Contacts of the helix formed by residues 748 - 755 (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 GLU 748 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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742A PHE* 3.3 25.1 - - + +
743A ARG* 2.4 38.5 + - - +
746A THR* 3.1 8.5 - - - +
747A PRO* 1.3 78.9 - - - +
749A THR* 1.3 74.1 + - - +
751A TYR* 3.3 18.9 + - - +
769A ILE* 4.9 5.9 - - - +
776A PRO* 4.3 22.4 - - + +
777A TRP 5.0 0.4 - - - +
779A PHE* 4.9 3.1 - - - -
780A SER* 2.7 29.3 + - - +
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Residues in contact with THR 749 (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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743A ARG* 4.4 24.2 + - - +
746A THR 4.7 2.1 + - - -
747A PRO* 3.2 1.3 - - - -
748A GLU* 1.3 90.7 + - - +
750A GLU* 1.3 73.5 + - - +
751A TYR 3.1 5.1 + - - -
752A GLY 4.2 5.0 + - - -
753A ARG* 5.6 0.3 - - - +
913A ARG* 5.5 3.4 + - - -
947A TYR* 5.8 0.2 - - - +
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Residues in contact with GLU 750 (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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747A PRO* 3.4 14.6 + - + +
749A THR* 1.3 90.3 - - - +
751A TYR* 1.3 63.4 + - - +
752A GLY 3.4 0.9 - - - -
753A ARG* 2.8 37.7 + - - +
909A LEU* 4.0 17.0 - - + +
912A ILE* 5.6 3.0 - - - +
913A ARG* 5.5 5.1 + - - +
947A TYR* 2.5 32.2 + - - -
955A LEU* 3.4 31.9 - - + -
959A MET* 3.4 24.5 - - + +
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Residues in contact with TYR 751 (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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178A PRO* 2.5 44.1 + - + +
747A PRO 3.7 2.9 + - - -
748A GLU 3.3 16.9 + - - +
749A THR 3.1 3.2 + - - -
750A GLU* 1.3 78.8 - - - +
752A GLY* 1.3 66.9 + - - +
753A ARG 3.1 1.8 + - - -
754A MET* 3.4 42.1 + - + +
755A ASN 4.9 0.7 + - - -
756A ILE* 4.1 10.8 - - + +
775A ILE* 3.5 19.0 - - + +
776A PRO* 4.1 23.8 - - + -
779A PHE* 4.0 33.9 - + + -
959A MET* 4.8 0.2 - - - -
969A THR* 4.5 4.3 - - + -
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Residues in contact with GLY 752 (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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234A GLN* 5.9 0.3 - - - -
749A THR 4.2 4.4 + - - -
750A GLU 3.4 1.4 - - - -
751A TYR* 1.3 86.1 - - - +
753A ARG* 1.3 57.3 + - - +
754A MET 3.4 0.6 + - - -
755A ASN* 3.1 24.2 + - - -
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Residues in contact with ARG 753 (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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230A ILE* 5.4 2.3 - - - +
231A ARG 4.7 3.3 - - - +
749A THR 5.6 0.2 - - - +
750A GLU* 2.8 44.0 + - - +
751A TYR 3.1 1.0 - - - -
752A GLY* 1.3 77.8 - - - +
754A MET* 1.3 65.5 + - - +
755A ASN* 3.2 12.4 + - - +
946A GLU* 3.2 30.3 + - - +
947A TYR* 2.9 36.9 + - - -
952A GLU* 2.6 35.5 + - - +
955A LEU* 5.1 2.5 - - - -
956A ILE* 4.0 29.8 - - + +
959A MET* 4.8 0.4 - - + -
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Residues in contact with MET 754 (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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181A SER* 4.3 11.2 - - - +
230A ILE* 5.7 0.4 - - - +
231A ARG* 3.8 16.5 + - - +
751A TYR* 3.4 42.4 - - + +
752A GLY 3.4 0.6 - - - -
753A ARG* 1.3 77.0 - - - +
755A ASN* 1.3 66.9 + - - +
756A ILE* 3.9 25.1 - - + +
779A PHE* 3.5 26.5 - - + -
956A ILE* 4.3 17.3 - - + -
959A MET* 3.7 34.3 - - + +
960A LYS* 4.4 23.8 + - + +
963A ALA* 6.1 0.4 - - - -
969A THR* 4.7 2.2 - - + -
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Residues in contact with ASN 755 (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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231A ARG* 2.7 46.9 + - - +
232A ARG* 3.6 9.2 - - - +
233A ALA* 3.6 25.8 - - - +
234A GLN* 3.9 24.8 + - - +
235A PRO* 3.5 3.8 - - - +
751A TYR 4.9 0.4 + - - -
752A GLY 3.1 22.4 + - - -
753A ARG* 3.3 10.4 + - - +
754A MET* 1.3 81.2 - - - +
756A ILE* 1.3 53.5 + - - +
757A GLY 3.5 2.5 - - - -
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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