Contacts of the helix formed by residues 724 - 742 (chain A) in PDB entry 5MJ6
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 724 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A ASN* 2.7 29.9 + - - -
723A LEU* 1.3 72.8 - - - +
725A ASP* 1.3 64.6 + - - +
726A LYS* 3.7 5.6 + - - -
727A ASP* 3.1 20.9 + - - -
728A ARG* 2.9 35.1 + - - +
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Residues in contact with ASP 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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508A TYR* 2.5 37.1 + - - -
509A GLU* 4.5 2.4 - - - +
724A SER* 1.3 75.4 - - - +
726A LYS* 1.3 68.1 + - - +
728A ARG* 3.4 13.2 + - - +
729A ALA* 2.9 30.2 + - - +
761A HIS* 3.5 44.6 + - + +
763A ALA* 4.4 8.3 + - + +
764A PRO* 3.6 12.9 - - + +
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Residues in contact with LYS 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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508A TYR* 3.7 50.9 - - + +
511A PHE* 6.2 0.6 - - - -
512A LEU* 3.9 31.5 - - + +
515A ARG* 4.7 10.1 - - - +
557A LEU* 5.9 1.6 - - - +
695A ASN* 3.8 48.9 + - - +
697A ASN* 4.9 5.5 + - - -
724A SER* 3.2 7.4 - - - +
725A ASP* 1.3 83.8 + - - +
727A ASP* 1.3 55.5 + - - +
729A ALA* 3.2 1.7 + - - +
730A ASN* 2.8 34.5 + - - +
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Residues in contact with ASP 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A VAL* 4.8 4.7 - - - +
691A LYS* 3.4 25.8 + - - +
694A ILE* 3.7 10.3 - - - +
695A ASN* 2.9 27.9 + - - +
723A LEU* 3.6 23.5 - - + +
724A SER* 3.1 37.7 + - - +
726A LYS* 1.3 76.9 - - - +
728A ARG* 1.3 61.9 + - - +
730A ASN* 3.2 6.7 - - - +
731A LEU* 3.2 27.2 + - - +
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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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716A LEU* 3.6 17.9 - - + -
720A PRO* 3.3 36.4 + - - +
721A TYR* 3.8 17.3 - - - +
723A LEU* 2.7 38.0 + - + -
724A SER* 2.9 21.6 + - - +
725A ASP* 3.6 19.7 - - - +
727A ASP* 1.3 73.1 - - - +
729A ALA* 1.3 64.0 + - - +
731A LEU* 3.5 9.5 + - - +
732A ILE* 3.2 29.7 + - - +
755A TYR* 3.6 12.9 + - + +
759A GLU* 2.5 40.9 + - - -
761A HIS* 3.6 18.0 + - - -
764A PRO* 4.0 2.7 - - + -
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Residues in contact with ALA 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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512A LEU* 3.9 20.4 - - + -
516A PHE* 3.7 11.6 - - + -
725A ASP 2.9 17.9 + - - +
726A LYS 3.5 4.5 - - - +
728A ARG* 1.3 74.1 - - - +
730A ASN* 1.3 65.8 + - - +
732A ILE* 3.1 5.4 + - - +
733A ASN* 2.9 24.1 + - - +
763A ALA* 4.1 22.7 - - + +
764A PRO* 4.2 8.7 - - - +
767A GLU* 3.9 3.3 - - + +
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Residues in contact with ASN 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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516A PHE* 3.8 11.4 - - - -
691A LYS* 3.5 23.4 - - - +
692A VAL 4.8 2.2 + - - -
693A ASN* 4.7 6.0 + - - +
696A MET* 2.9 48.6 - - + +
702A VAL* 5.8 0.8 - - - +
726A LYS 2.8 16.8 + - - +
727A ASP* 3.2 13.9 - - - +
729A ALA* 1.3 71.1 - - - +
731A LEU* 1.3 60.9 + - - +
733A ASN* 3.3 2.4 + - - +
734A ASN* 2.8 61.9 + - - +
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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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691A LYS* 3.7 22.9 - - + +
704A TYR* 4.3 8.5 - - + +
709A TRP* 4.0 22.6 - - + -
712A LEU* 4.1 19.5 - - + -
716A LEU* 4.3 19.1 - - + -
723A LEU* 3.9 28.7 - - + -
727A ASP 3.2 12.6 + - - +
728A ARG* 3.8 9.6 - - - +
729A ALA 3.3 0.4 - - - -
730A ASN* 1.3 82.1 - - - +
732A ILE* 1.3 64.4 + - - +
734A ASN* 3.9 3.7 - - + +
735A ILE* 3.0 27.9 + - - +
752A LEU* 4.4 14.4 - - + +
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Residues in contact with ILE 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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728A ARG 3.2 15.9 + - - +
729A ALA 3.1 6.5 + - - +
731A LEU* 1.3 76.5 - - - +
733A ASN* 1.3 65.5 + - - +
735A ILE* 3.2 17.5 - - - +
736A PHE* 3.2 24.7 + - + -
752A LEU* 3.7 24.5 - - + -
753A ILE* 4.0 17.3 - - + -
755A TYR* 3.8 15.0 - - + +
756A LEU* 4.4 3.8 - - + -
764A PRO* 3.5 37.2 - - + +
767A GLU* 3.8 16.2 - - + +
768A ALA* 4.2 11.2 - - + -
771A GLN* 4.9 0.4 - - + -
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Residues in contact with ASN 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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516A PHE* 3.4 44.1 + - + +
519A MET* 5.6 2.6 - - - +
696A MET* 5.4 0.7 - - - +
701A ILE* 4.8 2.1 - - - +
729A ALA 2.9 11.8 + - - +
730A ASN 3.5 7.0 - - - +
732A ILE* 1.3 76.6 - - - +
734A ASN* 1.3 78.0 - - - +
736A PHE* 3.1 4.9 + - - +
737A GLU* 2.9 46.3 + - - +
767A GLU* 3.1 28.3 + - - +
771A GLN* 4.2 8.3 + - - +
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Residues in contact with ASN 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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519A MET* 5.9 0.3 - - - +
693A ASN* 5.7 0.6 - - - +
696A MET* 5.0 4.3 - - - +
700A TYR 4.7 2.6 + - - +
701A ILE* 3.7 28.3 - - + +
702A VAL* 3.2 38.8 + - - +
704A TYR* 6.2 0.4 - - - -
709A TRP* 4.8 3.8 - - + -
730A ASN* 2.8 44.8 + - - +
731A LEU* 4.0 6.0 - - + +
733A ASN* 1.3 90.0 - - - +
735A ILE* 1.3 58.1 + - - +
737A GLU* 3.5 3.1 + - - +
738A LEU* 2.9 37.1 + - + +
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Residues in contact with ILE 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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709A TRP* 3.5 43.2 - - + +
731A LEU 3.0 16.1 + - - +
732A ILE* 3.2 17.7 - - - +
734A ASN* 1.3 76.7 - - - +
736A PHE* 1.3 70.9 + - + +
738A LEU* 3.4 3.3 + - + +
739A ALA* 2.9 28.1 + - - +
744A VAL* 3.7 23.6 - - + -
748A ARG* 4.3 12.6 - - + +
749A ALA* 3.8 28.0 - - + +
752A LEU* 4.2 17.5 - - + -
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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
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732A ILE* 3.2 27.8 - - + +
733A ASN 3.1 4.9 + - - +
735A ILE* 1.3 82.9 - - + +
737A GLU* 1.3 64.9 + - - +
739A ALA* 3.1 6.1 + - - +
740A GLY* 3.0 19.2 + - - -
746A LEU* 4.4 11.5 - - + +
749A ALA* 3.9 22.9 - - + -
750A PHE* 3.7 39.3 - + - -
753A ILE* 3.9 33.0 - - + -
768A ALA* 5.5 2.0 - - - -
771A GLN* 3.7 47.3 - - + +
772A THR* 5.7 1.3 - - - -
775A ILE* 4.5 8.5 - - + -
1013A TRP* 5.7 0.9 + - - -
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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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516A PHE 3.7 15.4 - - - +
519A MET* 4.4 4.7 - - - +
520A LYS* 3.9 35.3 + - + +
523A SER* 4.9 0.9 + - - -
635A PHE* 4.0 19.7 - - + -
701A ILE* 3.6 30.0 - - + +
733A ASN* 2.9 39.4 + - - +
734A ASN* 4.0 3.6 - - - +
736A PHE* 1.3 75.4 - - - +
738A LEU* 1.3 59.1 + - - +
740A GLY* 3.4 3.3 + - - +
741A LEU* 3.2 24.6 + - - +
771A GLN* 5.5 4.5 - - - +
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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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618A LEU* 3.8 24.0 - - + -
635A PHE* 4.1 15.7 - - + -
701A ILE* 4.3 6.5 - - + -
702A VAL 3.7 22.2 - - - +
703A HIS* 3.7 24.5 - - + +
709A TRP* 4.0 12.8 - - + +
734A ASN 2.9 22.5 + - - +
735A ILE* 3.8 4.3 - - - +
736A PHE 3.2 0.2 - - - -
737A GLU* 1.3 73.7 - - - +
739A ALA* 1.3 60.0 + - - +
740A GLY 3.2 0.4 - - - -
741A LEU* 3.8 2.4 - - + +
742A GLY 3.0 22.2 + - - -
743A LYS* 3.0 36.3 + - + -
744A VAL* 3.6 11.1 + - + -
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Residues in contact with ALA 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 ILE 2.9 17.2 + - - +
736A PHE* 3.1 5.6 + - - +
738A LEU* 1.3 74.6 - - - +
740A GLY* 1.3 61.6 + - - +
742A GLY* 3.9 6.6 + - - -
744A VAL* 3.4 21.8 - - + +
746A LEU* 3.7 42.2 - - + -
749A ALA* 4.5 3.1 - - + -
1013A TRP* 5.0 0.2 - - - -
1016A LYS* 6.0 0.9 - - - +
1017A ASN* 3.8 19.2 + - - +
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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
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637A LEU* 4.5 4.9 - - - +
736A PHE 3.0 12.2 + - - -
737A GLU* 3.4 4.7 + - - -
738A LEU 3.2 0.2 - - - -
739A ALA* 1.3 77.9 - - - +
741A LEU* 1.3 66.1 + - - +
1013A TRP* 3.8 31.1 - - - +
1016A LYS* 3.6 12.5 + - - +
1017A ASN* 5.0 1.2 + - - -
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Residues in contact with LEU 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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618A LEU* 4.8 2.0 - - + -
635A PHE* 3.4 36.3 - - + -
636A PHE 4.4 14.6 - - - +
637A LEU* 3.7 34.1 - - + +
737A GLU 3.2 13.1 + - - +
738A LEU* 3.8 9.6 - - + +
740A GLY* 1.3 76.7 - - - +
742A GLY* 1.3 60.3 - - - +
743A LYS* 3.5 41.5 - - + +
1016A LYS* 3.1 20.3 + - - -
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Residues in contact with GLY 742 (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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738A LEU 3.0 5.3 + - - -
739A ALA 4.2 8.1 - - - -
740A GLY 3.4 1.2 - - - -
741A LEU* 1.3 81.0 - - - +
743A LYS* 1.3 59.6 + - - +
744A VAL* 3.0 18.9 + - - +
1016A LYS* 4.9 10.8 - - - -
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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
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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