Contacts of the helix formed by residues 834 - 848 (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 ASN 834 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A GLY* 1.3 75.8 - - - +
835A CYS* 1.3 64.1 + - - +
836A SER* 3.2 3.6 - - - +
837A THR* 3.0 29.0 + - - +
838A THR* 3.2 16.4 + - - -
1139A BR 3.4 12.2 - - - +
1L NAG 1.4 66.3 + - - +
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Residues in contact with CYS 835 (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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803A ILE* 4.4 6.1 - - - -
808A TRP* 3.7 14.9 - - + -
824A LEU* 4.2 17.9 - - + +
827A ALA* 3.5 29.6 - - + -
828A CYS* 3.5 19.3 - - - +
832A LEU 3.9 4.0 + - - +
833A GLY 3.5 1.4 - - - -
834A ASN* 1.3 77.7 - - - +
836A SER* 1.3 56.7 + - - +
838A THR* 3.2 5.9 + - - -
839A ALA* 2.9 30.0 + - - +
1139A BR 3.7 24.0 - - - -
1L NAG 5.8 3.8 - - - -
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Residues in contact with SER 836 (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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828A CYS* 3.6 19.3 - - - +
831A ASN* 4.2 23.7 + - - -
832A LEU 5.0 1.6 + - - -
833A GLY 5.7 1.6 - - - -
834A ASN* 4.9 2.0 - - - -
835A CYS* 1.3 78.3 - - - +
837A THR* 1.3 57.0 + - - +
839A ALA* 3.3 3.8 + - - +
840A MET* 2.9 30.1 + - - +
866A VAL* 3.9 15.1 - - - +
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Residues in contact with THR 837 (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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834A ASN* 3.0 25.5 + - + +
836A SER* 1.3 78.5 + - - +
838A THR* 1.3 65.6 + - - +
840A MET* 3.9 4.9 - - - +
841A LYS* 3.2 23.8 + - + +
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Residues in contact with THR 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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808A TRP* 3.6 40.5 + - + +
834A ASN* 3.2 13.7 + - - -
835A CYS* 3.2 9.1 + - - -
837A THR* 1.3 77.4 - - - +
839A ALA* 1.3 66.1 + - - +
841A LYS* 3.4 7.3 + - + +
842A LEU* 3.2 28.0 + - + +
1L NAG 4.2 17.5 + - - +
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Residues in contact with ALA 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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808A TRP* 3.8 22.4 - - + -
828A CYS* 4.2 4.5 - - - -
835A CYS 2.9 17.0 + - - +
836A SER 3.6 4.5 - - - +
838A THR* 1.3 78.6 - - - +
840A MET* 1.3 56.6 + - - +
842A LEU* 3.2 5.0 + - - +
843A PHE* 2.9 27.7 + - - +
862A THR* 4.4 0.9 - - + +
863A VAL* 3.8 16.8 - - - +
866A VAL* 4.1 24.9 - - + -
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Residues in contact with MET 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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836A SER* 2.9 19.1 + - - +
837A THR* 3.9 5.8 - - - +
838A THR 3.3 0.2 - - - -
839A ALA* 1.3 73.2 - - - +
841A LYS* 1.3 66.1 + - - +
843A PHE* 3.1 5.6 + - - +
844A ASP* 2.9 55.3 + - - +
866A VAL* 3.4 37.0 - - + +
867A GLY* 4.4 11.2 - - - -
869A LYS* 5.5 2.2 - - + -
870A THR* 4.5 16.2 - - - +
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Residues in contact with LYS 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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837A THR* 3.2 15.0 + - + +
838A THR* 3.6 11.7 - - - +
840A MET* 1.3 76.4 - - - +
842A LEU* 1.3 64.1 + - + +
844A ASP* 3.6 7.0 + - + +
845A ASP* 2.5 66.0 + - - +
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Residues in contact with LEU 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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808A TRP* 3.5 43.1 - - + +
838A THR* 3.2 18.9 + - + +
839A ALA 3.5 5.6 - - - +
840A MET 3.2 0.2 - - - -
841A LYS* 1.3 77.6 - - + +
843A PHE* 1.3 64.4 + - - +
845A ASP* 3.4 7.9 + - + +
846A TRP* 3.0 23.7 + - - +
855A LEU* 4.0 13.7 - - + +
856A PRO* 5.5 7.4 - - + -
859A VAL* 5.0 4.3 - - + -
863A VAL* 4.0 18.2 - - + -
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Residues in contact with PHE 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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839A ALA 2.9 14.3 + - - +
840A MET* 3.1 12.1 + - - +
842A LEU* 1.3 76.6 - - - +
844A ASP* 1.3 63.3 + - - +
846A TRP* 3.0 33.5 + + - +
847A MET* 2.7 52.7 + - + +
863A VAL* 3.5 26.8 - - + +
864A PHE* 4.2 3.4 - + - -
867A GLY* 3.4 33.0 - - - -
870A THR* 6.3 0.2 - - - -
873A GLY* 3.6 35.9 - - - -
876A PHE* 4.8 1.1 - + - -
877A LEU* 4.0 16.4 - - + -
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Residues in contact with ASP 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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840A MET* 2.9 44.4 + - - +
841A LYS* 4.0 7.8 + - + +
843A PHE* 1.3 82.0 - - - +
845A ASP* 1.3 61.6 + - - +
847A MET* 3.8 8.2 - - - +
848A ALA* 2.8 33.3 + - - +
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Residues in contact with ASP 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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841A LYS* 2.5 51.2 + - - +
842A LEU* 3.8 8.2 - - + +
844A ASP* 1.3 77.6 - - - +
846A TRP* 1.3 65.5 + - - +
848A ALA* 4.2 4.0 - - - +
849A SER* 3.4 22.9 + - - -
853A GLN* 4.4 10.2 - - + +
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Residues in contact with TRP 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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842A LEU 3.0 13.6 + - - +
843A PHE* 3.0 29.2 + + - +
845A ASP* 1.3 77.3 - - - +
847A MET* 1.3 70.2 + - - +
849A SER* 3.0 11.3 + - - -
851A GLY* 2.9 55.0 + - - -
852A THR 4.5 0.2 - - - -
853A GLN* 3.8 17.5 - - - +
854A SER* 5.3 0.6 - - - +
855A LEU* 3.5 34.9 - - + +
864A PHE* 3.4 36.5 - + - -
876A PHE* 3.5 30.1 - + - -
877A LEU* 4.0 8.3 - - + -
880A LYS* 3.9 21.3 - - + -
889A GLU* 4.5 12.6 + - - -
893A ILE* 5.1 1.3 - - + -
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Residues in contact with MET 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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843A PHE* 2.7 44.4 + - + +
844A ASP* 3.8 8.7 - - - +
846A TRP* 1.3 70.2 - - + +
848A ALA* 1.3 57.9 + - - +
849A SER 3.1 4.9 - - - -
850A ASN* 3.1 18.2 + - - -
872A LYS* 3.3 60.3 - - + +
873A GLY* 4.2 1.6 - - - -
876A PHE* 3.6 49.0 - - + -
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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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844A ASP 2.8 22.3 + - - +
845A ASP* 4.2 5.6 - - - +
847A MET* 1.3 73.3 - - - +
849A SER* 1.3 57.7 + - - +
850A ASN 3.3 1.6 + - - -
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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