Contacts of the helix formed by residues 724 - 741 (chain A) in PDB entry 3JWR
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 ASP 724 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A ASN* 3.9 9.0 + - - +
679A SER* 2.5 36.0 + - - +
682A GLU* 3.7 24.4 - - + +
721A LEU 2.9 16.2 + - - +
722A ALA 3.5 3.9 - - - +
723A THR* 1.3 77.3 + - - +
725A LEU* 1.3 68.4 + - - +
726A ALA* 3.1 23.8 + - - +
727A LEU* 2.9 21.2 + - + +
728A TYR* 3.1 9.2 + - - -
71C GLU* 6.1 0.7 - - - +
86C ILE* 5.4 0.7 - - - +
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Residues in contact with LEU 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A THR* 3.4 16.4 - - - +
724A ASP* 1.3 73.6 + - - +
726A ALA* 1.3 57.5 + - - +
728A TYR* 3.4 17.0 + - + +
729A ILE* 3.0 32.7 + - - +
761A THR* 5.5 4.7 - - + +
764A ASP* 4.3 11.0 - - - +
765A LEU* 4.5 15.3 - - + -
820A PHE* 4.9 8.1 - - + -
824A VAL* 4.4 25.4 - - + -
901A IBM 5.6 17.7 - - + -
86C ILE* 3.9 33.0 - - + -
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Residues in contact with ALA 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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724A ASP* 3.0 18.9 + - - +
725A LEU* 1.3 77.0 - - - +
727A LEU* 1.3 63.8 + - + +
729A ILE* 3.4 2.6 + - - +
730A LYS* 2.9 29.1 + - - +
71C GLU* 5.2 8.3 - - + -
73C PHE* 3.5 26.0 - - + -
86C ILE* 3.6 17.6 - - + +
87C ILE* 4.8 7.9 - - - +
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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
----------------------------------------------------------
678A HIS* 6.5 0.4 - - + -
679A SER* 3.6 22.9 - - - +
721A LEU* 3.3 37.0 - - + +
722A ALA* 4.4 7.6 - - - +
724A ASP* 2.9 10.3 + - + +
726A ALA* 1.3 76.2 - - + +
728A TYR* 1.3 68.3 + - - +
730A LYS* 3.5 32.5 - - + -
731A ARG* 3.0 38.1 + - + +
758A MET* 5.7 0.2 - - - -
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Residues in contact with TYR 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ALA 4.5 3.0 + - - +
724A ASP 3.1 8.3 + - - +
725A LEU* 3.4 16.6 - - + +
726A ALA 3.3 0.2 - - - -
727A LEU* 1.3 79.1 - - - +
729A ILE* 1.3 69.2 + - + +
732A ARG* 2.9 79.1 + - + +
736A PHE* 4.0 4.4 - + - -
758A MET* 3.9 24.4 - - + +
761A THR* 3.6 43.1 - - + +
824A VAL* 2.6 39.9 + - + -
827A GLN* 4.7 0.2 - - - +
828A LEU* 3.2 24.2 + - + +
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Residues in contact with ILE 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 LEU 3.0 17.0 + - - +
726A ALA* 3.7 5.6 - - - +
727A LEU 3.1 0.2 - - - -
728A TYR* 1.3 85.1 - - + +
730A LYS* 1.3 58.5 + - - +
731A ARG 3.0 9.3 + - - -
732A ARG* 3.2 53.2 + - - +
733A GLY 4.5 2.4 + - - -
823A PHE* 4.0 17.3 - - + -
824A VAL* 4.9 1.3 - - + -
73C PHE* 4.3 9.9 - - + -
77C GLU* 4.4 17.3 - - - +
81C LEU* 4.0 20.0 - - + -
86C ILE* 4.2 16.8 - - + -
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Residues in contact with LYS 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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726A ALA 2.9 15.0 + - - +
727A LEU* 3.2 34.0 + - + +
729A ILE* 1.3 76.5 - - - +
731A ARG* 1.3 71.8 + - + +
734A GLU* 5.6 0.2 - - - +
72C ALA 5.9 2.5 - - - +
73C PHE* 3.6 23.1 - - + -
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Residues in contact with ARG 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A LEU* 3.0 27.1 + - - +
730A LYS* 1.3 101.4 - - + +
732A ARG* 1.3 67.2 + - - +
733A GLY 3.1 3.9 + - - -
734A GLU* 3.2 34.1 + - - +
735A PHE 3.7 1.7 + - - -
750A HIS* 3.6 12.3 - - - -
753A GLU* 3.4 29.9 + - - +
754A LEU* 3.4 34.5 - - + +
757A ALA* 4.3 18.5 - - - +
758A MET* 4.0 12.8 - - + -
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Residues in contact with ARG 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A TYR* 2.9 61.2 + - + +
729A ILE* 3.2 40.5 + - - +
731A ARG* 1.3 77.8 - - - +
733A GLY* 1.3 67.8 + - - +
735A PHE* 3.0 4.8 + - - +
736A PHE* 2.8 47.6 + - + -
758A MET* 3.8 16.1 - - - +
823A PHE* 2.8 44.1 + - - -
824A VAL* 3.9 0.8 + - - +
827A GLN* 4.6 8.6 - - - +
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Residues in contact with GLY 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 ILE 4.5 2.8 + - - -
730A LYS 5.4 0.4 - - - -
731A ARG 3.1 1.6 + - - -
732A ARG* 1.3 85.7 - - - +
734A GLU* 1.3 67.2 + - - +
736A PHE* 3.0 17.0 + - - +
737A GLU* 3.3 18.7 + - - +
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Residues in contact with GLU 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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731A ARG* 3.2 29.0 + - - +
733A GLY* 1.3 75.7 - - - +
735A PHE* 1.3 62.8 + - + +
737A GLU* 3.2 13.8 + - - +
738A LEU* 3.3 26.9 + - + +
750A HIS* 3.0 30.4 + - - -
754A LEU* 4.7 13.4 - - + +
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Residues in contact with PHE 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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731A ARG 3.7 0.4 + - - +
732A ARG 3.0 8.0 + - - +
734A GLU* 1.3 75.3 - - - +
736A PHE* 1.3 78.6 + + - +
737A GLU 3.1 5.8 + - - -
738A LEU* 3.5 6.1 + - - +
739A ILE* 3.3 32.4 + - + +
744A PHE* 4.2 24.2 - + - -
754A LEU* 3.4 37.2 - - + -
755A PHE* 4.2 18.2 - + - -
758A MET* 3.7 34.1 - - + -
828A LEU* 4.7 4.5 - - + -
831A ALA* 3.5 32.8 - - + -
832A LEU* 4.9 2.0 - - - -
835A VAL* 4.6 9.2 - - + -
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Residues in contact with PHE 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A TYR* 4.0 10.1 - + - -
732A ARG* 2.8 48.4 + - + +
733A GLY* 3.0 9.2 + - - +
735A PHE* 1.3 92.3 - + - +
737A GLU* 1.3 66.8 + - - +
739A ILE* 3.7 6.3 - - - +
740A ARG* 3.0 26.5 + - - +
827A GLN* 3.0 63.3 - - + +
828A LEU* 3.9 10.1 - - + -
831A ALA* 3.8 16.6 - - + -
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Residues in contact with GLU 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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733A GLY* 3.5 14.3 - - - +
734A GLU* 3.2 8.7 + - - +
735A PHE 3.1 0.6 - - - -
736A PHE* 1.3 90.1 - - - +
738A LEU* 1.3 63.1 + - + +
739A ILE 3.0 1.8 - - - -
740A ARG* 2.9 45.5 + - - +
741A LYS* 2.6 46.3 + - + +
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Residues in contact with LEU 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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734A GLU* 3.3 26.9 - - + +
735A PHE* 3.5 4.9 + - - +
737A GLU* 1.3 77.2 - - + +
739A ILE* 1.3 59.2 + - - +
742A ASN 3.8 0.2 - - - -
743A GLN* 2.8 28.5 + - + +
744A PHE* 2.7 41.8 + - + +
750A HIS* 6.4 0.9 - - + +
751A GLN* 3.3 37.9 - - + +
754A LEU* 4.3 19.7 - - + -
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Residues in contact with ILE 739 (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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735A PHE* 3.3 27.9 + - + +
736A PHE* 3.7 10.3 - - - +
737A GLU 3.0 0.2 - - - -
738A LEU* 1.3 74.2 - - - +
740A ARG* 1.3 70.9 + - - +
742A ASN* 2.8 16.8 + - - -
744A PHE* 3.9 21.5 - - + -
831A ALA* 4.2 16.4 - - + +
834A HIS* 3.9 36.3 - - + +
835A VAL* 3.7 30.5 - - + +
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Residues in contact with ARG 740 (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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736A PHE 3.0 17.3 + - - +
737A GLU* 2.9 34.1 + - - +
739A ILE* 1.3 82.1 - - - +
741A LYS* 1.3 91.2 + - - +
742A ASN* 3.1 5.2 + - - +
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Residues in contact with LYS 741 (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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737A GLU* 2.6 27.3 + - + +
740A ARG* 1.3 107.7 - - - +
742A ASN* 1.3 70.7 + - - +
743A GLN* 2.8 43.3 + - + +
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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