Contacts of the helix formed by residues 740 - 757 (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 TYR 740 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A ILE* 4.0 25.1 - - + -
708A ARG* 3.1 38.1 + - + -
711A ILE* 4.0 17.0 - - + -
712A ASP* 2.4 41.4 + - - -
735A ALA* 2.9 22.4 + - + +
738A HIS 3.4 1.7 - - - +
739A ASN* 1.3 73.4 - - - +
741A GLN* 1.3 65.9 + - - +
742A PRO* 3.8 30.1 - - + +
743A CYS* 3.0 35.9 - - + +
744A VAL* 3.0 5.1 + - - +
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Residues in contact with GLN 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A ASN 3.3 7.5 + - - +
740A TYR* 1.3 71.0 - - - +
742A PRO* 1.4 81.1 - - + +
744A VAL* 4.3 7.4 - - - -
745A GLN* 2.9 57.4 + - + +
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Residues in contact with PRO 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A ARG* 5.7 2.7 - - - +
712A ASP* 5.1 2.7 - - - +
740A TYR* 3.5 38.4 - - + +
741A GLN* 1.4 101.3 - - + +
743A CYS* 1.3 54.6 + - - +
745A GLN* 4.4 2.8 - - + +
746A ARG* 3.3 30.5 + - - +
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Residues in contact with CYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A ILE* 3.7 20.2 - - - -
716A TRP* 3.7 25.4 - - - -
732A LEU* 3.9 11.7 - - - -
735A ALA* 3.4 28.0 - - + -
736A CYS* 3.5 11.4 - - - -
740A TYR* 3.0 16.6 - - + +
742A PRO* 1.3 76.5 - - - +
744A VAL* 1.3 61.8 + - + +
746A ARG 3.4 0.2 + - - -
747A ALA* 2.8 31.4 + - - +
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A CYS* 3.9 24.9 - - + +
739A ASN* 3.7 35.4 - - - +
740A TYR 3.0 16.6 + - - +
741A GLN* 3.1 7.1 + - - +
743A CYS* 1.3 79.7 - - - +
745A GLN* 1.3 75.0 + - - +
747A ALA* 3.1 5.0 + - - +
748A GLU* 2.8 45.7 + - + +
774A VAL* 4.0 9.6 - - + +
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Residues in contact with GLN 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A GLN* 2.9 47.1 + - - +
742A PRO* 4.5 2.7 - - + +
744A VAL* 1.3 92.2 - - - +
746A ARG* 1.3 64.4 + - - +
748A GLU* 3.3 18.8 + - - +
749A GLY* 3.1 19.9 + - - -
752A ARG* 5.8 1.2 + - - -
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Residues in contact with ARG 746 (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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714A GLN 4.6 4.9 + - - -
715A THR* 5.7 0.8 - - - +
716A TRP* 3.0 63.9 - - + +
742A PRO 3.3 20.2 + - - +
743A CYS 3.8 3.1 - - - +
745A GLN* 1.3 72.3 - - - +
747A ALA* 1.3 66.9 + - - +
749A GLY* 3.4 2.1 + - - -
750A TYR* 3.1 40.9 + - + -
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Residues in contact with ALA 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A TRP* 3.9 12.9 - - + -
736A CYS* 4.0 7.6 - - - -
743A CYS 2.8 22.6 + - - +
744A VAL 3.4 5.2 - - - +
746A ARG* 1.3 75.7 - - - +
748A GLU* 1.3 60.4 + - - +
750A TYR* 3.4 2.8 + - - +
751A PHE* 3.0 23.0 + - - +
770A ALA 4.1 7.4 - - - +
771A VAL* 4.1 10.7 - - - +
774A VAL* 3.4 30.2 - - + +
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Residues in contact with GLU 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A VAL* 2.8 38.2 + - + +
745A GLN* 3.3 24.9 + - - +
747A ALA* 1.3 71.8 - - - +
749A GLY* 1.3 58.0 + - - +
751A PHE* 3.4 7.8 + - - +
752A ARG* 3.0 44.1 + - - +
774A VAL* 4.0 23.3 - - + +
775A GLY* 5.4 2.6 + - - -
777A GLN* 5.8 2.4 - - - +
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Residues in contact with GLY 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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745A GLN 3.1 13.7 + - - -
746A ARG* 3.9 3.4 - - - -
748A GLU* 1.3 74.2 - - - +
750A TYR* 1.3 63.6 + - - +
752A ARG* 3.4 23.0 + - - +
753A LYS* 3.1 28.4 + - - +
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Residues in contact with TYR 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A TRP* 3.5 54.6 + + + +
746A ARG* 3.1 35.0 + - + -
747A ALA 3.7 6.5 - - - +
749A GLY* 1.3 73.3 - - - +
751A PHE* 1.3 58.6 + - - +
753A LYS* 3.4 6.7 + - + +
754A TRP* 2.9 30.0 + - - +
763A LEU* 3.5 22.5 - - + +
764A PRO* 4.3 18.3 - - + +
767A VAL* 4.8 2.0 - - + -
771A VAL* 3.8 16.8 - - + -
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Residues in contact with PHE 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ALA 3.0 16.9 + - - +
748A GLU* 3.7 9.9 - - - +
749A GLY 3.3 0.2 - - - -
750A TYR* 1.3 75.5 - - - +
752A ARG* 1.3 55.3 + - + +
754A TRP* 3.0 31.6 + + - +
755A LYS* 2.7 53.5 + - + +
771A VAL* 3.7 24.0 - - + +
772A PHE* 4.6 1.3 - + - -
775A GLY* 3.5 30.7 - - - +
778A SER* 5.4 0.9 - - - -
781A GLY* 3.6 38.1 - - - -
784A PHE* 4.5 6.7 - + - -
785A LEU* 3.6 20.9 - - + -
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Residues in contact with ARG 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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745A GLN* 5.8 1.4 + - - -
748A GLU* 3.0 34.1 + - - +
749A GLY* 3.8 20.3 + - - +
751A PHE* 1.3 78.6 - - + +
753A LYS* 1.3 63.4 + - + +
755A LYS* 3.1 6.8 + - - +
756A GLU* 2.8 63.1 + - - +
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Residues in contact with LYS 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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749A GLY 3.1 19.8 + - - +
750A TYR* 3.8 8.5 - - + +
752A ARG* 1.3 81.3 - - + +
754A TRP* 1.3 61.9 + - - +
756A GLU* 3.8 18.0 - - - +
757A SER* 3.3 23.2 + - - -
761A LEU* 3.7 22.3 - - + +
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Residues in contact with TRP 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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750A TYR 2.9 18.7 + - - +
751A PHE* 3.4 22.9 - + - +
753A LYS* 1.3 76.6 - - - +
755A LYS* 1.3 60.9 + - - +
757A SER* 2.9 9.8 + - - -
759A GLY* 2.8 57.5 + - - -
761A LEU* 3.3 28.8 + - + -
763A LEU* 4.0 26.2 - - + +
772A PHE* 3.6 33.6 - + - -
784A PHE* 3.4 31.0 - + - -
785A LEU* 3.7 26.2 - - + -
788A LYS* 4.0 17.0 - - + -
797A GLU* 4.1 15.5 + - - -
801A ILE* 5.2 0.4 - - + -
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Residues in contact with LYS 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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751A PHE* 2.7 42.3 + - + +
752A ARG* 3.8 5.2 - - - +
754A TRP* 1.3 71.3 - - + +
756A GLU* 1.3 63.4 + - + +
757A SER 3.0 2.0 - - - -
758A ASN* 2.8 23.2 + - - -
780A GLU* 4.0 28.3 + - - +
781A GLY* 4.7 0.4 - - - -
784A PHE* 3.7 52.5 - - + -
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Residues in contact with GLU 756 (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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752A ARG* 2.8 49.1 + - + +
753A LYS* 3.8 21.4 - - + +
755A LYS* 1.3 74.1 - - + +
757A SER* 1.3 58.0 + - - +
758A ASN 3.2 1.7 + - - -
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Residues in contact with SER 757 (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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753A LYS 3.3 6.6 + - - -
754A TRP 2.9 15.1 + - - -
755A LYS 3.0 2.0 + - - -
756A GLU* 1.3 78.3 - - - +
758A ASN* 1.3 58.5 + - - +
759A GLY 3.7 0.2 - - - -
760A ASN* 2.9 43.9 + - - +
761A LEU* 3.0 39.9 + - - +
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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
------------------------------------------------------------
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