Contacts of the helix formed by residues 817 - 832 (chain B) in PDB entry 4QUN
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 817 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806B TYR* 3.8 3.5 + - - -
808B ALA* 5.7 1.0 - - + +
815B PRO* 3.1 3.9 - - - +
816B ASP* 1.3 83.0 - - + +
818B SER* 1.3 64.0 + - - +
819B SER* 3.0 17.5 + - - -
820B ASP* 2.9 51.2 + - + +
821B PHE* 3.0 21.5 + - - +
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Residues in contact with SER 818 (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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815B PRO 4.6 1.8 + - - -
816B ASP 4.3 0.2 - - - -
817B ASP* 1.3 72.6 + - - +
819B SER* 1.3 58.4 + - - +
821B PHE* 3.2 5.9 + - - +
822B LEU* 3.0 33.2 + - - +
893B PHE* 3.8 30.3 - - - -
897B ALA* 5.9 2.9 - - - -
900B ARG* 3.4 18.7 + - - -
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Residues in contact with SER 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817B ASP* 3.0 9.2 + - - -
818B SER* 1.3 79.4 + - - +
820B ASP* 1.3 66.5 + - - +
822B LEU* 3.2 2.9 + - - +
823B GLU* 3.0 31.6 + - - +
900B ARG* 2.8 35.7 + - - +
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Residues in contact with ASP 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781B ILE* 3.6 30.8 - - - +
782B ALA* 3.9 13.5 - - + +
783B TYR* 5.6 1.7 - - - -
806B TYR* 3.5 12.2 + - - +
808B ALA* 6.0 0.2 - - - +
817B ASP* 2.9 36.3 + - + +
819B SER* 1.3 78.7 - - - +
821B PHE* 1.3 62.3 + - - +
823B GLU* 3.5 8.3 + - - +
824B PHE* 3.0 23.9 + - - +
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Residues in contact with PHE 821 (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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806B TYR* 3.2 13.6 + + - +
809B TRP* 3.7 29.6 - + - -
815B PRO* 3.7 27.1 - - + -
817B ASP 3.0 12.7 + - - +
818B SER* 3.2 7.8 + - - +
820B ASP* 1.3 78.8 - - - +
822B LEU* 1.3 69.0 + - + +
824B PHE* 3.1 6.9 + + - +
825B VAL* 2.9 49.1 + - + +
851B VAL* 3.9 15.5 - - + -
852B LEU* 4.6 6.3 - - + -
855B MET* 3.7 38.1 - - + -
893B PHE* 3.5 24.0 - + - -
897B ALA* 4.8 0.4 - - + -
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Residues in contact with LEU 822 (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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818B SER* 3.0 18.1 + - - +
819B SER* 3.2 4.5 + - - +
821B PHE* 1.3 88.1 - - + +
823B GLU* 1.3 64.1 + - - +
825B VAL* 3.3 3.1 + - - +
826B ASN* 3.0 30.7 + - - +
855B MET* 3.8 16.2 - - - -
859B MET* 3.7 25.9 - - + +
897B ALA* 4.3 11.2 - - + +
900B ARG* 3.6 43.3 - - - +
901B VAL* 3.7 22.0 - - + -
904B GLU* 5.4 2.5 - - - +
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Residues in contact with GLU 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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783B TYR* 5.8 3.6 - - + -
819B SER* 3.0 22.5 + - - +
820B ASP* 3.7 8.7 - - - +
822B LEU* 1.3 76.3 - - - +
824B PHE* 1.3 57.9 + - - +
826B ASN* 3.4 11.8 + - - +
827B TYR* 3.0 26.7 + - - +
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Residues in contact with PHE 824 (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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741B VAL* 3.9 26.5 - - + -
743B LEU* 3.9 13.5 - - + -
783B TYR* 3.5 47.7 - + + -
804B LEU* 3.9 30.5 - - + -
806B TYR* 3.5 28.9 - + + -
809B TRP* 6.2 0.2 - + - -
820B ASP 3.0 13.7 + - - +
821B PHE* 3.4 11.4 - + - +
823B GLU* 1.3 75.3 - - - +
825B VAL* 1.3 69.5 + - + +
827B TYR* 3.0 9.0 + + - +
828B VAL* 2.9 38.1 + - + +
852B LEU* 4.6 8.3 - - + -
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Residues in contact with VAL 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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821B PHE* 2.9 46.7 + - + +
822B LEU 3.3 4.2 + - - +
824B PHE* 1.3 75.5 - - + +
826B ASN* 1.3 63.8 + - - +
828B VAL* 3.2 10.2 + - + +
829B ARG* 2.9 25.6 + - + +
852B LEU* 3.5 27.4 - - + -
855B MET* 4.2 8.7 - - + -
856B GLU* 4.2 19.1 - - + +
859B MET* 3.7 27.6 - - + -
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Residues in contact with ASN 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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822B LEU* 3.0 23.9 + - - +
823B GLU* 3.9 12.0 + - - +
825B VAL* 1.3 75.7 - - - +
827B TYR* 1.3 57.4 + - - +
829B ARG* 3.4 22.2 + - - +
830B SER* 3.0 27.2 + - - -
859B MET* 3.6 27.0 - - - +
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Residues in contact with TYR 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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783B TYR* 3.6 31.9 - + - +
785B SER* 4.2 7.7 + - - -
802B THR* 5.4 2.4 - - - +
804B LEU* 3.9 37.4 - - + +
823B GLU 3.0 13.6 + - - +
824B PHE* 3.0 13.1 + + - +
826B ASN* 1.3 73.3 - - - +
828B VAL* 1.3 63.9 - - - +
830B SER* 2.6 33.5 + - - -
831B LEU* 3.3 31.1 + - + +
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Residues in contact with VAL 828 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714B TYR* 6.2 0.2 - - + -
739B LEU* 4.3 10.0 - - + +
741B VAL* 4.0 27.8 - - + -
804B LEU* 4.3 6.5 - - + -
824B PHE* 2.9 44.9 + - + +
825B VAL* 3.5 10.5 - - + +
827B TYR* 1.3 75.3 - - - +
829B ARG* 1.3 65.4 + - - +
831B LEU* 3.0 19.9 + - - +
832B ARG* 3.1 11.3 + - - +
838B VAL* 4.8 9.6 - - + -
852B LEU* 4.8 13.7 - - + -
856B GLU* 4.7 15.5 - - - +
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Residues in contact with ARG 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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825B VAL* 2.9 19.7 + - + +
826B ASN* 3.6 21.2 + - - +
828B VAL* 1.3 76.2 - - - +
830B SER* 1.3 63.2 + - - +
831B LEU 3.2 0.7 + - - -
832B ARG* 3.3 17.2 + - - +
856B GLU* 3.6 32.5 + - + +
859B MET* 3.7 39.3 - - - +
860B CYS* 3.4 32.1 - - - +
863B GLU* 2.8 43.8 + - - -
864B ARG* 4.4 2.8 - - - +
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Residues in contact with SER 830 (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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826B ASN 3.0 14.1 + - - -
827B TYR* 2.6 35.3 + - - -
829B ARG* 1.3 77.3 - - - +
831B LEU* 1.3 64.6 + - - +
832B ARG 4.6 2.9 - - - +
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Residues in contact with LEU 831 (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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738B SER* 5.6 1.0 + - - -
739B LEU* 4.0 26.7 - - + +
802B THR* 4.5 12.8 - - + +
804B LEU* 3.9 20.2 - - + -
827B TYR* 3.4 42.8 - - + +
828B VAL 3.0 8.0 + - - +
830B SER* 1.3 86.3 - - - +
832B ARG* 1.3 65.4 - - - +
833B VAL* 3.3 13.0 + - - +
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Residues in contact with ARG 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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711B VAL 5.3 0.2 + - - -
712B ASN* 3.8 22.0 + - - +
713B LYS 2.9 35.0 + - - +
714B TYR* 3.1 27.5 - - - -
739B LEU* 5.3 0.2 - - - -
828B VAL* 3.1 10.4 + - + +
829B ARG* 3.3 17.3 + - - +
830B SER 4.6 2.3 - - - +
831B LEU* 1.3 78.7 - - - +
833B VAL* 1.3 71.8 + - - +
834B ASP* 4.0 3.9 + - - +
836B GLU 3.9 7.5 + - - -
838B VAL* 3.7 29.5 - - + +
856B GLU* 2.8 39.6 + - - -
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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