Contacts of the helix formed by residues 774 - 784 (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 ALA 774 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602A SER* 4.5 26.0 - - - +
603A ASP* 4.6 11.0 - - - +
606A LYS* 4.0 20.2 - - + -
647A ARG* 4.8 3.1 - - + -
773A ARG* 1.3 73.7 - - - +
775A ILE* 1.3 68.2 + - + +
776A PRO 3.3 1.8 - - - -
777A TRP* 3.1 8.8 + - + +
778A ILE* 3.0 28.3 + - + +
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Residues in contact with ILE 775 (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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177A HIS* 4.9 16.6 - - + -
178A PRO* 4.0 21.5 - - + +
179A THR* 5.0 4.3 - - - -
602A SER* 5.6 0.2 - - - +
647A ARG* 2.9 54.1 - - - +
751A TYR* 3.5 29.8 - - + +
774A ALA* 1.3 75.6 - - + +
776A PRO* 1.3 72.7 - - + +
778A ILE* 3.4 2.1 + - - +
779A PHE* 3.0 24.1 + - - +
969A THR* 5.6 0.4 - - + -
970A GLY* 4.1 14.3 - - - +
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Residues in contact with PRO 776 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A GLU* 4.3 22.4 - - + +
751A TYR* 4.1 29.8 - - + -
773A ARG* 3.4 33.4 - - + +
774A ALA 3.5 0.9 - - - -
775A ILE* 1.3 98.0 - - + +
777A TRP* 1.3 53.5 + - - +
779A PHE* 3.4 9.1 - - + +
780A SER* 2.7 42.5 + - - -
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Residues in contact with TRP 777 (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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605A GLY 5.3 0.4 + - - -
606A LYS* 3.7 29.9 - - + +
728A TYR* 3.4 27.8 + + - -
732A VAL* 4.3 9.9 - - + -
738A PHE* 3.9 26.2 - + - -
742A PHE* 3.3 47.3 - + - -
748A GLU* 5.0 0.4 - - - +
773A ARG 3.7 16.4 - - - +
774A ALA* 3.1 10.5 + - + +
776A PRO* 1.3 83.5 - - - +
778A ILE* 1.3 77.6 + - + +
780A SER* 3.5 6.3 + - - -
781A TRP* 3.3 32.4 - + - -
788A LEU* 4.6 2.5 - - + -
789A PRO* 3.3 30.2 - - + +
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Residues in contact with ILE 778 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A THR* 3.4 26.2 - - - +
646A GLY* 4.1 24.0 - - - +
647A ARG* 3.7 22.0 - - + -
774A ALA* 3.0 16.3 + - + +
775A ILE 3.9 0.2 - - - +
777A TRP* 1.3 89.9 - - + +
779A PHE* 1.3 63.7 + - - +
781A TRP* 3.3 7.8 + - - +
782A THR* 3.1 32.0 + - - +
789A PRO* 4.0 18.8 - - + +
790A VAL* 5.1 7.0 - - + -
970A GLY* 3.5 16.2 - - - +
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Residues in contact with PHE 779 (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* 3.8 24.2 - - + -
751A TYR* 4.0 26.0 - + + -
754A MET* 3.5 30.3 - - + -
775A ILE 3.0 19.2 + - - +
776A PRO* 3.4 9.0 - - + +
778A ILE* 1.3 76.3 - - - +
780A SER* 1.3 72.4 + - - +
782A THR* 2.7 27.1 + - - -
783A GLN* 3.0 46.8 + - + +
959A MET* 4.0 16.2 - - + -
963A ALA* 5.3 1.6 - - + -
969A THR* 2.9 39.0 - - + +
970A GLY* 4.2 2.7 - - - -
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Residues in contact with SER 780 (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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742A PHE* 4.0 10.1 - - - -
746A THR* 3.3 30.2 - - - +
747A PRO* 3.9 3.4 - - - +
748A GLU* 2.7 38.7 - - - +
776A PRO 2.7 27.2 + - - -
777A TRP 3.7 6.3 - - - -
778A ILE 3.4 0.2 - - - -
779A PHE* 1.3 81.8 - - - +
781A TRP* 1.3 59.2 + - - +
783A GLN* 3.8 4.6 + - - +
784A THR* 3.6 12.6 + - - -
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Residues in contact with TRP 781 (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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738A PHE* 4.2 6.5 - + - -
741A TYR* 4.2 26.2 - + - -
742A PHE* 3.1 45.8 - + - -
745A ALA* 5.2 4.9 - - + -
746A THR* 3.8 19.5 - - + -
777A TRP* 3.3 34.7 - - - -
778A ILE 3.3 5.1 + - - +
779A PHE 3.2 0.6 - - - -
780A SER* 1.3 73.6 - - - +
782A THR* 1.3 60.2 + - - +
783A GLN 3.3 0.4 - - - -
784A THR* 3.2 16.3 - - + +
785A ARG 3.2 4.0 + - - -
786A PHE* 2.9 54.3 + + - -
787A HIS* 3.1 18.3 + - - +
788A LEU* 3.7 27.6 - - + +
789A PRO* 3.2 24.6 - - + +
860A LEU* 5.8 0.4 - - + -
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Residues in contact with THR 782 (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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644A THR* 5.2 4.1 - - + +
778A ILE* 3.1 24.7 + - - +
779A PHE* 2.7 12.6 + - - -
781A TRP* 1.3 75.7 - - - +
783A GLN* 1.3 68.5 + - - +
785A ARG* 3.3 10.6 + - - -
787A HIS* 3.8 23.4 + - + -
963A ALA* 6.1 0.2 - - - -
966A MET* 3.8 29.2 - - + +
968A ASN* 4.1 26.5 - - + +
969A THR 4.9 3.4 - - - +
970A GLY* 5.6 0.2 - - - -
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Residues in contact with GLN 783 (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* 3.9 12.5 - - + +
779A PHE* 3.0 47.6 + - + +
780A SER 3.8 8.5 - - - +
782A THR* 1.3 77.0 - - - +
784A THR* 1.3 57.2 + - - +
785A ARG* 2.9 12.1 + - - +
844A TYR* 4.4 1.8 - - - -
902A ASN* 3.1 23.2 + - - -
905A GLN* 2.7 32.0 + - - +
959A MET* 3.3 31.5 - - - +
962A ILE* 3.1 34.6 - - - +
963A ALA* 3.5 8.0 + - - +
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Residues in contact with THR 784 (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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745A ALA* 3.5 14.0 + - - +
746A THR* 4.2 1.3 - - + -
747A PRO* 5.2 0.4 - - - -
780A SER 3.6 6.2 + - - +
781A TRP* 3.2 36.8 - - + +
783A GLN* 1.3 75.0 - - - +
785A ARG* 1.3 66.4 + - - +
786A PHE* 3.2 20.8 + - + -
840A ILE* 3.5 14.5 - - - +
841A ALA* 3.8 14.1 + - + +
844A TYR* 3.4 37.4 - - - +
905A GLN* 4.9 0.2 - - - +
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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