Contacts of the helix formed by residues 748 - 765 (chain B) in PDB entry 5JO3
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 748 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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745B ASN* 3.0 24.1 + - - +
746B LEU 3.7 0.6 - - - +
747B GLU* 1.3 76.7 - - - +
749B PRO* 1.3 66.2 - - - +
750B HIS* 3.1 17.2 + - - +
751B GLU* 3.0 40.9 + - + +
752B LYS* 2.8 28.2 + - - +
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Residues in contact with PRO 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747B GLU 3.4 8.7 - - - +
748B ASP* 1.3 89.1 - - - +
750B HIS* 1.3 61.4 + - - +
752B LYS* 3.3 8.4 + - + +
753B GLU* 3.0 24.1 + - - +
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Residues in contact with HIS 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B ARG* 3.9 23.8 + - - -
734B GLU* 2.7 34.6 + - - -
738B LEU* 5.8 0.2 - - + -
748B ASP* 3.1 11.7 + - - +
749B PRO* 1.3 78.0 - - - +
751B GLU* 1.3 68.7 + - + +
753B GLU* 3.3 9.6 + - - +
754B LEU* 3.0 28.0 + - + +
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Residues in contact with GLU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B LEU* 3.7 27.2 - - + +
743B GLN 3.4 13.0 - - - +
744B PHE* 3.2 25.6 - - + -
745B ASN* 2.7 48.0 + - - +
746B LEU* 4.9 0.7 - - - -
748B ASP* 3.0 22.7 + - - +
750B HIS* 1.3 79.6 - - + +
752B LYS* 1.3 60.1 + - - +
754B LEU* 3.3 7.9 + - - +
755B PHE* 2.9 30.3 + - - +
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Residues in contact with LYS 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637B LYS 3.6 23.0 + - - -
638B LEU* 3.9 15.1 - - + +
639B THR* 4.6 7.1 - - - +
642B GLU* 2.9 43.6 + - - +
746B LEU* 3.5 46.6 + - + +
748B ASP 2.8 8.7 + - - +
749B PRO* 3.6 11.2 - - + +
751B GLU* 1.3 77.1 - - - +
753B GLU* 1.3 63.0 + - - +
755B PHE* 3.2 3.9 + - + +
756B LEU* 2.9 34.8 + - + +
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Residues in contact with GLU 753 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B GLN* 3.5 52.3 + - + +
731B ARG* 2.7 42.8 + - - -
749B PRO 3.0 14.2 + - - +
750B HIS* 3.6 13.3 + - - +
752B LYS* 1.3 75.7 - - - +
754B LEU* 1.3 62.8 + - - +
756B LEU* 3.2 14.3 + - + +
757B ALA* 3.0 22.3 + - - +
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Residues in contact with LEU 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731B ARG* 3.7 56.8 - - + +
734B GLU* 3.8 23.6 - - + +
735B PHE* 3.7 38.4 - - + +
738B LEU* 3.9 12.8 - - + -
744B PHE* 5.7 0.2 - - + -
750B HIS* 3.0 15.7 + - - +
751B GLU* 3.5 9.9 - - - +
753B GLU* 1.3 75.9 - - - +
755B PHE* 1.3 63.5 + - - +
757B ALA* 3.2 4.7 + - - +
758B MET* 3.1 36.0 + - + +
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Residues in contact with PHE 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634B ILE* 4.0 29.6 - - + -
637B LYS* 5.7 0.4 - - + -
638B LEU* 4.5 9.2 - - + -
735B PHE* 4.1 21.9 - + - -
744B PHE* 3.9 12.6 - + + -
746B LEU* 3.8 26.2 - - + -
751B GLU 2.9 17.6 + - - +
752B LYS* 3.5 3.6 - - + +
754B LEU* 1.3 76.6 - - - +
756B LEU* 1.3 67.5 + - + +
758B MET* 3.1 6.9 + - + +
759B LEU* 2.8 42.0 + - + +
832B LEU* 3.9 27.1 - - + -
835B VAL* 3.7 29.2 - - + -
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Residues in contact with LEU 756 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B LEU* 4.0 25.1 - - + -
642B GLU* 4.0 30.1 - - + +
646B LEU* 3.7 35.2 - - + +
715B ILE* 4.2 20.6 - - + -
719B ALA* 5.9 3.8 - - + -
752B LYS* 2.9 24.9 + - + +
753B GLU* 3.2 13.9 + - + +
755B PHE* 1.3 79.3 - - + +
757B ALA* 1.3 58.4 + - - +
759B LEU* 3.6 6.1 - - + +
760B MET* 2.9 34.4 + - - +
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Residues in contact with ALA 757 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B GLN 5.3 1.1 - - - +
719B ALA* 5.7 0.7 - - - +
722B ALA* 3.6 27.9 - - + +
731B ARG* 3.9 20.2 - - - +
753B GLU* 3.0 15.7 + - - +
754B LEU* 3.2 9.4 + - - +
756B LEU* 1.3 78.3 - - - +
758B MET* 1.3 71.2 + - + +
760B MET* 3.3 5.5 + - - +
761B THR* 3.2 24.4 + - - -
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Residues in contact with MET 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727B LEU 5.1 0.2 - - - +
728B TYR* 3.8 42.0 - - + +
731B ARG* 4.3 6.5 - - + -
732B ARG* 3.9 26.0 - - - +
735B PHE* 3.4 47.3 - - + -
736B PHE* 5.2 0.2 - - - -
754B LEU* 3.1 26.8 + - + +
755B PHE* 3.1 8.0 + - + +
757B ALA* 1.3 81.9 - - + +
759B LEU* 1.3 59.9 + - - +
761B THR* 3.2 6.8 + - - +
762B ALA* 2.9 28.3 + - - +
828B LEU* 3.7 12.3 - - + +
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Residues in contact with LEU 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B MET* 3.8 25.1 - - + -
628B ALA* 4.2 13.0 - - + -
629B LEU* 5.1 1.6 - - + -
634B ILE* 3.7 44.6 - - + -
638B LEU* 4.7 0.9 - - + -
646B LEU* 4.2 17.3 - - + -
755B PHE* 2.8 29.9 + - + +
756B LEU* 3.6 6.3 - - + +
758B MET* 1.3 73.2 - - - +
760B MET* 1.3 65.0 + - - +
762B ALA* 3.2 5.0 + - + +
763B CYS* 2.9 30.3 + - - -
832B LEU* 4.1 20.0 - - + -
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Residues in contact with MET 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B THR* 4.9 3.9 - - + +
625B MET* 3.6 24.7 - - - -
646B LEU* 3.8 14.4 - - + +
649B ALA* 3.9 24.7 - - + +
650B ALA* 4.0 15.5 - - - +
653B HIS* 4.3 3.4 - - + -
719B ALA* 3.5 42.4 - - + +
722B ALA* 4.3 2.5 - - + -
723B THR* 3.7 21.9 - - + +
756B LEU 2.9 17.6 + - - +
757B ALA 3.4 9.2 - - - +
759B LEU* 1.3 76.9 - - - +
761B THR* 1.3 58.1 + - - +
763B CYS* 3.2 3.7 + - - +
764B ASP* 2.8 30.3 + - - +
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Residues in contact with THR 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722B ALA 3.5 16.5 + - - -
723B THR* 4.9 3.1 - - - +
725B LEU* 4.3 5.6 - - + -
728B TYR* 3.7 35.8 - - + +
757B ALA 3.2 11.6 + - - -
758B MET* 3.2 7.8 + - - +
760B MET* 1.3 77.4 - - - +
762B ALA* 1.3 64.5 + - - +
764B ASP* 3.2 6.8 + - + +
765B LEU* 3.0 41.8 + - + +
828B LEU* 3.5 18.8 - - + -
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Residues in contact with ALA 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624B CYS* 4.5 2.3 - - - -
758B MET 2.9 14.9 + - - +
759B LEU* 3.2 11.9 + - + +
761B THR* 1.3 75.9 - - - +
763B CYS* 1.3 61.7 + - - +
766B SER* 3.4 8.8 + - - -
828B LEU* 3.6 18.5 - - + +
829B TYR* 2.7 43.4 + - + -
832B LEU* 4.0 21.8 - - + -
842B LEU* 5.4 0.9 - - + -
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Residues in contact with CYS 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B THR* 3.7 33.1 + - + +
624B CYS* 3.8 15.5 - - + -
625B MET* 3.5 48.2 - - + -
628B ALA* 4.8 1.6 - - - -
759B LEU* 2.9 30.1 + - - +
760B MET 3.7 3.1 - - - +
762B ALA* 1.3 78.1 - - - +
764B ASP* 1.3 63.4 + - - +
766B SER* 2.8 22.5 + - - -
842B LEU* 6.4 0.2 - - - -
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Residues in contact with ASP 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B TYR* 3.7 7.3 + - - -
617B HIS* 2.9 23.4 + - - -
621B THR* 3.8 10.0 - - + +
653B HIS* 3.0 7.4 + - - +
723B THR* 3.6 29.5 - - + +
760B MET 2.8 17.1 + - - +
761B THR* 3.6 9.8 - - + +
763B CYS* 1.3 76.9 - - - +
765B LEU* 1.3 69.0 + - + +
766B SER 3.3 0.9 + - - -
767B ALA 5.0 0.3 + - - -
901B ZN 2.1 36.3 - - - -
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Residues in contact with LEU 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B TYR* 5.9 0.2 - - - +
725B LEU* 4.3 10.5 - - + -
761B THR* 3.0 35.3 + - + +
763B CYS 3.2 0.2 - - - -
764B ASP* 1.3 85.7 - - + +
766B SER* 1.3 58.5 + - - +
767B ALA 3.2 2.9 - - - -
768B ILE* 2.9 32.7 + - + +
820B PHE* 3.9 18.8 - - + -
824B ILE* 3.6 30.3 - - + +
825B CYS* 4.3 10.8 - - - -
828B LEU* 4.7 6.7 - - + -
829B TYR* 3.4 12.3 - - + +
903B 6LK 3.2 22.4 - - + +
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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