.3 - - + -
126A LEU* 4.0 16.2 - - + -
127A ARG 3.2 20.4 - - - +
128A PHE* 3.0 43.1 - - + -
155A THR* 5.2 1.3 - - + +
156A GLY* 1.3 72.1 - - - +
158A GLN* 1.3 53.4 + - - +
159A TYR* 3.7 26.7 - - + -
167A LEU 2.7 23.6 - - - +
168A ARG* 3.2 2.8 - - - +
169A VAL* 3.2 38.2 + - + +
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Residues in contact with GLN 158 (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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125A ASP 3.8 3.1 - - - +
127A ARG* 3.0 60.5 + - + +
156A GLY 4.2 1.2 + - - -
157A LEU* 1.3 72.0 - - - +
159A TYR* 1.3 60.1 + - - +
166A ALA* 3.2 27.5 - - + +
167A LEU 3.4 4.5 - - - +
168A ARG* 4.4 22.3 + - + +
198A PRO* 3.7 22.2 - - + +
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Residues in contact with TYR 159 (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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125A ASP* 3.4 6.5 - - + +
126A LEU* 3.1 44.6 - - + -
157A LEU* 3.7 26.9 - - + -
158A GLN* 1.3 73.3 - - - +
160A THR* 1.3 61.9 + - - +
161A PHE 4.0 0.2 + - - -
166A ALA* 3.1 5.0 - - - +
167A LEU* 3.1 67.4 + - + +
169A VAL* 4.4 16.8 - - + +
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Residues in contact with THR 160 (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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125A ASP* 2.5 45.3 + - - +
158A GLN 5.8 0.2 - - - +
159A TYR* 1.3 75.7 - - - +
161A PHE* 1.3 59.3 + - - +
162A ASN 3.2 1.6 + - - -
163A GLU* 2.8 25.9 + - + +
164A THR 2.6 27.6 + - - +
165A VAL 3.1 20.6 + - - -
166A ALA* 3.4 8.7 - - + +
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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