Contacts of the helix formed by residues 837 - 853 (chain A) in PDB entry 5A7R
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 VAL 837 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A LEU 4.0 3.3 + - - +
834A ASP* 3.4 25.9 + - - +
836A PHE* 1.3 75.8 - - - +
838A PRO* 1.4 67.5 - - + +
839A GLU* 4.0 21.1 - - + +
840A LYS* 2.8 39.6 + - + +
841A MET* 3.0 10.6 + - - -
936A TYR* 3.9 20.0 - - + +
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Residues in contact with PRO 838 (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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836A PHE 3.6 2.5 - - - +
837A VAL* 1.4 86.1 - - + +
839A GLU* 1.3 62.9 + - - +
841A MET* 3.3 13.2 + - + +
842A ARG* 2.9 34.1 + - - +
929A TYR* 4.4 5.5 + - - +
933A LEU* 3.7 28.0 - - + -
936A TYR* 3.4 39.0 - - + -
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Residues in contact with GLU 839 (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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837A VAL* 4.0 11.7 - - + +
838A PRO* 1.3 80.9 - - - +
840A LYS* 1.3 64.4 + - - +
842A ARG* 3.7 29.0 + - - +
843A ARG* 3.0 26.9 + - - +
1971A SO4 3.0 34.7 + - - +
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Residues in contact with LYS 840 (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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827A LEU* 4.3 8.6 - - + +
829A PHE* 3.9 9.0 - - + -
834A ASP* 3.4 27.6 - - - +
835A GLN 4.4 5.6 - - - +
837A VAL* 2.8 23.4 + - + +
839A GLU* 1.3 81.9 + - - +
841A MET* 1.3 62.0 + - - +
843A ARG* 3.4 8.0 + - - +
844A GLU* 3.2 29.2 + - - +
1971A SO4 3.3 28.7 + - - +
1978A GOL 3.2 42.0 + - - +
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Residues in contact with MET 841 (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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835A GLN 3.3 18.8 - - - +
836A PHE* 3.4 29.8 - - - +
837A VAL 3.0 9.3 + - - +
838A PRO* 3.8 17.0 - - + +
840A LYS* 1.3 74.6 - - - +
842A ARG* 1.3 59.5 + - - +
844A GLU* 3.2 3.9 + - - +
845A LEU* 2.9 35.8 + - + +
881A LEU* 4.2 17.3 - - + -
885A ILE* 4.3 18.9 - - + +
929A TYR* 5.0 8.7 - - + -
932A LEU* 3.9 46.4 - - + +
933A LEU* 4.2 11.4 - - + -
936A TYR* 4.8 0.2 - - + -
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Residues in contact with ARG 842 (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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706A PRO 5.7 1.1 - - - -
708A TRP* 3.8 26.5 - - + -
838A PRO* 2.9 18.8 + - - +
839A GLU* 3.7 37.6 + - - +
841A MET* 1.3 73.1 - - - +
843A ARG* 1.3 61.1 + - - +
845A LEU* 3.7 8.7 - - - +
846A ASN* 2.9 48.6 + - - +
929A TYR* 4.0 17.8 + - - +
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Residues in contact with ARG 843 (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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775A LEU 5.8 0.2 + - - -
776A ASP 5.3 0.2 - - - -
777A HIS* 3.0 45.0 + - + +
825A ASP* 2.8 46.3 + - - -
826A ALA 3.7 6.7 - - - -
827A LEU* 3.7 23.9 - - + +
839A GLU 3.0 12.0 + - - +
840A LYS* 3.6 6.7 - - - +
841A MET 3.3 0.4 - - - -
842A ARG* 1.3 75.8 - - - +
844A GLU* 1.3 86.7 + - - +
846A ASN* 3.4 6.2 + - - +
847A LYS* 3.0 48.7 + - - +
1971A SO4 3.2 28.0 - - - +
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Residues in contact with GLU 844 (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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826A ALA* 3.6 3.5 - - - +
827A LEU* 2.9 35.5 + - + +
829A PHE* 4.0 5.7 - - + -
835A GLN 6.2 0.2 - - - +
840A LYS 3.2 15.7 + - - +
841A MET* 3.2 6.0 + - - +
843A ARG* 1.3 106.4 + - - +
845A LEU* 1.3 64.7 + - - +
847A LYS* 3.4 2.8 + - - +
848A ALA* 3.0 25.6 + - - +
870A TRP* 3.7 10.8 - - + -
882A LYS* 3.0 32.8 + - - +
885A ILE* 3.9 23.1 - - + -
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Residues in contact with LEU 845 (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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708A TRP* 3.8 32.7 - - + -
841A MET* 2.9 21.7 + - + +
842A ARG* 3.7 7.6 - - - +
844A GLU* 1.3 76.6 - - - +
846A ASN* 1.3 56.7 + - - +
848A ALA* 3.4 1.1 + - - -
849A TYR* 2.9 30.0 + - - +
885A ILE* 3.5 42.1 - - + +
888A LEU* 3.7 25.8 - - + -
889A ALA* 3.8 6.8 - - - +
929A TYR* 3.8 35.4 - - + -
932A LEU* 5.3 1.3 - - + -
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Residues in contact with ASN 846 (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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705A PHE* 3.4 57.6 - - + +
706A PRO 5.5 0.2 + - - -
708A TRP* 2.8 27.9 + - - +
777A HIS 4.9 4.5 - - - +
842A ARG* 2.9 41.3 + - - +
843A ARG* 3.9 6.1 - - - +
845A LEU* 1.3 71.3 - - - +
847A LYS* 1.3 60.8 + - - +
849A TYR* 4.2 2.0 - - - -
850A CYS* 2.9 25.3 + - - +
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Residues in contact with LYS 847 (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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775A LEU* 4.2 2.0 - - - +
776A ASP 2.9 19.6 + - - -
777A HIS 3.4 20.5 + - - +
779A GLU 2.9 26.8 + - - +
824A ILE* 3.7 20.0 - - + +
825A ASP* 2.7 44.3 + - - +
843A ARG* 3.0 40.7 + - - +
844A GLU 3.7 4.5 - - - +
846A ASN* 1.3 76.6 - - - +
848A ALA* 1.3 63.6 + - - +
850A CYS* 3.3 6.4 + - + +
851A GLY 3.1 17.0 + - - -
870A TRP* 3.8 15.7 - - + -
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Residues in contact with ALA 848 (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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824A ILE* 4.2 11.9 - - + -
844A GLU 3.0 17.2 + - - +
845A LEU* 4.6 0.7 - - - -
847A LYS* 1.3 76.8 - - - +
849A TYR* 1.3 63.1 + - - +
851A GLY* 3.1 2.9 + - - -
852A PHE* 3.0 41.9 + - + -
870A TRP* 4.0 16.6 - - + -
885A ILE* 5.0 1.1 - - + -
886A GLN* 4.8 6.1 - - + -
889A ALA* 3.7 21.1 - - + -
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Residues in contact with TYR 849 (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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702A LEU* 4.3 6.5 - - + -
704A ASP 4.4 7.2 + - - -
705A PHE* 3.8 22.0 - + - -
706A PRO* 3.7 24.5 - - + +
708A TRP* 4.1 11.7 - + + -
845A LEU 2.9 19.5 + - - +
846A ASN 3.6 3.6 - - - +
848A ALA* 1.3 77.4 - - - +
850A CYS* 1.3 63.4 + - - +
852A PHE* 3.1 4.0 + - - +
853A LEU* 2.9 66.4 + - + +
889A ALA* 3.7 13.6 - - + +
892A ALA* 3.8 42.3 + - + -
893A ALA* 4.0 3.6 - - + -
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Residues in contact with CYS 850 (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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700A GLN* 2.8 48.2 + - - -
702A LEU* 3.7 30.3 - - + -
705A PHE* 4.3 3.6 - - + -
778A ASN 3.5 27.4 - - - +
779A GLU 4.0 2.0 - - - +
780A CYS* 3.7 16.4 - - - -
846A ASN 2.9 18.3 + - - +
847A LYS* 3.7 5.8 - - - +
849A TYR* 1.3 77.1 - - - +
851A GLY* 1.3 61.0 + - - +
853A LEU 3.8 1.2 + - - -
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Residues in contact with GLY 851 (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 LEU* 3.8 3.3 - - - +
780A CYS* 3.9 5.1 - - - -
822A VAL* 3.7 26.8 - - - +
824A ILE* 3.9 11.0 - - - +
847A LYS 3.1 11.1 + - - -
848A ALA 3.1 4.9 + - - -
850A CYS* 1.3 77.0 - - - +
852A PHE* 1.4 64.3 + - - +
854A ARG* 2.9 26.5 + - - -
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Residues in contact with PHE 852 (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 LEU* 4.2 14.4 - - + -
736A VAL* 4.0 14.1 - - + -
822A VAL* 5.1 1.1 - - + -
824A ILE* 4.4 10.8 - - + -
848A ALA* 3.0 33.4 + - + +
849A TYR* 4.0 1.6 - - - +
851A GLY* 1.4 82.0 - - - +
853A LEU* 1.3 63.0 + - - +
854A ARG* 3.6 1.8 + - - -
862A LEU* 5.2 0.7 - - - +
865A VAL* 3.7 30.7 - - + -
867A THR* 5.3 0.4 - - + -
886A GLN* 3.8 41.3 - - + -
889A ALA* 4.0 3.1 - - + -
890A ALA* 3.7 28.0 - - + -
893A ALA* 3.9 16.2 - - + +
895A ARG* 2.9 36.1 + - - -
897A VAL* 6.0 0.4 - - + -
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Residues in contact with LEU 853 (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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700A GLN* 3.0 17.2 + - - -
702A LEU* 3.9 23.8 - - + -
704A ASP 6.1 0.4 - - - +
849A TYR* 2.9 52.6 + - + +
850A CYS 3.8 2.4 + - - +
851A GLY 3.6 0.2 - - - -
852A PHE* 1.3 76.4 - - - +
854A ARG* 1.3 83.2 + - - +
855A PRO* 3.6 22.8 - - + +
862A LEU* 6.6 0.2 - - + -
892A ALA 5.1 1.1 - - - +
893A ALA* 4.1 20.4 - - + +
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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