Contacts of the helix formed by residues 778 - 792 (chain A) in PDB entry 3RJO
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 SER 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751A PHE* 5.4 1.0 - - - -
774A VAL 4.5 0.4 + - - -
775A GLY 3.4 11.7 + - - -
776A ALA 3.3 1.8 - - - +
777A GLN* 1.3 79.4 - - - +
779A THR* 1.3 59.3 + - - +
780A GLU* 4.4 6.2 - - - +
781A GLY* 3.4 11.4 + - - -
782A TRP* 3.0 30.2 + - - +
808A THR* 5.9 0.4 - - - -
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Residues in contact with THR 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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778A SER* 1.3 71.5 - - - +
780A GLU* 1.3 73.4 + - - +
782A TRP* 4.3 4.3 - - - -
783A ASP* 2.9 41.1 + - - +
810A ASN* 4.0 19.2 + - - -
813A LYS* 4.2 14.2 - - - +
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Residues in contact with GLU 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A LYS* 4.0 18.5 + - - +
778A SER* 3.4 5.7 + - - +
779A THR* 1.3 85.4 - - - +
781A GLY* 1.3 56.0 + - - +
783A ASP* 4.7 10.7 - - - +
784A PHE* 2.8 28.4 + - - +
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Residues in contact with GLY 781 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A PHE* 3.6 21.7 - - - -
755A LYS* 4.7 2.2 - - - -
775A GLY 3.5 19.7 - - - -
778A SER* 3.4 9.3 + - - -
779A THR 3.3 0.6 - - - -
780A GLU* 1.3 77.0 - - - +
782A TRP* 1.3 56.0 + - - +
784A PHE* 3.4 4.0 + - - +
785A LEU* 2.8 39.1 + - - +
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Residues in contact with TRP 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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775A GLY 3.9 1.8 + - - -
776A ALA* 3.5 23.1 - - + +
778A SER 3.0 19.0 + - - +
779A THR* 3.7 6.7 - - - +
781A GLY* 1.3 73.4 - - - +
783A ASP* 1.3 71.5 + - - +
785A LEU* 3.3 0.7 + - - -
786A TYR* 2.7 52.3 + + + +
805A LEU* 3.1 41.3 + - + +
808A THR* 3.5 20.4 - - + +
813A LYS* 3.8 35.7 - - + -
816A TRP* 3.9 30.7 - + - -
817A LEU* 3.7 29.6 - - + -
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Residues in contact with ASP 783 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A THR* 2.9 35.5 + - - +
780A GLU* 3.9 12.6 - - - +
782A TRP* 1.3 82.7 - - - +
784A PHE* 1.3 67.6 + - - +
786A TYR* 3.2 5.7 + - - +
787A SER* 2.9 23.3 + - - -
813A LYS* 2.8 26.1 + - - -
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Residues in contact with PHE 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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751A PHE* 4.5 2.7 - + - -
754A TRP* 3.4 38.6 - + - -
755A LYS* 3.7 50.3 - - + -
758A ASN* 3.8 19.1 - - - -
759A GLY 3.8 15.7 - - - -
780A GLU 2.8 22.1 + - - +
781A GLY 3.5 4.3 - - - +
782A TRP 3.3 0.2 - - - -
783A ASP* 1.3 72.8 - - - +
785A LEU* 1.3 62.2 + - - +
787A SER* 2.7 29.4 + - - -
788A LYS* 3.2 30.5 + - + +
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Residues in contact with LEU 785 (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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751A PHE* 3.6 17.3 - - + -
754A TRP* 3.7 30.5 - - + -
772A PHE* 3.7 41.1 - - + +
776A ALA* 3.8 18.6 - - + +
781A GLY 2.8 23.2 + - - +
782A TRP 3.5 3.8 - - - +
784A PHE* 1.3 75.4 - - - +
786A TYR* 1.3 63.2 + - - +
788A LYS* 3.3 6.1 + - - +
789A TYR* 3.1 21.0 + - - +
801A ILE* 3.8 26.3 - - + +
804A ALA* 4.6 3.1 - - + -
805A LEU* 3.9 9.9 - - + -
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Residues in contact with TYR 786 (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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782A TRP* 2.7 39.7 + + + +
783A ASP* 3.2 6.2 + - - +
785A LEU* 1.3 73.4 - - - +
787A SER* 1.3 66.0 + - - +
789A TYR* 3.1 21.6 + + + +
790A GLN* 3.3 50.4 + - + +
805A LEU* 4.0 21.9 - - + +
816A TRP* 3.2 43.3 - + - -
817A LEU* 5.4 0.7 - - + -
826A LYS* 3.4 24.8 + - - +
827A ILE* 4.8 12.6 - - + -
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Residues in contact with SER 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ASP 2.9 12.8 + - - -
784A PHE* 2.7 28.7 + - - -
786A TYR* 1.3 81.7 - - - +
788A LYS* 1.3 69.7 + - - +
790A GLN* 3.3 23.7 - - - +
791A PHE* 3.3 19.4 - - - -
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Residues in contact with LYS 788 (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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754A TRP* 4.0 18.4 - - + -
758A ASN* 3.2 40.7 + - - +
759A GLY* 4.7 2.5 - - - +
784A PHE* 3.2 52.1 + - + +
785A LEU 3.7 6.7 - - - +
786A TYR 3.2 0.4 - - - -
787A SER* 1.3 83.8 + - - +
789A TYR* 1.3 64.6 + - - +
790A GLN 3.2 1.8 - - - -
791A PHE* 3.2 8.9 + - + +
792A SER* 3.0 28.8 + - - -
797A GLU* 5.2 5.8 - - - +
801A ILE* 4.2 12.6 - - + -
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Residues in contact with TYR 789 (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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785A LEU 3.1 12.0 + - - +
786A TYR* 3.1 23.8 + + + +
788A LYS* 1.3 77.8 - - - +
790A GLN* 1.3 63.6 + - + +
791A PHE 3.5 0.3 + - - -
792A SER* 3.8 3.5 + - - -
798A LYS* 3.1 87.3 + - + +
801A ILE* 3.8 24.6 - - + +
802A GLU* 4.1 21.5 + - + +
805A LEU* 5.2 4.9 - - + -
826A LYS 4.1 19.7 - - - -
827A ILE* 3.7 31.0 - - + +
828A LYS* 5.0 1.0 + - - +
831A GLU* 4.2 7.3 - - - +
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Residues in contact with GLN 790 (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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786A TYR* 3.3 47.3 + - + +
787A SER* 3.3 14.0 - - - +
789A TYR* 1.3 83.3 - - + +
791A PHE* 1.3 75.5 + - + +
792A SER 3.5 1.3 - - - +
798A LYS* 5.3 2.2 + - - +
826A LYS* 4.2 21.8 + - - +
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Residues in contact with PHE 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A SER* 3.3 26.6 + - - +
788A LYS* 3.2 11.8 + - + +
790A GLN* 1.3 93.6 - - + +
792A SER* 1.3 64.5 + - - +
793A LEU* 3.6 3.6 + - - +
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Residues in contact with SER 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A LYS 3.0 18.6 + - - -
789A TYR* 4.0 7.6 - - - -
790A GLN 3.5 1.9 - - - +
791A PHE* 1.3 78.6 - - - +
793A LEU* 1.3 59.5 + - - +
794A SER* 3.2 19.6 + - - -
797A GLU* 2.5 28.1 + - - +
798A LYS* 3.6 28.8 - - - +
801A ILE* 5.4 0.4 - - - -
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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