Contacts of the helix formed by residues 853 - 865 (chain Z) in PDB entry 5WTI
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 ARG 853 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E C 3.2 28.7 + - - +
14E T 2.9 26.4 + - - +
830Z LEU* 3.7 21.0 - - - +
831Z SER* 3.3 34.4 - - - +
852Z ARG* 1.3 94.0 - - + +
854Z GLU* 1.3 64.6 + - - +
855Z ILE 3.2 1.6 - - - -
856Z PRO* 3.4 15.7 - - - +
857Z ARG* 3.6 40.8 + - - +
872Z GLU* 3.1 32.5 + - - -
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Residues in contact with GLU 854 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E C 4.1 15.8 + - - +
792Z LEU* 4.2 19.0 - - + +
851Z SER* 3.4 12.1 + - - +
852Z ARG 3.3 0.8 - - - -
853Z ARG* 1.3 77.1 - - - +
855Z ILE* 1.3 58.7 + - - +
856Z PRO 3.6 0.2 - - - -
857Z ARG* 3.6 26.1 + - - +
858Z GLN* 2.9 60.6 + - + +
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Residues in contact with ILE 855 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575Z LEU* 3.7 27.8 - - + -
580Z ALA 5.6 0.2 - - - +
792Z LEU* 3.5 26.5 - - + +
795Z MET* 3.5 27.8 - - + -
796Z ALA* 4.5 4.4 - - - +
799Z ILE* 3.9 28.3 - - + -
827Z PHE* 4.1 4.9 - - + -
850Z TRP* 4.4 12.1 - - + +
851Z SER 4.0 1.6 - - - +
852Z ARG* 3.6 21.1 - - - +
854Z GLU* 1.3 77.3 - - - +
856Z PRO* 1.3 66.1 - - + +
858Z GLN* 3.8 2.8 - - - +
859Z VAL* 3.0 33.4 + - + +
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Residues in contact with PRO 856 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575Z LEU* 4.7 4.7 - - + -
827Z PHE* 3.7 47.3 - - + -
828Z GLU 5.8 1.1 - - - +
852Z ARG 3.3 16.4 - - - +
853Z ARG* 3.4 15.0 - - - +
855Z ILE* 1.3 91.1 - - + +
857Z ARG* 1.3 55.1 + - - +
859Z VAL* 4.1 0.3 - - - +
860Z ALA* 3.0 29.6 + - - +
870Z VAL* 4.2 8.0 - - + +
872Z GLU* 4.3 19.1 - - - +
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Residues in contact with ARG 857 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E T 2.4 37.9 + - - +
853Z ARG* 3.6 32.8 + - - +
854Z GLU* 3.4 22.7 + - - +
855Z ILE 3.2 0.8 - - - -
856Z PRO* 1.3 80.4 - - - +
858Z GLN* 1.3 64.3 + - + +
860Z ALA* 3.6 5.5 + - - +
861Z LEU* 3.3 33.3 + - + +
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Residues in contact with GLN 858 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789Z GLU* 5.3 3.0 + - - +
792Z LEU* 3.7 19.5 - - - +
793Z LYS* 3.6 34.5 - - - +
796Z ALA* 3.7 16.2 - - + +
854Z GLU* 2.9 44.2 + - + +
855Z ILE* 3.9 1.1 - - - +
857Z ARG* 1.3 77.5 - - + +
859Z VAL* 1.3 60.4 + - - +
860Z ALA 3.1 1.6 - - - -
861Z LEU* 3.1 10.6 + - + +
862Z GLN* 2.8 38.9 + - + +
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Residues in contact with VAL 859 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796Z ALA* 3.6 29.8 - - - +
799Z ILE* 4.1 15.7 - - + -
800Z ILE* 3.4 24.3 - - + +
825Z ILE* 3.8 20.6 - - + -
827Z PHE* 3.8 30.1 - - + -
855Z ILE* 3.0 22.1 + - + +
856Z PRO 4.1 1.6 - - - +
858Z GLN* 1.3 76.5 - - - +
860Z ALA* 1.3 57.9 + - - +
863Z GLY* 3.0 24.1 + - - -
870Z VAL* 4.1 4.6 - - + +
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Residues in contact with ALA 860 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856Z PRO 3.0 19.1 + - - +
857Z ARG* 3.8 6.7 - - - +
859Z VAL* 1.3 78.1 - - - +
861Z LEU* 1.3 58.6 + - + +
863Z GLY* 3.9 0.4 - - - -
864Z GLU* 3.1 27.9 + - - +
868Z LEU 5.2 2.5 - - - +
870Z VAL* 3.6 25.7 - - + +
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Residues in contact with LEU 861 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B C 3.8 36.1 - - + +
4Z ARG* 2.8 50.0 + - - +
857Z ARG* 3.3 23.0 + - + +
858Z GLN* 3.1 12.4 + - + +
860Z ALA* 1.3 79.9 - - + +
862Z GLN* 1.3 66.1 + - + +
864Z GLU* 3.4 14.1 + - - +
865Z ILE* 4.4 3.5 + - - +
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Residues in contact with GLN 862 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B C 2.9 37.6 + - - -
103B C 4.9 9.4 + - - +
793Z LYS* 3.6 21.6 + - - +
796Z ALA* 3.8 7.2 - - + +
797Z ASN* 3.7 24.3 + - - +
800Z ILE* 3.7 22.0 - - + +
858Z GLN* 2.8 27.8 + - + +
861Z LEU* 1.3 79.2 - - + +
863Z GLY* 1.3 60.7 + - - +
864Z GLU 3.6 0.3 + - - -
865Z ILE* 4.0 6.4 - - - +
866Z TYR* 3.7 21.7 - - - -
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Residues in contact with GLY 863 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800Z ILE* 3.5 16.5 - - - +
859Z VAL 3.0 13.4 + - - -
860Z ALA 3.9 1.1 - - - -
862Z GLN* 1.3 75.4 - - - +
864Z GLU* 1.3 63.0 + - - +
865Z ILE 3.3 1.3 - - - -
866Z TYR* 3.2 13.3 + - - -
868Z LEU* 2.9 42.6 + - - +
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Residues in contact with GLU 864 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Z MET* 4.9 4.0 - - - +
2Z ALA* 4.1 21.1 - - + +
4Z ARG* 2.6 32.2 + - - +
518Z PRO* 3.4 13.8 - - + +
520Z GLU* 5.1 0.5 - - - +
860Z ALA 3.1 18.7 + - - +
861Z LEU* 3.7 15.1 - - - +
862Z GLN 3.3 1.2 - - - -
863Z GLY* 1.3 78.1 - - - +
865Z ILE* 1.3 58.1 + - - +
867Z GLY* 3.0 18.9 + - - -
868Z LEU 4.5 7.6 - - - -
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Residues in contact with ILE 865 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z ALA* 4.1 21.3 - - + -
4Z ARG* 4.2 19.3 - - + +
468Z TYR* 3.6 35.9 - - + +
477Z LEU* 3.6 15.8 - - + +
516Z ILE* 4.6 16.8 - - + -
518Z PRO* 3.2 12.7 - - + +
519Z THR* 3.0 26.2 + - - +
861Z LEU 4.5 2.5 - - - +
862Z GLN 4.0 6.0 + - - +
864Z GLU* 1.3 76.3 - - - +
866Z TYR* 1.3 87.4 + - + +
867Z GLY 3.4 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