Contacts of the helix formed by residues 721 - 738 (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 721 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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720A GLY* 1.3 75.4 - - - +
722A VAL* 1.3 67.7 + - - +
723A SER* 3.7 9.3 - - - -
724A GLU* 2.7 36.7 + - - +
725A ARG* 3.0 23.3 + - - +
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Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A SER* 1.3 74.2 - - - +
723A SER* 1.3 58.2 + - - +
725A ARG* 3.5 8.0 + - - +
726A MET* 3.0 42.6 + - + +
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Residues in contact with SER 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670A ILE* 3.4 33.5 - - - +
721A SER* 3.7 11.2 + - - -
722A VAL* 1.3 78.0 - - - +
724A GLU* 1.3 64.5 + - - +
726A MET* 3.3 1.5 + - - -
727A LEU* 2.8 31.9 + - - +
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Residues in contact with GLU 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A GLN* 4.3 3.3 - - - +
719A GLU 4.7 1.1 - - - +
720A GLY* 3.0 15.2 - - - -
721A SER* 2.7 41.6 + - - +
723A SER* 1.3 77.1 - - - +
725A ARG* 1.3 59.8 + - - +
727A LEU* 3.8 8.0 - - - +
728A ARG* 3.0 35.2 + - - +
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Residues in contact with ARG 725 (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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718A ASP* 3.2 36.6 + - - +
719A GLU 3.2 17.9 - - - +
720A GLY 3.8 11.2 - - - +
721A SER 3.0 17.9 + - - +
722A VAL* 3.8 6.7 - - - +
724A GLU* 1.3 75.8 - - - +
726A MET* 1.3 60.6 + - - +
728A ARG* 3.5 5.4 - - - +
729A SER* 2.9 30.5 + - - -
765A VAL* 4.1 15.2 - - - +
766A ASP* 2.9 41.2 + - - +
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Residues in contact with MET 726 (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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670A ILE* 4.3 8.1 - - + -
674A PHE* 3.9 25.0 - - + -
722A VAL* 3.0 30.0 + - + +
723A SER* 3.8 4.0 - - - +
725A ARG* 1.3 77.3 - - - +
727A LEU* 1.3 59.4 + - - +
729A SER* 3.9 4.7 - - - -
730A GLN* 3.0 38.9 + - + +
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Residues in contact with LEU 727 (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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668A THR 3.8 22.9 - - - +
669A GLU 4.8 0.2 - - - -
670A ILE* 4.0 25.3 - - + +
673A VAL* 4.1 17.9 - - + -
674A PHE* 4.0 21.1 - - + -
710A LEU* 4.2 16.2 - - + -
714A GLN* 4.8 6.3 - - - +
723A SER 2.8 22.5 + - - +
724A GLU* 3.8 8.7 - - - +
726A MET* 1.3 69.5 - - - +
728A ARG* 1.3 67.4 - - - +
730A GLN* 3.9 0.9 - - - +
731A LEU* 3.0 47.7 + - + +
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Residues in contact with ARG 728 (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* 3.3 24.3 + - + +
715A THR* 3.0 48.3 + - - +
717A THR* 3.1 25.4 + - - +
719A GLU* 2.9 36.4 + - - +
720A GLY* 5.0 0.6 - - - -
724A GLU* 3.0 25.6 + - - +
725A ARG* 3.5 10.7 - - - +
727A LEU* 1.3 76.7 - - - +
729A SER* 1.3 65.0 + - - +
731A LEU* 3.5 0.5 - - - +
732A LEU* 3.0 43.5 + - + +
766A ASP* 2.7 38.0 + - + -
767A VAL* 4.8 0.9 - - - -
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Residues in contact with SER 729 (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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725A ARG 2.9 16.1 + - - -
726A MET* 3.9 6.7 - - - -
727A LEU 3.3 0.2 - - - -
728A ARG* 1.3 79.3 - - - +
730A GLN* 1.3 72.5 + - - +
732A LEU* 3.8 1.9 + - - +
733A LEU* 3.3 21.5 + - - +
765A VAL 5.1 1.0 + - - -
766A ASP* 3.0 36.6 + - - +
769A LEU* 4.3 15.8 - - - +
770A ALA* 5.2 1.9 + - - +
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Residues in contact with GLN 730 (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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674A PHE* 3.8 28.9 - - + -
677A LEU* 5.8 4.7 - - + +
726A MET* 3.0 29.4 + - + +
729A SER* 1.3 81.0 + - - +
731A LEU* 1.3 58.1 - - - +
733A LEU* 3.6 21.5 + - - +
734A LEU* 3.0 28.9 + - - +
769A LEU* 4.1 18.6 - - - +
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Residues in contact with LEU 731 (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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673A VAL* 4.3 15.5 - - + -
674A PHE* 5.6 1.3 - - + -
677A LEU* 5.3 4.7 - - + -
707A LEU* 4.4 19.1 - - + -
710A LEU* 3.7 27.1 - - + +
711A ILE* 4.0 23.3 - - + +
714A GLN* 3.8 20.2 - - + +
727A LEU* 3.0 48.0 + - + +
728A ARG* 3.5 3.8 - - - +
730A GLN* 1.3 74.9 - - - +
732A LEU* 1.3 61.9 + - - +
734A LEU* 3.3 7.0 + - + +
735A ALA* 2.9 30.2 + - - +
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Residues in contact with LEU 732 (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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711A ILE* 4.4 8.3 - - + +
714A GLN* 4.1 17.9 - - + -
715A THR 4.2 4.3 - - - +
716A TRP* 3.8 45.8 - - + +
728A ARG* 3.0 32.1 + - + +
729A SER* 4.1 2.9 - - - +
731A LEU* 1.3 72.6 - - - +
733A LEU* 1.3 65.8 + - - +
735A ALA* 3.4 4.7 + - - +
736A CYS* 3.0 29.5 + - - -
743A CYS* 3.9 11.0 - - - -
766A ASP 4.8 0.7 - - - +
767A VAL* 3.8 27.4 - - + -
770A ALA* 3.9 14.4 - - + -
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Residues in contact with LEU 733 (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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729A SER 3.3 16.1 + - - +
730A GLN* 3.6 23.3 - - - +
731A LEU 3.3 0.6 - - - -
732A LEU* 1.3 78.9 - - - +
734A LEU* 1.3 57.9 + - - +
736A CYS* 3.0 3.1 + - + +
737A VAL* 2.9 43.4 + - + +
769A LEU* 3.9 29.4 - - + +
770A ALA* 3.9 10.4 - - + +
773A ALA* 3.8 28.9 - - + -
803A PHE* 4.0 28.7 - - + -
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Residues in contact with LEU 734 (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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677A LEU* 4.1 19.5 - - + -
681A ILE* 4.8 8.1 - - + -
684A TYR* 4.5 5.2 - - - +
703A LEU* 4.4 10.5 - - + -
704A ILE* 4.2 13.7 - - + -
707A LEU* 3.7 29.6 - - + -
711A ILE* 4.8 4.3 - - + -
730A GLN 3.0 15.7 + - - +
731A LEU* 3.5 9.6 - - + +
733A LEU* 1.3 80.0 - - - +
735A ALA* 1.3 64.1 + - - +
737A VAL* 3.5 7.1 + - + +
738A HIS* 3.2 52.6 + - + +
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Residues in contact with ALA 735 (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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704A ILE* 4.2 11.2 - - - -
711A ILE* 3.9 16.2 - - + -
731A LEU 2.9 16.5 + - - +
732A LEU 3.5 1.3 - - - +
733A LEU 3.2 0.2 - - - -
734A LEU* 1.3 78.2 - - - +
736A CYS* 1.3 58.3 + - - +
738A HIS* 3.4 1.6 + - - +
739A ASN 3.1 7.4 + - - -
740A TYR* 2.9 34.2 + - + +
743A CYS* 3.4 32.5 - - + -
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Residues in contact with CYS 736 (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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716A TRP* 4.5 2.5 - - - -
732A LEU 3.0 25.2 + - - +
733A LEU* 3.0 7.1 + - + +
735A ALA* 1.3 73.1 - - - +
737A VAL* 1.3 65.5 + - - +
738A HIS 3.1 1.3 - - - -
739A ASN* 3.0 20.3 + - - +
743A CYS* 3.5 37.9 - - - -
744A VAL* 3.9 9.6 - - + +
747A ALA* 4.0 6.7 - - - -
770A ALA* 4.2 11.7 - - - +
773A ALA* 5.8 0.9 - - + -
774A VAL* 3.5 31.5 - - + +
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Residues in contact with VAL 737 (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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684A TYR* 5.2 2.9 - - + +
700A LYS* 5.9 1.5 - - - -
733A LEU* 2.9 40.1 + - + +
734A LEU* 3.8 8.1 - - + +
736A CYS* 1.3 75.1 - - - +
738A HIS* 1.3 75.2 + - + +
739A ASN* 3.3 9.8 + - - -
773A ALA* 5.3 6.2 - - + +
803A PHE* 5.2 4.7 - - + -
807A ARG* 3.6 35.7 - - + +
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Residues in contact with HIS 738 (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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684A TYR* 3.0 41.3 + + - -
700A LYS* 3.7 37.9 - - + +
703A LEU* 4.2 5.9 - - + +
704A ILE* 3.6 37.5 - - + +
734A LEU* 3.2 43.2 + - + +
735A ALA 3.4 0.6 + - - +
736A CYS 3.1 0.8 - - - -
737A VAL* 1.3 88.5 + - + +
739A ASN* 1.3 72.8 + - - +
740A TYR* 3.4 1.6 + - - -
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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
------------------------------------------------------------
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