Contacts of the helix formed by residues 147 - 158 (chain A) in PDB entry 1JSA
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 PRO 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A LEU* 4.1 11.0 - - + +
125A VAL* 3.8 24.6 - - + +
126A THR* 2.9 42.2 - - + +
129A PHE* 4.5 18.1 - - + -
146A THR* 1.3 93.3 - - + +
148A GLU* 1.3 63.9 + - + +
150A ARG* 4.6 1.3 - - + +
151A ALA* 3.3 23.0 + - - +
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Residues in contact with GLU 148 (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* 4.4 23.1 - - + +
146A THR* 3.1 5.7 - - - +
147A PRO* 1.3 86.0 - - + +
149A LYS* 1.3 53.0 + - - +
151A ALA* 4.1 3.5 + - - +
152A GLU* 2.5 31.9 - - - +
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Residues in contact with LYS 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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142A GLU 3.7 12.5 + - - -
143A ASP* 3.3 25.0 - - - +
144A GLU* 3.9 3.3 - - - +
145A ASN* 2.9 26.9 - - - +
146A THR* 2.7 28.8 + - - +
148A GLU* 1.3 76.5 - - - +
150A ARG* 1.3 59.1 + - - +
152A GLU* 3.1 22.5 - - - +
153A LYS* 4.3 1.7 + - - +
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Residues in contact with ARG 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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125A VAL* 4.7 8.1 - - + +
128A ILE* 5.0 9.9 - - - +
129A PHE* 4.3 20.8 - - - -
132A ILE* 4.8 15.8 - - - +
140A LEU* 6.1 4.0 - - - +
144A GLU* 3.0 47.4 + - + +
146A THR 2.8 14.8 + - - +
147A PRO* 4.2 5.2 - - + +
149A LYS* 1.3 77.8 - - - +
151A ALA* 1.3 54.7 + - - +
152A GLU 2.6 7.2 + - - -
153A LYS* 2.4 32.4 + - + +
154A ILE* 3.1 31.0 + - + +
184A LEU* 3.3 58.3 + - - +
185A ILE* 5.4 0.6 - - - +
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Residues in contact with ALA 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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118A LYS* 6.0 3.1 - - + +
121A VAL* 5.4 9.1 - - + +
122A LEU* 4.9 15.5 - - + -
125A VAL* 5.2 2.9 - - + +
147A PRO 3.3 15.6 + - - +
148A GLU* 4.2 4.3 - - - +
150A ARG* 1.3 78.4 - - - +
152A GLU* 1.3 70.3 + - - +
154A ILE* 4.5 10.0 - - - +
155A TRP* 2.9 34.6 + - + +
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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
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148A GLU* 2.5 29.7 - - - +
149A LYS* 3.1 17.2 - - - +
150A ARG 2.6 3.8 + - - -
151A ALA* 1.3 80.4 - - - +
153A LYS* 1.3 62.1 + - + +
155A TRP* 4.8 1.1 - - - -
156A GLY* 2.9 25.8 + - - +
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Residues in contact with LYS 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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141A PRO* 6.0 1.6 - - - +
143A ASP* 4.2 24.0 - - + +
144A GLU* 3.3 43.7 - - + +
149A LYS 4.4 1.6 - - - +
150A ARG* 2.4 32.5 + - + +
152A GLU* 1.3 68.3 - - + +
154A ILE* 1.3 60.7 + - + +
156A GLY* 3.7 0.7 - - - -
157A PHE* 2.9 68.5 + - + -
184A LEU* 5.8 0.9 - - + -
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Residues in contact with ILE 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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108A TYR* 5.4 2.9 - - + +
121A VAL* 4.5 13.7 - - + -
125A VAL* 3.4 33.7 - - + -
150A ARG* 3.1 41.0 + - + +
151A ALA* 4.5 2.0 - - - +
153A LYS* 1.3 73.2 - - + +
155A TRP* 1.3 62.9 + - + +
156A GLY 2.9 0.9 - - - -
157A PHE* 2.8 32.6 + - + +
158A PHE* 3.3 26.3 + - + -
184A LEU* 5.4 2.5 - - + -
185A ILE* 3.4 35.2 - - + -
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Residues in contact with TRP 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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116A ILE* 4.2 15.7 - - + -
117A SER* 4.3 10.3 - - - -
118A LYS* 4.4 26.6 - - + +
121A VAL* 4.1 30.7 - - + +
151A ALA 2.9 20.7 + - - +
152A GLU* 4.7 1.8 - - - +
154A ILE* 1.3 81.2 - - + +
156A GLY* 1.3 61.0 + - - +
158A PHE* 3.7 14.3 + + - +
159A GLY* 3.2 19.2 + - - -
160A LYS* 3.6 41.7 + - + +
164A ASP* 3.7 26.2 - - + +
166A LEU* 4.6 12.1 - - + -
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLU 2.9 23.0 + - - -
153A LYS 3.7 1.1 - - - -
154A ILE 2.9 1.0 - - - -
155A TRP* 1.3 79.8 - - - +
157A PHE* 1.3 65.9 + - - +
158A PHE 3.5 0.3 + - - -
159A GLY* 3.8 8.9 + - - -
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Residues in contact with PHE 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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153A LYS* 2.9 53.9 + - - -
154A ILE* 2.8 12.1 + - + +
156A GLY* 1.3 79.1 - - - +
158A PHE* 1.3 68.3 + - + +
178A ASN* 6.1 2.0 - - + -
180A GLU 6.0 0.4 - - - -
181A ILE* 4.6 30.5 - - + +
184A LEU* 3.0 36.1 - - + -
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Residues in contact with PHE 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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154A ILE* 3.3 41.6 + - + -
155A TRP* 4.0 15.5 - + + +
157A PHE* 1.3 84.9 - - + +
159A GLY* 1.3 65.2 + - - +
160A LYS* 3.3 24.1 + - - +
166A LEU* 4.0 30.1 - - + -
171A PHE* 5.1 13.9 - + - -
174A GLY* 4.1 34.3 - - - -
175A THR* 4.8 12.8 - - + -
181A ILE* 5.0 10.5 - - + -
185A ILE* 5.3 7.0 - - + -
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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