Contacts of the helix formed by residues 819 - 829 (chain B) in PDB entry 5TKD
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 819 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818B ARG* 1.3 76.6 - - - +
820B PRO* 1.4 75.0 - - - +
821B SER* 3.6 8.2 + - - -
822B GLU* 3.2 21.4 + - - +
823B LYS* 3.1 20.1 + - - +
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Residues in contact with PRO 820 (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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770B GLU* 5.9 9.2 - - + +
773B VAL* 3.3 27.4 - - + +
774B GLU* 5.8 8.5 - - + -
818B ARG 4.6 1.3 - - - +
819B SER* 1.4 85.0 - - - +
821B SER* 1.4 56.4 + - - +
823B LYS* 3.4 9.1 + - + -
824B GLU* 2.9 28.4 + - - +
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Residues in contact with SER 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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819B SER* 3.2 7.7 + - - -
820B PRO* 1.4 81.1 - - - +
822B GLU* 1.3 56.5 + - - +
824B GLU* 3.9 8.0 - - - +
825B HIS* 2.9 31.6 + - - +
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Residues in contact with GLU 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 ARG* 4.3 16.8 - - + -
819B SER* 3.2 19.1 + - - +
821B SER* 1.3 74.7 - - - +
823B LYS* 1.4 59.7 + - - +
825B HIS* 3.5 6.4 + - - +
826B PHE* 3.0 29.1 + - - +
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Residues in contact with LYS 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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773B VAL* 3.9 12.2 + - + +
774B GLU* 3.6 30.3 + - - +
776B ILE* 3.6 49.4 + - + +
778B TRP* 6.2 0.4 - - - -
815B LEU* 3.8 28.3 + - + +
818B ARG* 3.8 20.6 + - + -
819B SER 3.1 11.1 + - - +
820B PRO* 3.7 15.0 - - - +
822B GLU* 1.4 72.8 - - - +
824B GLU* 1.4 64.3 + - - +
826B PHE* 3.3 20.9 + - - +
827B TYR 3.4 5.0 + - - -
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Residues in contact with GLU 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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769B ARG* 2.8 41.4 + - - +
773B VAL* 4.1 19.3 - - + +
776B ILE* 4.1 9.5 - - - +
784B LEU* 4.2 5.1 - - + +
820B PRO 2.9 17.9 + - - +
821B SER* 3.9 7.9 - - - +
823B LYS* 1.4 75.4 - - - +
825B HIS* 1.4 57.4 + - - +
827B TYR* 3.3 4.5 + - - +
828B GLN* 3.0 51.7 + - - +
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Residues in contact with HIS 825 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821B SER 2.9 20.7 + - - +
822B GLU* 3.7 7.2 - - - +
824B GLU* 1.4 72.3 - - - +
826B PHE* 1.4 56.6 + - - +
828B GLN* 4.2 10.7 + - - +
829B ARG* 2.8 73.6 + - - +
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Residues in contact with PHE 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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776B ILE* 5.7 2.2 - - + -
815B LEU* 5.4 14.1 - - + -
822B GLU 3.0 13.6 + - - +
823B LYS* 3.3 14.1 - - - +
824B GLU 3.3 0.4 - - - -
825B HIS* 1.4 76.4 - - - +
827B TYR* 1.4 73.1 + + - +
829B ARG 3.7 0.9 + - - -
830B GLN 3.3 2.6 + - - -
831B HIS* 3.0 74.3 + + + +
832B ARG 3.3 28.0 - - - -
833B LEU* 4.0 23.3 - - + -
834B PRO* 5.4 2.7 - - + -
851B TYR* 4.6 0.2 - - - -
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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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776B ILE* 3.6 42.0 - - + -
777B PRO* 3.1 27.3 + - + +
779B LEU* 2.6 33.3 + - + -
780B ALA 4.2 0.9 - - - -
781B PRO* 3.6 27.3 - - + +
784B LEU* 3.9 20.2 - - + -
798B TRP* 3.3 21.0 + + - -
823B LYS 3.4 2.8 + - - +
824B GLU 3.3 8.0 + - - +
826B PHE* 1.4 89.9 - + - +
828B GLN* 1.3 60.4 + - - +
830B GLN* 2.9 30.5 + - - +
833B LEU* 5.4 1.3 - - + -
851B TYR* 3.4 19.7 - - + -
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Residues in contact with GLN 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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769B ARG* 3.5 11.1 - - - +
784B LEU* 4.7 8.1 - - + -
824B GLU* 3.0 50.3 + - + +
825B HIS* 3.3 10.7 + - - +
827B TYR* 1.3 74.6 - - - +
829B ARG* 1.3 64.2 + - + +
830B GLN* 3.2 12.3 + - - +
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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 HIS* 2.8 44.8 + - - +
828B GLN* 1.3 76.0 - - + +
830B GLN* 1.4 69.7 + - - +
831B HIS* 3.3 38.1 + - + +
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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