Contacts of the strand formed by residues 148 - 158 (chain A) in PDB entry 5JSJ
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 LYS 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A MET* 3.6 45.2 - - - +
141A PHE 3.5 5.6 - - - +
142A GLU* 4.2 21.3 - - + +
143A THR* 5.6 0.2 - - - -
146A GLY 4.8 1.8 - - - +
147A SER* 1.3 84.0 + - - +
149A ASP* 1.3 61.0 + - - +
189A ASP* 4.7 8.1 + - - -
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Residues in contact with ASP 149 (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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140A MET* 3.4 7.0 - - - +
141A PHE* 2.9 53.3 + - + -
143A THR* 5.4 7.6 - - - -
147A SER 4.1 0.2 + - - -
148A LYS* 1.3 74.5 - - - +
150A GLU* 1.3 84.5 + - - +
151A TRP* 3.4 22.4 + - - -
172A LYS* 3.9 9.5 + - - -
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Residues in contact with GLU 150 (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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138A GLU* 3.3 39.8 - - + +
139A HIS 3.3 10.5 - - - +
140A MET* 4.2 24.7 - - - +
149A ASP* 1.3 88.1 + - - +
151A TRP* 1.3 65.1 + - - +
172A LYS* 4.1 6.8 + - - -
191A ARG* 3.1 23.7 + - - +
302A MG 4.2 7.3 - - - -
303A CL 4.1 3.8 - - - +
149B ASP* 4.9 5.0 - - - +
150B GLU* 5.2 3.3 - - - +
172B LYS* 3.6 23.0 + - - -
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Residues in contact with TRP 151 (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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138A GLU* 3.5 5.0 - - - +
139A HIS* 2.8 36.0 + - - +
141A PHE* 3.4 33.0 - + + -
149A ASP* 3.4 17.1 + - - -
150A GLU* 1.3 83.6 - - - +
152A ARG* 1.3 61.6 + - - +
153A GLY 3.9 0.5 + - - -
170A TYR* 3.8 32.4 - + + -
172A LYS* 3.6 36.8 - - + +
173A ASP* 4.1 18.2 - - + -
177A TYR* 4.0 15.9 - - - -
301A 6PD 3.4 47.6 - - + -
303A CL 3.8 3.6 - - + -
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Residues in contact with ARG 152 (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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136A ALA* 5.7 5.7 - - + +
137A VAL 3.5 9.6 - - - +
138A GLU* 3.0 32.8 + - - +
151A TRP* 1.3 72.6 - - - +
153A GLY* 1.3 62.7 + - - +
170A TYR* 3.4 7.9 - - - +
171A GLU* 3.0 40.6 + - + +
172A LYS 4.8 0.3 + - - -
193A MET* 4.7 15.1 - - - +
303A CL 3.3 18.6 - - + +
152B ARG* 2.9 52.4 - - - +
171B GLU* 2.9 25.1 + - - -
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Residues in contact with GLY 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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136A ALA* 3.3 8.1 - - - +
137A VAL* 2.8 38.0 + - - +
151A TRP 3.9 1.6 + - - -
152A ARG* 1.3 78.4 - - - +
154A MET* 1.3 60.0 + - - -
169A THR 3.1 14.8 - - - -
170A TYR* 3.9 9.1 - - - -
171A GLU* 4.5 2.7 - - - -
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Residues in contact with MET 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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134A GLY* 4.5 2.5 - - - +
135A LYS 3.5 15.0 - - - +
136A ALA* 4.7 3.8 - - + -
153A GLY* 1.3 74.5 - - - +
155A VAL* 1.3 75.7 + - - +
156A LEU* 3.6 23.8 + - + +
168A ILE* 3.1 17.9 - - - +
169A THR* 2.9 29.6 + - + +
239A LYS* 3.8 32.3 - - - -
242A VAL* 4.0 24.5 - - + -
255A VAL* 5.2 0.4 - - + -
257A ASP* 6.2 0.9 - - + -
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Residues in contact with VAL 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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132A MET* 3.5 29.8 - - + +
133A ILE* 4.0 12.1 - - + -
134A GLY* 2.8 31.9 + - - -
135A LYS 3.0 6.2 + - - +
137A VAL* 3.7 25.4 - - + -
154A MET* 1.3 74.9 - - - +
156A LEU* 1.3 59.2 + - - +
157A ALA 4.5 0.9 - - - +
166A PHE* 4.2 23.1 - - + -
167A TYR 3.7 10.8 - - - +
168A ILE* 4.1 5.4 - - + -
181A LEU* 3.6 25.8 - - + -
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Residues in contact with LEU 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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133A ILE* 3.4 14.5 - - - +
134A GLY* 5.4 0.2 - - - -
154A MET* 3.7 42.0 - - + +
155A VAL* 1.3 74.2 - - - +
157A ALA* 1.3 63.5 + - + +
167A TYR* 2.8 20.8 + - + +
168A ILE* 4.1 1.1 - - - -
169A THR* 4.1 14.4 - - + +
176A LEU* 3.8 19.1 - - + -
236A VAL* 3.6 37.3 - - + +
238A ALA* 4.0 2.8 - - - +
239A LYS* 6.5 0.4 - - + -
242A VAL* 4.7 0.7 - - + -
244A PHE* 3.7 25.4 - - + -
255A VAL* 3.9 20.6 - - + -
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Residues in contact with ALA 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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133A ILE* 4.0 17.4 - - + +
155A VAL* 3.9 0.8 - - - +
156A LEU* 1.3 83.9 - - + +
158A ARG* 1.3 69.4 + - - +
166A PHE* 3.4 7.2 - - - +
167A TYR* 2.8 38.5 + - + +
234A HIS* 6.2 2.5 - - - +
236A VAL* 5.5 2.2 - - + -
244A PHE* 6.3 0.4 - - + -
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Residues in contact with ARG 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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123A ILE* 3.1 50.9 - - - +
126A ALA* 4.7 5.5 - - - +
129A ALA* 3.6 25.5 - - - +
130A ASP* 4.5 10.7 + - - -
133A ILE* 3.6 16.2 - - + +
157A ALA* 1.3 82.4 - - - +
159A ALA* 1.3 77.3 + - - +
160A PRO* 3.7 3.8 - - - +
163A ASN* 3.1 28.3 + - - +
165A TRP 3.9 6.3 - - - -
166A PHE* 3.9 16.8 - - - -
167A TYR* 4.6 2.4 - - - -
182A LEU* 4.5 1.0 - - - +
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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