Contacts of the helix formed by residues 808 - 821 (chain B) in PDB entry 5WRZ
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 808 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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804B VAL* 3.5 10.2 - - - +
805B ASP* 2.7 32.8 + - - +
807B ASP* 1.3 83.2 - - - +
809B GLU* 1.3 59.0 + - - +
810B GLU* 3.6 11.7 - - - +
811B ALA* 3.3 17.2 + - - +
812B GLU* 3.0 28.5 + - - +
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Residues in contact with GLU 809 (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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808B SER* 1.3 70.8 - - - +
810B GLU* 1.3 66.5 + - - +
812B GLU* 3.1 18.4 + - - +
813B ILE* 3.0 37.0 + - + +
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Residues in contact with GLU 810 (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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804B VAL* 3.6 24.2 - - + +
805B ASP 5.6 0.2 + - - -
808B SER* 3.6 14.3 + - - +
809B GLU* 1.3 77.6 - - - +
811B ALA* 1.3 59.6 + - - +
813B ILE* 3.3 7.3 + - - +
814B ILE* 3.0 35.3 + - - +
838B LYS* 4.0 10.4 - - - +
964B LEU* 4.3 19.0 - - + +
965B ASP* 5.4 1.3 - - - +
1001B TYR* 2.8 44.4 + - + +
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Residues in contact with ALA 811 (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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804B VAL* 4.0 9.9 - - + -
805B ASP 3.3 26.2 - - - +
806B ARG* 3.3 17.9 - - - +
808B SER* 3.3 4.6 + - - +
809B GLU 3.3 0.4 - - - -
810B GLU* 1.3 81.3 - - - +
812B GLU* 1.3 57.7 + - - +
814B ILE* 3.7 1.9 - - - +
815B ARG* 2.9 43.1 + - - +
836B ILE* 4.2 15.5 - - + +
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Residues in contact with GLU 812 (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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807B ASP 3.4 18.2 - - - +
808B SER 3.0 14.6 + - - +
809B GLU* 3.1 18.0 + - - +
811B ALA* 1.3 75.2 - - - +
813B ILE* 1.3 67.3 + - + +
815B ARG* 3.5 23.9 + - - +
816B LYS* 3.1 23.0 + - - +
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Residues in contact with ILE 813 (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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809B GLU* 3.0 32.2 + - + +
810B GLU* 3.3 4.9 + - - +
812B GLU* 1.3 74.1 - - + +
814B ILE* 1.3 57.8 + - + +
816B LYS* 3.1 8.9 + - + +
817B TYR* 2.8 33.5 + - + +
859B LEU* 5.9 0.7 - - + -
962B ILE* 4.6 14.6 - - + -
963B SER 4.5 12.6 - - - +
964B LEU* 4.3 37.7 - - + -
969B VAL* 4.4 15.9 - - + -
971B LEU* 3.9 18.2 - - + +
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Residues in contact with ILE 814 (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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810B GLU* 3.0 24.5 + - + +
811B ALA* 3.7 3.8 - - - +
813B ILE* 1.3 79.5 - - + +
815B ARG* 1.3 64.4 + - - +
817B TYR* 3.0 10.3 + - - +
818B VAL* 3.0 22.4 + - + +
833B VAL* 5.7 0.2 - - + -
836B ILE* 3.7 35.4 - - + -
859B LEU* 5.5 1.3 - - + -
861B TRP* 4.8 0.9 - - + -
921B LEU* 4.0 17.0 - - + -
964B LEU* 5.2 3.6 - - + -
1001B TYR* 3.9 35.7 - - + -
1003B LEU* 3.7 32.5 - - + -
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Residues in contact with ARG 815 (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 ARG* 3.1 40.0 + - - +
807B ASP* 5.4 0.8 - - - +
811B ALA* 2.9 27.0 + - - +
812B GLU* 3.8 27.3 - - - +
814B ILE* 1.3 75.8 - - - +
816B LYS* 1.3 56.7 + - - +
818B VAL* 3.4 9.4 + - - +
819B LYS* 2.9 30.5 + - - +
833B VAL* 4.5 21.1 - - + -
836B ILE* 4.5 9.7 - - + +
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Residues in contact with LYS 816 (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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812B GLU 3.1 17.3 + - - +
813B ILE* 3.1 7.6 + - + +
815B ARG* 1.3 74.2 - - - +
817B TYR* 1.3 64.7 + - - +
819B LYS* 4.0 11.2 - - + -
820B ASN* 3.0 53.2 + - - +
962B ILE* 5.3 4.0 - - + -
971B LEU* 4.3 24.1 - - + +
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Residues in contact with TYR 817 (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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813B ILE 2.8 13.1 + - - +
814B ILE* 3.4 11.4 - - - +
816B LYS* 1.3 76.5 - - - +
818B VAL* 1.3 56.2 + - - +
821B THR* 2.6 40.9 + - + +
859B LEU* 2.8 32.6 + - + -
860B LEU* 4.0 1.6 - - - +
861B TRP* 3.4 29.0 - + + -
899B ASP* 3.4 32.0 + - - -
921B LEU* 3.6 24.7 - - + -
969B VAL* 3.6 18.8 - - + -
970B PRO* 3.4 30.7 - - + +
971B LEU* 3.9 17.7 - - + +
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Residues in contact with VAL 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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814B ILE 3.0 16.3 + - - +
815B ARG 3.6 7.2 - - - +
817B TYR* 1.3 75.0 - - - +
819B LYS* 1.3 65.2 + - - +
820B ASN 3.4 0.3 + - - -
821B THR 3.7 2.4 + - - -
822B HIS* 3.9 7.6 + - - +
831B LEU* 4.4 25.4 - - + +
833B VAL* 4.1 21.5 - - + -
861B TRP* 3.6 23.8 - - + -
901B VAL* 3.4 32.9 - - + +
1003B LEU* 3.9 15.7 - - + -
1005B LEU* 4.9 3.6 - - + -
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Residues in contact with LYS 819 (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 ARG 2.9 18.7 + - - +
816B LYS* 3.1 13.4 + - + +
818B VAL* 1.3 80.0 - - - +
820B ASN* 1.3 72.1 + - - +
821B THR 3.8 0.2 + - - -
822B HIS* 4.4 7.3 + - - +
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Residues in contact with ASN 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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816B LYS* 3.0 47.2 + - - +
819B LYS* 1.3 95.3 + - - +
821B THR* 1.3 61.3 + - + +
822B HIS 3.5 4.1 + - - +
900B MET* 5.3 0.9 - - - +
971B LEU* 3.1 29.4 + - - +
972B GLY* 5.1 0.6 - - - -
973B THR* 3.6 43.2 - - + +
974B GLY 4.4 2.4 + - - -
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Residues in contact with THR 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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817B TYR* 2.6 35.3 + - + +
818B VAL 3.7 0.2 + - - -
819B LYS 3.5 0.6 - - - -
820B ASN* 1.3 79.9 - - - +
822B HIS* 1.3 60.6 + - - +
823B ALA 3.5 3.2 + - - -
861B TRP* 3.9 3.5 + - - -
899B ASP 3.9 12.1 - - - +
900B MET* 3.7 30.0 - - - +
901B VAL* 3.0 43.3 + - - +
902B SER 3.8 1.2 + - - -
956B PRO* 5.1 0.4 - - + -
970B PRO 4.0 5.6 - - - +
971B LEU* 4.3 4.5 - - - +
972B GLY 3.8 17.7 - - - +
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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