Contacts of the helix formed by residues 142 - 152 (chain A) in PDB entry 1JQO
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 ASP 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A SER* 1.3 81.5 + - - +
143A ILE* 1.3 82.5 + - - +
144A GLU* 2.9 29.3 + - - +
145A GLU* 3.2 20.1 + - + +
146A THR* 3.1 24.2 + - - -
262A ARG* 5.9 2.1 - - - +
692A GLN* 2.7 17.6 + - - +
696A ALA* 4.7 2.5 - - - -
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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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142A ASP* 1.3 73.4 + - - +
144A GLU* 1.3 66.4 + - - +
145A GLU 2.8 2.5 + - - -
146A THR* 2.9 6.9 + - - +
147A LEU* 2.7 56.9 + - + +
165A LEU* 5.6 6.1 - - + -
259A PHE* 3.6 32.5 - - + -
263A VAL* 3.7 26.5 - - + -
266A ALA* 4.4 7.9 - - + -
282A LEU* 5.6 1.1 - - + -
692A GLN* 2.9 27.5 - - - +
695A THR* 3.9 10.3 - - - +
696A ALA* 4.5 9.6 - - + +
699A LEU* 5.5 4.5 - - + -
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Residues in contact with GLU 144 (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 ASP* 2.9 19.3 + - - +
143A ILE* 1.3 78.2 - - - +
145A GLU* 1.3 64.4 + - - +
147A LEU* 3.9 4.3 - - - +
148A LYS* 3.0 57.6 + - + +
262A ARG* 5.1 5.7 - - - +
265A THR* 5.1 0.5 - - - +
266A ALA* 4.0 24.5 + - + +
269A ASN* 2.9 30.1 + - + +
270A ILE* 5.9 0.7 - - + -
208B ASP* 3.2 30.8 - - - +
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Residues in contact with GLU 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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141A SER* 2.4 43.5 + - - -
142A ASP* 3.2 24.2 + - + +
143A ILE 2.8 0.6 + - - -
144A GLU* 1.3 77.6 - - - +
146A THR* 1.3 69.2 + - - +
147A LEU 2.9 0.7 + - - -
148A LYS* 3.0 7.2 + - - +
149A ARG* 2.8 60.5 + - + +
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Residues in contact with THR 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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141A SER* 4.8 1.2 + - - -
142A ASP 3.1 10.6 + - - -
143A ILE* 2.9 6.6 + - - -
145A GLU* 1.3 92.4 + - - +
147A LEU* 1.3 57.3 + - - +
149A ARG* 4.0 8.3 + - - +
150A LEU* 2.9 33.9 + - + +
696A ALA* 3.8 29.3 - - - +
699A LEU* 4.9 6.1 - - + -
700A GLU* 3.3 42.0 + - + +
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Residues in contact with LEU 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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143A ILE* 2.7 43.2 + - + +
144A GLU* 3.9 2.9 - - - +
146A THR* 1.3 70.8 - - - +
148A LYS* 1.3 62.2 + - - +
150A LEU* 3.0 4.5 + - - -
151A VAL* 2.8 39.6 + - + +
161A VAL* 3.5 28.3 - - + -
165A LEU* 5.1 6.3 - - + -
263A VAL* 5.4 0.7 - - + +
266A ALA* 3.6 31.0 - - + -
267A LEU* 4.3 13.2 - - + +
270A ILE* 3.9 17.3 - - + -
699A LEU* 3.7 21.5 - - + -
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Residues in contact with LYS 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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144A GLU* 3.0 50.9 + - + +
145A GLU* 3.0 5.3 + - - +
147A LEU* 1.3 78.2 - - - +
149A ARG* 1.3 52.4 + - - +
151A VAL* 4.7 1.6 - - - -
152A SER* 2.6 47.6 + - - +
269A ASN* 3.5 32.1 - - - +
270A ILE* 3.3 18.2 - - + -
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Residues in contact with ARG 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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145A GLU* 2.8 49.8 + - + +
146A THR* 4.0 6.1 + - - +
148A LYS* 1.3 73.8 - - - +
150A LEU* 1.3 60.7 + - - +
152A SER* 4.6 0.9 - - - -
153A GLU* 2.9 66.0 + - + +
154A VAL* 3.1 18.6 + - - -
700A GLU* 3.2 38.2 + - - -
704A HIS* 5.4 0.9 - - - -
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Residues in contact with LEU 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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146A THR* 2.9 30.5 + - + +
147A LEU* 3.6 3.4 - - - +
149A ARG* 1.3 76.8 - - - +
151A VAL* 1.3 55.0 + - + +
154A VAL* 3.3 30.3 - - + +
155A GLY 2.7 28.4 + - - -
156A LYS* 3.2 15.7 + - + +
161A VAL* 5.0 5.4 - - + -
699A LEU* 4.2 23.6 - - + -
700A GLU* 3.9 26.5 - - + -
703A MET* 4.2 23.8 - - + -
704A HIS* 3.9 20.6 - - + -
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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
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147A LEU* 2.8 28.3 + - - +
148A LYS* 4.0 2.7 - - - +
150A LEU* 1.3 72.6 - - + +
152A SER* 1.3 58.8 + - - +
155A GLY* 2.9 20.3 - - - -
156A LYS 3.0 23.5 + - - +
158A PRO* 3.7 20.0 - - + -
161A VAL* 3.8 23.8 - - + -
270A ILE* 3.6 26.0 - - + -
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Residues in contact with SER 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 LYS* 2.6 32.8 + - - +
149A ARG* 4.6 1.1 - - - -
151A VAL* 1.3 72.2 - - - +
153A GLU* 1.3 74.2 + - - +
155A GLY* 3.1 9.2 + - - -
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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