Contacts of the helix formed by residues 822 - 837 (chain B) in PDB entry 5QSY
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 ASP 822 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777B GLN* 4.8 6.1 + - - +
820B ASN 3.7 2.6 + - - -
821B PRO* 1.3 76.5 - - - +
823B THR* 1.3 65.0 + - - +
824B GLY* 3.1 22.0 + - - -
825B LEU* 3.1 30.4 + - - +
826B GLN* 3.2 10.5 + - - +
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Residues in contact with THR 823 (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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821B PRO 3.9 1.2 + - - -
822B ASP* 1.3 73.5 - - - +
824B GLY* 1.3 63.4 + - - +
826B GLN* 3.7 12.5 - - + +
827B SER* 3.0 26.8 + - - -
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Residues in contact with GLY 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B GLN* 3.9 7.4 + - - -
822B ASP* 3.1 12.5 + - - +
823B THR* 1.3 79.8 - - - +
825B LEU* 1.3 60.1 + - - +
827B SER* 3.8 6.2 + - - -
828B GLU* 3.3 20.4 + - - +
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Residues in contact with LEU 825 (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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773B LEU* 5.5 4.5 - - + +
777B GLN* 3.5 44.1 - - + +
780B LEU* 4.8 3.4 - - + -
795B LEU* 4.4 19.5 - - + -
799B LEU* 4.5 15.0 - - + -
821B PRO* 3.7 24.2 - - + -
822B ASP* 3.1 21.8 + - - +
824B GLY* 1.3 74.5 - - - +
826B GLN* 1.3 54.4 + - - +
828B GLU* 2.6 24.1 + - + +
829B LEU* 2.7 42.2 + - + +
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Residues in contact with GLN 826 (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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821B PRO* 3.6 26.4 + - + +
822B ASP 3.2 12.6 + - - +
823B THR* 3.7 11.1 - - + +
825B LEU* 1.3 76.4 - - - +
827B SER* 1.3 63.8 + - - +
829B LEU* 3.7 10.2 - - + +
830B LEU* 3.0 26.6 + - - +
872B PHE* 4.8 2.4 - - - -
880B ILE 3.4 21.2 + - - -
881B VAL* 3.6 21.7 - - + +
882B ASP* 3.3 26.8 + - - +
885B ALA* 4.8 11.7 - - + +
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Residues in contact with SER 827 (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 THR* 3.0 19.3 + - - -
824B GLY* 3.9 7.2 - - - -
826B GLN* 1.3 75.4 - - - +
828B GLU* 1.3 51.7 + - - +
830B LEU* 3.6 13.1 - - - +
831B SER* 2.8 37.1 + - - -
885B ALA* 6.2 1.5 - - - +
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Residues in contact with GLU 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B GLN* 3.0 37.1 + - - +
780B LEU* 4.2 24.4 - - + +
781B SER* 3.8 18.2 + - - -
824B GLY 3.3 10.3 + - - +
825B LEU* 2.6 14.4 + - + +
827B SER* 1.3 72.2 - - - +
829B LEU* 1.3 62.3 + - - +
831B SER* 3.8 8.8 - - - +
832B PHE* 3.3 21.1 + - - +
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Residues in contact with LEU 829 (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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780B LEU* 4.6 3.4 - - + -
792B PHE* 3.8 27.2 - - + -
795B LEU* 4.1 29.2 - - + -
796B CYS* 4.6 1.6 - - - -
799B LEU* 3.7 28.5 - - + -
821B PRO* 5.8 0.7 - - + -
825B LEU* 2.7 30.3 + - + +
826B GLN* 3.7 9.4 - - + +
828B GLU* 1.3 68.2 - - - +
830B LEU* 1.3 65.8 + - - +
832B PHE* 2.9 17.5 + - - +
833B VAL* 3.0 14.4 + - - +
872B PHE* 3.6 19.3 - - + -
875B LEU* 4.1 16.6 - - + -
881B VAL* 4.6 7.0 - - + -
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Residues in contact with LEU 830 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826B GLN 3.0 15.9 + - - +
827B SER* 3.6 13.0 - - - +
829B LEU* 1.3 77.0 - - - +
831B SER* 1.3 73.3 + - - +
833B VAL* 3.0 14.9 + - - +
834B MET* 3.1 25.6 + - + +
872B PHE* 3.8 19.0 - - + -
885B ALA* 3.2 27.1 - - + +
886B ALA* 3.3 25.6 - - + +
888B ASP* 3.4 31.0 - - + +
889B ILE* 5.1 0.4 - - + -
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Residues in contact with SER 831 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B SER* 2.8 24.7 + - - -
828B GLU* 3.8 13.2 + - - +
829B LEU 3.3 0.2 - - - -
830B LEU* 1.3 78.5 - - - +
832B PHE* 1.3 60.9 + - - +
834B MET* 3.7 5.0 + - - +
835B ASP* 3.3 32.1 + - - +
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Residues in contact with PHE 832 (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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780B LEU* 4.6 16.4 - - + -
788B LYS* 3.9 23.8 - - + -
789B GLU* 4.1 20.4 - - + -
792B PHE* 3.4 53.8 - + + -
828B GLU 3.3 11.3 + - - +
829B LEU* 2.9 10.8 + - - +
831B SER* 1.3 77.6 + - - +
833B VAL* 1.3 66.9 + - - +
835B ASP* 3.3 2.6 + - - -
836B HIS* 3.1 66.3 + + + +
868B LEU* 4.1 12.8 - - + -
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Residues in contact with VAL 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B PHE* 3.8 17.3 - - + -
829B LEU 3.0 13.8 + - - +
830B LEU* 3.0 10.6 + - - +
832B PHE* 1.3 74.1 - - - +
834B MET* 1.3 60.1 + - - +
837B VAL* 2.8 52.9 + - + +
838B PHE* 3.6 24.6 - - + -
868B LEU 5.4 0.7 - - - +
869B LEU* 4.5 8.5 - - + -
872B PHE* 3.7 34.1 - - + -
889B ILE* 3.6 15.9 - - + -
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Residues in contact with MET 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B LEU* 3.1 31.6 + - + +
831B SER* 4.0 9.2 - - - +
833B VAL* 1.3 80.6 - - - +
835B ASP* 1.3 67.1 + - - +
836B HIS 3.4 0.2 + - - -
838B PHE* 3.5 36.5 + - + +
888B ASP* 3.3 51.1 - - + +
889B ILE* 3.6 23.8 - - + -
892B HIS* 6.1 4.5 - - + -
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Residues in contact with ASP 835 (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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831B SER* 3.3 25.1 + - - +
832B PHE* 3.8 5.4 - - - +
833B VAL 3.2 0.6 - - - -
834B MET* 1.3 84.9 - - - +
836B HIS* 1.3 73.8 + - + +
839B ILE* 3.4 14.8 - - - +
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Residues in contact with HIS 836 (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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785B THR* 3.9 24.1 + - + +
788B LYS* 3.4 33.4 + - - -
789B GLU* 4.8 5.2 - - - -
832B PHE* 3.1 63.4 + + + +
835B ASP* 1.3 91.8 - - + +
837B VAL* 1.3 62.4 + - + +
839B ILE* 3.8 8.3 - - - +
865B ARG* 3.2 23.6 - - - +
868B LEU* 4.5 8.8 - - + +
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Residues in contact with VAL 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B PHE* 5.9 0.2 - - + -
833B VAL* 2.8 41.7 + - + +
836B HIS* 1.3 74.7 - - + +
838B PHE* 1.3 78.5 + - + +
839B ILE* 3.5 6.5 + - - +
865B ARG* 3.5 24.7 + - - +
868B LEU* 4.3 17.3 - - + -
869B LEU* 4.2 16.2 - - + +
900B TYR* 2.8 51.4 + - + +
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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