Contacts of the helix formed by residues 721 - 748 (chain U) in PDB entry 4UJ3
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 MET 721 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720U LEU* 1.3 75.0 - - - +
722U GLU* 1.3 63.6 + - + +
723U ALA 3.3 2.9 - - - -
724U ILE* 3.0 49.7 - - + +
725U GLN* 3.3 13.9 + - + +
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Residues in contact with GLU 722 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720U LEU 3.3 5.6 - - - +
721U MET* 1.3 81.8 - - + +
723U ALA* 1.3 62.5 + - - +
725U GLN* 3.8 10.1 - - + +
726U LYS* 3.2 23.2 + - - +
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Residues in contact with ALA 723 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720U LEU* 4.0 11.1 + - - +
721U MET 3.3 0.8 - - - -
722U GLU* 1.3 79.7 - - - +
724U ILE* 1.3 60.3 + - + +
726U LYS* 3.6 5.9 + - - +
727U GLN* 3.3 24.5 + - - +
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Residues in contact with ILE 724 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720U LEU 4.7 4.5 + - - +
721U MET* 3.0 46.2 - - + +
723U ALA* 1.3 77.5 - - + +
725U GLN* 1.3 66.7 + - - +
726U LYS 3.3 0.4 - - - -
727U GLN* 3.3 24.5 + - + +
728U GLU* 3.5 10.9 + - - +
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Residues in contact with GLN 725 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721U MET* 3.3 25.7 + - + +
722U GLU* 3.8 10.1 - - - +
723U ALA 3.3 0.2 - - - -
724U ILE* 1.3 87.3 - - + +
726U LYS* 1.3 62.0 + - - +
728U GLU* 3.5 18.7 + - - +
729U GLU* 4.0 3.5 + - - +
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Residues in contact with LYS 726 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722U GLU 3.2 18.1 + - - +
723U ALA* 3.8 6.3 - - - +
724U ILE 3.3 0.2 - - - -
725U GLN* 1.3 76.0 - - - +
727U GLN* 1.3 59.1 + - - +
728U GLU 3.2 0.9 - - - -
729U GLU* 3.0 27.9 + - + +
730U ILE* 3.1 14.0 + - + +
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Residues in contact with GLN 727 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723U ALA 3.3 14.7 + - - +
724U ILE* 3.5 21.9 - - + +
725U GLN 3.2 0.4 - - - -
726U LYS* 1.3 75.5 - - - +
728U GLU* 1.3 61.1 + - - +
729U GLU 3.1 1.3 - - - -
730U ILE* 3.0 44.9 - - + +
731U ASN* 3.2 15.4 + - - +
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Residues in contact with GLU 728 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724U ILE 3.5 8.7 + - - +
725U GLN* 3.7 12.6 - - - +
726U LYS 3.2 0.6 - - - -
727U GLN* 1.3 78.4 - - - +
729U GLU* 1.3 59.6 + - - +
731U ASN* 3.9 4.5 + - - +
732U PHE* 3.3 23.6 + - - +
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Residues in contact with GLU 729 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725U GLN 4.0 2.4 + - - +
726U LYS* 3.0 20.4 + - + +
728U GLU* 1.3 79.7 - - - +
730U ILE* 1.3 60.8 + - + +
732U PHE* 3.8 9.7 + - + +
733U ARG* 3.5 27.1 + - - +
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Residues in contact with ILE 730 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726U LYS* 3.2 16.8 - - + +
727U GLN* 3.0 46.4 - - + +
729U GLU* 1.3 76.0 - - + +
731U ASN* 1.3 86.0 + - - +
733U ARG* 3.2 13.5 + - - +
734U LEU* 3.1 27.3 + - + +
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Residues in contact with ASN 731 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727U GLN* 3.2 17.3 + - - +
728U GLU* 4.3 5.2 - - - +
730U ILE* 1.3 93.9 - - - +
732U PHE* 1.3 63.5 + - - +
734U LEU* 3.0 19.2 + - - +
735U GLN* 2.9 23.7 + - - +
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Residues in contact with PHE 732 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728U GLU 3.3 17.3 + - - +
729U GLU* 3.9 9.2 - - + +
730U ILE 3.3 0.6 - - - -
731U ASN* 1.3 76.9 - - - +
733U ARG* 1.3 77.3 + - + +
735U GLN* 3.1 7.4 + - + +
736U ASP* 2.8 43.6 + - + +
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Residues in contact with ARG 733 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729U GLU 3.5 14.0 + - - +
730U ILE* 3.2 13.3 + - - +
731U ASN 3.2 0.6 - - - -
732U PHE* 1.3 94.3 - - + +
734U LEU* 1.3 62.7 + - - +
736U ASP* 3.4 5.9 + - - +
737U TYR* 3.0 23.7 + - - +
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Residues in contact with LEU 734 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730U ILE* 3.1 16.2 + - + +
731U ASN* 3.0 23.9 + - - +
733U ARG* 1.3 78.5 - - - +
735U GLN* 1.3 60.1 + - - +
737U TYR* 3.4 12.5 - - + +
738U ILE* 3.2 30.5 + - + +
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Residues in contact with GLN 735 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S ILE* 4.8 14.0 - - - +
45S GLY* 4.9 9.1 - - - +
731U ASN 2.9 11.6 + - - +
732U PHE* 3.1 9.6 + - + +
734U LEU* 1.3 73.4 - - - +
736U ASP* 1.3 64.5 - - - +
737U TYR 3.0 1.8 - - - -
738U ILE* 3.1 24.6 + - - +
739U ASP* 2.9 49.0 + - - +
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Residues in contact with ASP 736 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732U PHE* 2.8 41.6 + - + +
733U ARG* 3.9 6.3 - - - +
735U GLN* 1.3 73.7 - - - +
737U TYR* 1.3 61.0 + - - +
739U ASP* 3.7 8.8 + - - +
740U ARG* 3.5 23.6 + - - +
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Residues in contact with TYR 737 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733U ARG 3.0 12.8 + - - +
734U LEU* 3.4 17.7 - - + +
735U GLN 3.0 0.4 - - - -
736U ASP* 1.3 76.0 - - - +
738U ILE* 1.3 72.3 + - + +
739U ASP 3.3 0.2 + - - -
740U ARG* 3.4 34.1 + - - +
741U ILE* 3.2 53.0 + - + +
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Residues in contact with ILE 738 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44S ILE* 5.2 17.0 - - + -
45S GLY* 4.3 16.4 - - - -
734U LEU* 3.2 19.7 - - + +
735U GLN* 3.1 29.2 + - - +
737U TYR* 1.3 83.3 - - + +
739U ASP* 1.3 63.2 + - - +
741U ILE* 4.0 4.1 - - - +
742U ILE* 3.0 44.8 + - + +
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Residues in contact with ASP 739 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S ALA* 4.1 21.4 - - - +
76S ILE* 3.7 20.9 - - + +
735U GLN* 2.9 39.2 + - - +
736U ASP* 3.8 9.0 - - - +
737U TYR 3.2 0.2 - - - -
738U ILE* 1.3 78.6 - - - +
740U ARG* 1.3 61.9 + - - +
742U ILE* 3.7 4.5 - - - +
743U VAL* 3.0 26.2 + - - +
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Residues in contact with ARG 740 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S ILE* 4.3 4.6 - - - +
736U ASP 3.5 9.8 + - - +
737U TYR* 3.4 39.9 + - - +
739U ASP* 1.3 78.4 - - - +
741U ILE* 1.3 70.5 + - - +
743U VAL* 3.2 11.4 + - + +
744U ALA* 3.1 21.1 + - + +
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Residues in contact with ILE 741 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737U TYR* 3.2 52.5 + - + +
738U ILE* 4.0 6.3 - - - +
740U ARG* 1.3 86.2 - - + +
742U ILE* 1.3 54.8 + - + +
744U ALA* 3.1 11.0 + - + +
745U ILE* 2.8 59.9 + - + +
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Residues in contact with ILE 742 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45S GLY* 4.5 7.4 - - - -
46S VAL* 3.9 31.9 - - + +
738U ILE* 3.0 37.9 + - + +
739U ASP* 3.7 5.8 - - - +
741U ILE* 1.3 74.2 - - + +
743U VAL* 1.3 66.9 + - + +
745U ILE* 3.2 10.5 + - + +
746U MET* 3.0 43.5 + - + +
753U LEU* 3.6 33.0 - - + -
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Residues in contact with VAL 743 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S ILE* 3.1 46.7 - - + -
79S ALA* 5.3 7.4 - - + +
739U ASP 3.0 17.5 + - - +
740U ARG* 3.3 9.4 - - - +
742U ILE* 1.3 78.9 - - + +
744U ALA* 1.3 62.3 + - - +
746U MET* 4.1 9.1 - - + +
747U GLU* 3.1 25.7 + - + +
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Residues in contact with ALA 744 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740U ARG* 3.1 9.2 + - + +
741U ILE* 3.1 18.0 + - + +
743U VAL* 1.3 80.3 - - - +
745U ILE* 1.3 63.0 + - + +
747U GLU* 3.2 14.1 + - - +
748U THR* 3.3 22.7 + - + +
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Residues in contact with ILE 745 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741U ILE* 2.8 43.7 + - + +
742U ILE* 3.2 11.2 + - + +
744U ALA* 1.3 74.5 - - + +
746U MET* 1.3 56.7 + - - +
748U THR* 4.7 3.1 - - - -
749U ASN 3.0 40.6 + - - +
750U PRO* 3.1 1.5 - - + -
752U ILE* 3.6 45.5 - - + -
753U LEU* 3.9 30.5 - - + -
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Residues in contact with MET 746 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S VAL* 4.5 8.5 - - + -
65S TRP* 3.6 32.3 - - + -
76S ILE* 5.6 4.5 - - + +
79S ALA* 3.2 50.5 - - + +
80S TYR* 4.1 6.7 - - + +
82S ARG* 5.4 3.5 + - - +
742U ILE* 3.0 32.9 + - + +
743U VAL* 4.1 4.5 - - + +
745U ILE* 1.3 73.2 - - - +
747U GLU* 1.3 64.6 + - - +
748U THR 3.1 3.3 + - - -
750U PRO* 3.5 24.1 - - + +
753U LEU* 3.7 21.5 - - + -
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Residues in contact with GLU 747 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79S ALA* 5.9 0.4 - - - +
82S ARG* 5.1 12.5 - - - +
743U VAL* 3.1 22.2 + - + +
744U ALA* 3.2 7.8 + - - +
746U MET* 1.3 75.6 - - - +
748U THR* 1.3 65.4 + - + +
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Residues in contact with THR 748 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744U ALA* 3.3 18.5 + - + +
745U ILE* 4.1 2.6 + - - -
746U MET 3.1 2.2 - - - -
747U GLU* 1.3 88.1 - - + +
749U ASN* 1.3 79.9 + - - +
750U PRO* 3.3 11.2 - - - +
752U ILE* 6.1 0.2 - - - +
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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