Contacts of the helix formed by residues 734 - 754 (chain A) in PDB entry 3N57
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 THR 734 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LEU* 3.9 22.1 - - + +
539A PRO 5.4 0.7 + - - -
541A GLU* 3.7 14.9 - - - +
561A PHE* 3.6 3.6 - - - -
563A GLN* 4.5 3.6 + - - -
733A ILE* 1.3 79.8 + - - +
735A LYS* 1.3 51.6 + - - +
736A GLN* 3.2 29.9 + - + +
737A ALA* 2.9 29.8 + - + +
738A ALA* 2.8 34.0 + - - +
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Residues in contact with LYS 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 3.0 21.4 + - - +
543A GLU* 4.3 27.1 + - - -
551A ILE* 4.0 38.9 + - + +
561A PHE* 3.3 21.4 - - + -
734A THR* 1.3 69.1 - - - +
736A GLN* 1.3 72.3 + - - +
738A ALA* 3.0 5.2 + - - +
739A LEU* 3.0 40.0 + - + +
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Residues in contact with GLN 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLU* 2.4 37.7 + - - +
734A THR* 3.2 24.5 + - + +
735A LYS* 1.3 78.7 - - - +
737A ALA* 1.3 55.9 + - - +
739A LEU* 3.5 13.3 - - - +
740A GLY* 2.9 24.6 + - - -
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Residues in contact with ALA 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A LEU* 6.0 1.6 - - + -
733A ILE* 3.9 11.4 - - + -
734A THR* 2.9 34.9 + - + +
736A GLN* 1.3 73.6 - - - +
738A ALA* 1.3 60.1 + - - +
740A GLY* 3.3 4.0 + - - +
741A ILE* 2.9 33.3 + - + +
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Residues in contact with ALA 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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551A ILE* 4.2 8.5 - - + -
559A LEU* 4.2 3.8 - - + -
561A PHE* 3.6 26.9 - - + -
729A LEU* 3.8 23.8 - - + +
733A ILE* 4.3 6.7 - - + +
734A THR 2.8 15.2 + - - +
735A LYS 3.3 9.4 - - - +
737A ALA* 1.3 69.8 - - - +
739A LEU* 1.3 58.8 + - - +
741A ILE* 2.8 24.1 + - - +
742A MET* 3.0 12.8 + - - +
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Residues in contact with LEU 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ILE* 3.6 37.7 - - + +
552A LYS* 4.4 14.7 + - + -
559A LEU* 4.2 9.8 - - + +
735A LYS* 3.0 41.3 + - + +
736A GLN* 3.5 12.6 - - - +
738A ALA* 1.3 74.9 - - - +
740A GLY* 1.3 55.8 + - - +
742A MET* 3.5 2.3 + - - +
743A GLN* 3.0 35.5 + - + +
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Residues in contact with GLY 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736A GLN 2.9 16.4 + - - -
737A ALA* 3.5 6.7 - - - -
738A ALA 3.1 0.6 - - - -
739A LEU* 1.3 75.8 - - - +
741A ILE* 1.3 57.3 + - - +
743A GLN* 3.6 7.2 - - - +
744A MET* 3.2 27.1 + - - +
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Residues in contact with ILE 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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574A LEU* 4.3 20.4 - - + -
576A PHE* 4.2 9.9 - - + -
639A PRO* 4.8 22.2 - - + -
642A LEU* 3.7 26.5 - - + -
729A LEU* 4.1 14.8 - - + -
733A ILE* 3.5 30.7 - - + -
737A ALA* 2.9 12.7 + - + +
738A ALA* 2.8 15.6 + - - +
740A GLY* 1.3 70.0 - - - +
742A MET* 1.3 66.8 + - - +
744A MET* 3.2 12.9 + - + +
745A VAL* 3.0 21.7 + - - +
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Residues in contact with MET 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A LYS* 4.8 6.7 - - + +
557A SER* 3.5 34.8 - - - +
558A LYS 4.2 1.8 - - - +
559A LEU* 3.4 42.0 - - + -
576A PHE* 4.2 16.2 - - - -
725A ILE* 3.7 20.6 - - + +
727A ALA* 3.6 24.9 - - + -
729A LEU* 4.8 2.4 - - + +
738A ALA 3.0 4.9 + - - -
739A LEU* 3.8 7.2 - - - +
741A ILE* 1.3 76.5 - - - +
743A GLN* 1.3 53.9 + - - +
745A VAL* 3.1 10.1 + - - +
746A GLU* 2.8 47.5 + - - +
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Residues in contact with GLN 743 (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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552A LYS* 3.6 22.6 + - - +
739A LEU* 3.0 21.5 + - + +
740A GLY* 3.6 8.7 - - - +
742A MET* 1.3 75.2 - - - +
744A MET* 1.3 54.1 + - - +
746A GLU* 3.7 7.4 + - - +
747A ASP* 2.8 75.7 + - - +
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Residues in contact with MET 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A PRO* 4.2 27.4 - - + +
642A LEU* 5.1 10.3 - - - -
643A LYS* 3.6 45.8 - - + -
740A GLY 3.2 12.1 + - - +
741A ILE* 3.2 14.3 + - + +
743A GLN* 1.3 78.1 - - - +
745A VAL* 1.3 54.4 + - - +
747A ASP* 3.6 5.5 - - - +
748A THR* 2.6 48.4 + - + +
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Residues in contact with VAL 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A PHE* 4.1 23.6 - - + -
578A PHE* 4.5 5.8 - - + -
642A LEU* 4.0 29.8 - - + -
646A ILE* 3.9 22.0 - - + +
725A ILE* 4.3 20.9 - - + -
741A ILE 3.0 17.3 + - - +
742A MET* 3.1 11.6 + - - +
744A MET* 1.3 77.4 - - + +
746A GLU* 1.3 62.2 + - - +
748A THR* 3.7 7.6 - - - +
749A LEU* 3.2 29.2 + - + +
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Residues in contact with GLU 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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552A LYS* 2.8 33.7 + - - +
554A THR* 5.1 4.7 - - - +
556A MET* 3.4 31.9 - - + +
557A SER* 2.8 35.3 + - - +
725A ILE* 4.8 7.4 - - + -
742A MET* 2.8 27.7 + - - +
743A GLN* 3.7 7.9 - - - +
745A VAL* 1.3 68.7 - - - +
747A ASP* 1.3 60.7 + - - +
749A LEU* 3.0 8.8 + - - +
750A ILE* 2.8 42.3 + - + +
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Residues in contact with ASP 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A GLN* 2.8 54.0 + - - +
744A MET* 3.6 5.5 - - - +
746A GLU* 1.3 72.6 - - - +
748A THR* 1.3 57.6 + - - +
750A ILE* 3.4 10.5 + - - +
751A GLU* 2.8 33.3 + - - +
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Residues in contact with THR 748 (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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643A LYS* 5.2 9.6 - - + -
646A ILE* 3.8 22.1 - - + +
647A GLU* 4.1 23.7 + - - +
650A ALA* 4.3 1.9 - - - +
744A MET* 2.6 45.2 + - + +
745A VAL* 3.7 9.6 - - - +
747A ASP* 1.3 74.4 - - - +
749A LEU* 1.3 59.7 + - - +
751A GLU* 4.5 7.0 - - - -
752A HIS* 3.3 32.4 + - - +
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Residues in contact with LEU 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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556A MET* 6.2 0.9 - - - -
578A PHE* 4.0 15.5 - - + -
646A ILE* 4.0 14.8 - - + +
649A MET* 4.7 11.0 - - + -
650A ALA* 4.5 11.2 - - + -
720A LEU* 4.3 20.6 - - + -
723A LEU* 4.3 12.8 - - + -
725A ILE* 3.8 28.5 - - + -
745A VAL* 3.2 20.2 + - + +
746A GLU* 3.0 9.4 + - - +
748A THR* 1.3 74.2 - - - +
750A ILE* 1.3 60.2 + - + +
753A ALA* 2.8 35.9 + - + +
754A HIS 3.4 3.5 + - - -
755A THR* 3.9 23.8 - - + +
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Residues in contact with ILE 750 (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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556A MET* 3.6 28.7 - - + -
746A GLU* 2.8 27.1 + - + +
747A ASP* 3.8 10.5 - - - +
749A LEU* 1.3 71.4 - - + +
751A GLU* 1.3 60.0 + - + +
754A HIS* 3.2 28.5 + - - -
755A THR* 3.6 26.0 - - - +
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Residues in contact with GLU 751 (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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747A ASP 2.8 22.1 + - - +
748A THR* 4.3 3.6 - - - +
750A ILE* 1.3 77.1 - - + +
752A HIS* 1.3 91.1 + - - +
754A HIS* 4.7 10.3 + - - -
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Residues in contact with HIS 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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647A GLU* 5.2 14.6 - - + +
650A ALA* 3.5 29.9 - - + +
651A THR* 3.2 21.3 - - + -
748A THR* 3.3 29.2 + - - +
751A GLU* 1.3 111.6 + - - +
753A ALA* 1.3 60.6 + - - +
754A HIS* 3.7 8.8 + - - -
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Residues in contact with ALA 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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650A ALA* 4.2 9.6 - - + +
717A PRO* 5.2 3.4 - - + +
720A LEU* 3.9 32.0 - - + +
721A SER* 4.2 12.8 + - - -
749A LEU* 2.8 16.6 + - + +
752A HIS* 1.3 73.5 - - - +
754A HIS* 1.3 76.2 + - - +
755A THR* 3.1 14.5 + - - +
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Residues in contact with HIS 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721A SER* 4.0 4.7 - - - +
750A ILE* 3.2 23.1 + - - -
751A GLU 4.7 9.6 + - - -
752A HIS 4.5 8.4 + - - -
753A ALA* 1.3 82.8 + - - +
755A THR* 1.3 65.2 + - - +
756A LYS* 3.3 15.8 + - - +
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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) + - + + + + + -
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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