Contacts of the helix formed by residues 872 - 888 (chain B) in PDB entry 5B2R
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 872 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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864B ARG 3.1 11.2 + - - -
865B GLY* 4.1 13.3 - - - -
866B LYS 5.0 3.5 - - - +
870B VAL 3.3 4.3 + - - -
871B PRO* 1.3 78.2 - - - +
873B GLU* 1.3 65.8 + - - +
874B GLU* 3.7 8.1 + - - +
875B VAL* 3.3 25.5 + - - +
876B VAL* 3.2 17.3 + - - +
903B ALA* 3.8 2.2 - - - -
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Residues in contact with GLU 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872B SER* 1.3 75.1 - - - +
874B GLU* 1.3 59.4 + - - +
876B VAL* 3.1 6.4 + - - +
877B LYS* 2.8 29.9 + - - +
903B ALA* 3.7 33.9 - - + +
904B GLU* 5.2 5.6 - - + +
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Residues in contact with GLU 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872B SER* 3.3 8.1 + - - +
873B GLU* 1.3 78.3 - - - +
875B VAL* 1.3 64.0 + - + +
877B LYS* 3.4 8.0 + - - +
878B LYS* 3.1 44.4 + - - +
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Residues in contact with VAL 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B TYR* 3.8 44.9 - - + +
863B ASN 3.6 21.8 - - - +
864B ARG 3.7 9.0 - - - +
865B GLY* 5.2 0.4 - - - -
871B PRO* 4.5 3.4 - - + -
872B SER* 3.3 25.7 + - - +
873B GLU 3.2 0.6 - - - -
874B GLU* 1.3 77.0 - - + +
876B VAL* 1.3 58.4 + - - +
878B LYS* 2.9 7.7 + - - -
879B MET* 2.8 39.4 + - + +
883B TRP* 4.1 8.5 - - + -
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Residues in contact with VAL 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B PRO 3.9 7.9 - - - +
872B SER 3.2 13.0 + - - +
873B GLU* 3.1 9.5 + - - +
875B VAL* 1.3 73.7 - - - +
877B LYS* 1.3 59.8 + - - +
880B LYS* 2.8 38.6 + - + +
883B TRP* 3.8 12.1 - - + -
900B LEU 3.2 25.8 - - - +
901B THR* 3.9 28.9 - - + +
903B ALA* 4.2 9.0 - - + -
904B GLU* 3.8 28.5 - - + +
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Residues in contact with LYS 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873B GLU 2.8 18.8 + - - +
874B GLU* 3.7 9.0 - - - +
876B VAL* 1.3 74.3 - - - +
878B LYS* 1.3 64.4 + - + +
880B LYS* 4.3 5.5 + - - +
881B ASN* 5.5 3.3 + - - -
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Residues in contact with LYS 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B TYR 5.7 2.2 - - - +
825B ASP* 4.6 10.5 - - + +
874B GLU* 3.1 31.0 + - - +
875B VAL* 2.9 7.6 + - - +
877B LYS* 1.3 79.8 - - + +
879B MET* 1.3 75.3 + - + +
880B LYS 3.6 0.4 + - - -
881B ASN* 5.0 3.3 + - - +
882B TYR* 5.4 1.9 + - - +
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Residues in contact with MET 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820B ARG* 6.3 0.2 - - - +
821B ASP 3.6 13.5 - - - +
822B MET 3.7 12.8 - - - +
823B TYR 3.8 14.8 - - - +
824B VAL* 3.5 25.4 - - - +
825B ASP* 3.6 28.7 - - + +
875B VAL* 2.8 22.0 + - + +
878B LYS* 1.3 89.4 - - + +
880B LYS* 1.3 59.7 + - - +
881B ASN 3.3 2.2 - - - -
882B TYR* 3.2 27.2 + - + -
883B TRP* 2.8 51.1 + - + +
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Residues in contact with LYS 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876B VAL* 2.8 29.5 + - + +
877B LYS* 4.3 4.9 + - - +
878B LYS 3.6 1.2 - - - -
879B MET* 1.3 77.4 - - - +
881B ASN* 1.3 62.4 + - - +
883B TRP* 3.3 13.9 + - - +
884B ARG* 2.9 33.6 + - - +
897B PHE* 4.0 7.5 - - + -
901B THR* 4.7 7.2 - - + -
904B GLU* 5.5 3.8 - - - +
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Residues in contact with ASN 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B LYS 5.5 3.5 + - - -
878B LYS 5.0 2.8 + - - +
879B MET 3.3 0.4 - - - -
880B LYS* 1.3 80.6 - - - +
882B TYR* 1.3 61.7 + - - +
884B ARG* 3.3 14.8 + - - +
885B GLN* 3.3 34.0 + - - +
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Residues in contact with TYR 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817B GLN* 2.7 38.7 + - - +
818B ASN* 5.2 2.5 - - + -
820B ARG* 3.6 37.3 + - + +
821B ASP 3.7 13.2 - - - -
822B MET* 3.7 20.9 - - - -
825B ASP* 5.0 10.3 - - - +
878B LYS 5.4 1.7 + - - +
879B MET* 3.2 30.5 + - + +
881B ASN* 1.3 74.8 - - - +
883B TRP* 1.3 72.7 + + - +
885B GLN* 3.3 19.3 + - + +
886B LEU* 3.3 40.2 + - + +
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Residues in contact with TRP 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822B MET* 2.9 56.0 + - + +
823B TYR* 4.3 2.9 - + - -
871B PRO* 4.7 2.9 - - + -
875B VAL* 4.1 13.9 - - + -
876B VAL* 3.8 30.3 - - + -
879B MET* 2.8 29.0 + - + +
880B LYS* 3.6 12.8 - - - +
882B TYR* 1.3 85.4 - + - +
884B ARG* 1.3 55.4 + - - +
886B LEU* 3.3 6.1 + - + +
887B LEU* 3.0 23.0 + - - +
892B ILE* 3.6 13.6 - - + +
897B PHE* 3.9 12.8 - + + -
900B LEU* 3.3 58.3 - - + -
901B THR* 3.6 19.5 - - + -
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Residues in contact with ARG 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880B LYS* 2.9 22.0 + - - +
881B ASN* 3.7 14.6 + - - +
882B TYR 3.3 0.2 - - - -
883B TRP* 1.3 76.7 - - - +
885B GLN* 1.3 58.7 + - + +
887B LEU* 3.1 13.0 + - + +
888B ASN* 2.8 46.5 + - - +
897B PHE* 3.5 36.5 - - + -
904B GLU* 5.9 0.8 + - - -
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Residues in contact with GLN 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790B GLU* 5.5 0.2 - - - +
791B LEU* 3.5 19.3 - - + +
881B ASN* 3.3 21.0 + - - +
882B TYR* 3.7 19.8 - - + +
883B TRP 3.2 0.6 - - - -
884B ARG* 1.3 74.8 - - + +
886B LEU* 1.3 66.6 + - + +
888B ASN* 3.4 10.2 + - - +
889B ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791B LEU* 4.3 11.4 - - + -
816B LEU 3.7 17.5 - - - +
817B GLN* 4.3 10.8 - - - -
818B ASN* 4.7 0.9 - - + -
822B MET* 3.6 25.8 - - + -
882B TYR* 3.3 51.6 + - + +
883B TRP* 3.3 9.3 + - - +
885B GLN* 1.3 76.9 - - + +
887B LEU* 1.3 61.2 + - - +
889B ALA* 3.1 4.9 + - - -
890B LYS 3.1 3.6 + - - -
891B LEU* 2.9 42.7 + - + -
892B ILE* 3.5 17.0 + - + -
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Residues in contact with LEU 887 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A A 6.1 2.5 - - - -
883B TRP 3.0 13.7 + - - +
884B ARG* 3.1 18.4 + - + +
886B LEU* 1.3 77.7 - - - +
888B ASN* 1.3 64.8 + - - +
890B LYS* 3.1 17.8 + - - -
892B ILE* 3.7 21.7 - - + +
893B THR* 3.8 3.6 - - - +
894B GLN* 3.6 49.4 - - + +
897B PHE* 3.9 28.9 - - + -
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Residues in contact with ASN 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ASP* 5.1 9.1 + - - -
790B GLU* 3.0 27.5 - - + +
884B ARG* 2.8 42.6 + - - +
885B GLN* 3.4 9.4 + - - +
886B LEU 3.4 0.2 - - - -
887B LEU* 1.3 79.6 - - - +
889B ALA* 1.3 56.7 + - - +
890B LYS 3.5 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
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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