Contacts of the helix formed by residues 817 - 830 (chain B) in PDB entry 2O8C
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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534B ASN* 5.4 1.7 + - - -
768B PRO* 3.6 27.3 - - + +
769B PHE* 4.1 3.4 - - - -
772B ARG* 2.6 45.0 + - - -
816B PRO* 1.3 72.3 - - - +
818B LEU* 1.3 55.1 + - - +
819B GLU* 3.6 2.9 + - - +
820B ARG* 3.0 35.3 + - + +
821B LEU* 2.9 28.7 + - - +
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Residues in contact with LEU 818 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B PHE* 4.0 7.3 - - + -
815B LEU* 4.6 5.4 - - + -
816B PRO* 2.8 32.1 + - + +
817B ASP* 1.3 66.8 - - - +
819B GLU* 1.3 59.8 + - - +
820B ARG 3.3 0.2 - - - -
821B LEU* 3.7 7.6 - - + +
822B LEU* 2.9 36.9 + - + +
861B ALA* 3.7 35.7 - - + +
864B GLY* 3.9 25.1 - - - -
865B PHE* 3.9 16.8 - - + +
868B MET* 3.6 29.2 - - + -
1051B VAL* 3.8 14.1 - - + -
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Residues in contact with GLU 819 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B LEU* 3.7 20.3 - - + +
769B PHE* 4.1 10.3 - - + +
772B ARG* 2.8 45.5 + - - +
817B ASP* 3.2 1.2 + - - +
818B LEU* 1.3 79.9 - - - +
820B ARG* 1.3 61.9 + - - +
822B LEU* 3.6 3.8 + - - +
823B SER* 3.4 19.9 + - - -
1048B GLN* 3.7 33.9 + - - +
1051B VAL* 3.9 19.1 - - + +
1052B GLU* 5.5 2.9 - - - +
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Residues in contact with ARG 820 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 5.0 3.6 - - - -
531B PRO* 3.4 30.9 - - - +
533B GLU 3.1 22.6 + - - -
534B ASN* 3.4 24.0 + - - +
535B TYR 3.8 13.7 + - - -
536B SER* 4.1 2.4 + - - +
537B LYS* 5.2 1.0 - - - +
562B ASP* 3.5 21.0 + - - -
564B SER* 3.4 28.0 + - - +
565B LEU* 3.7 17.7 - - + +
772B ARG* 3.8 5.8 - - - +
817B ASP* 3.0 33.7 + - + +
819B GLU* 1.3 77.8 - - - +
821B LEU* 1.3 63.3 + - - +
823B SER* 3.1 7.6 + - - -
824B LYS* 3.0 29.8 + - + +
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Residues in contact with LEU 821 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816B PRO* 3.9 21.5 - - + -
817B ASP 2.9 16.4 + - - +
818B LEU* 3.9 10.5 - - + +
819B GLU 3.4 0.2 - - - -
820B ARG* 1.3 72.0 - - - +
822B LEU* 1.3 60.8 + - - +
824B LYS* 3.1 17.0 + - + +
825B ILE* 2.9 38.1 + - + +
857B ASP* 4.0 34.1 - - + +
860B SER* 3.4 26.2 - - - +
861B ALA* 4.0 22.4 - - + +
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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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703B MET* 5.7 0.9 - - - -
818B LEU 2.9 25.9 + - - +
819B GLU* 3.7 5.6 - - - +
820B ARG 3.2 0.4 - - - -
821B LEU* 1.3 75.8 - - + +
823B SER* 1.3 57.3 + - - +
825B ILE* 3.4 5.7 + - + +
826B HIS* 2.9 28.1 + - - +
861B ALA* 5.7 0.7 - - + -
865B PHE* 3.7 17.5 - - + -
1040B PHE* 3.7 22.4 - - + -
1041B ASP* 4.8 2.3 - - - +
1044B TYR* 5.4 1.8 - - - +
1047B TRP* 3.6 50.7 - - + +
1048B GLN* 3.9 23.8 - - + +
1051B VAL* 4.1 4.7 - - + -
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Residues in contact with SER 823 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B SER 3.5 22.2 - - - -
565B LEU* 2.9 27.5 + - - +
700B LEU* 6.6 0.2 - - - -
703B MET* 3.8 14.7 - - - +
819B GLU 3.4 12.1 + - - -
820B ARG 3.1 6.1 + - - -
822B LEU* 1.3 76.7 - - - +
824B LYS* 1.3 59.6 + - - +
826B HIS* 3.4 7.6 + - - +
827B ASN* 3.0 39.0 + - - -
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Residues in contact with LYS 824 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B THR 4.5 10.3 - - - +
524B TYR* 3.3 30.4 + - + +
525B SER* 4.3 14.5 + - - +
526B VAL* 5.1 3.0 - - - +
564B SER 5.8 1.6 - - - +
820B ARG* 3.0 21.0 + - + +
821B LEU* 3.5 24.2 - - + +
823B SER* 1.3 73.1 - - - +
825B ILE* 1.3 66.0 + - + +
827B ASN* 3.5 9.3 + - - +
828B VAL* 3.2 28.9 + - + +
857B ASP* 2.8 29.4 + - + +
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Residues in contact with ILE 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 LEU* 2.9 23.7 + - + +
822B LEU* 3.7 5.4 - - + +
824B LYS* 1.3 74.6 - - + +
826B HIS* 1.3 67.7 + - - +
828B VAL* 3.2 7.3 + - - +
829B GLY* 3.1 16.8 + - - -
857B ASP* 4.6 6.7 - - + +
858B PHE* 4.3 18.6 - - + +
861B ALA* 3.6 31.6 - - + -
1037B PHE* 3.7 39.8 - - + +
1040B PHE* 3.7 31.9 - - + -
1041B ASP* 4.9 1.6 - - + +
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Residues in contact with HIS 826 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LYS* 4.3 5.3 + - - -
699B GLU* 2.9 24.3 + - - -
702B SER* 2.9 21.1 + - - -
703B MET* 3.3 32.0 - - + +
822B LEU 2.9 13.7 + - - +
823B SER* 3.5 10.3 - - - +
824B LYS 3.3 0.2 - - - -
825B ILE* 1.3 78.0 - - - +
827B ASN* 1.3 82.7 + - - +
828B VAL 3.1 0.5 + - - -
829B GLY* 3.1 1.2 + - - -
830B SER* 3.0 27.5 + - - -
1041B ASP* 2.9 46.8 + - - +
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Residues in contact with ASN 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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523B THR* 4.4 20.8 + - - +
563B THR 5.3 1.6 + - - -
564B SER 5.7 1.4 + - - -
699B GLU* 3.1 44.5 + - - +
700B LEU* 4.4 6.8 + - - +
703B MET* 4.6 4.0 - - - +
823B SER* 3.0 25.9 + - - +
824B LYS* 3.8 8.7 - - - +
825B ILE 3.3 0.2 - - - -
826B HIS* 1.3 90.2 - - - +
828B VAL* 1.3 61.6 + - + +
830B SER* 3.5 15.1 - - - +
833B LYS* 4.4 15.3 + - - +
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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
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526B VAL* 6.5 0.2 - - + -
824B LYS* 3.2 17.9 + - + +
825B ILE* 3.2 6.7 + - - +
826B HIS 3.1 0.8 - - - -
827B ASN* 1.3 80.2 - - + +
829B GLY* 1.3 62.3 + - - +
830B SER 3.3 2.8 + - - +
854B LYS* 4.1 34.3 - - + +
1034B ARG* 3.3 18.4 - - + +
1037B PHE* 3.5 32.1 - - + -
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Residues in contact with GLY 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 ILE 3.1 10.3 + - - -
826B HIS* 3.7 2.5 - - - -
828B VAL* 1.3 77.3 - - - +
830B SER* 1.3 64.0 + - - +
831B PRO* 3.1 7.9 - - - +
1034B ARG* 3.2 37.6 + - - -
1037B PHE* 4.1 2.4 - - - +
1038B TYR* 3.4 26.0 - - - +
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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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698B GLN 4.2 4.2 + - - -
699B GLU* 4.4 4.1 - - - -
702B SER* 3.9 14.4 + - - -
826B HIS* 3.0 21.2 + - - -
827B ASN* 3.5 19.1 - - - -
828B VAL 3.2 3.8 - - - +
829B GLY* 1.3 75.5 - - - +
831B PRO* 1.3 70.7 - - - +
832B LEU* 3.9 5.5 + - - +
833B LYS* 3.8 21.0 + - - +
834B SER* 3.4 20.6 + - - -
1034B ARG* 4.3 1.0 - - - -
1038B TYR* 5.0 0.9 - - - -
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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