Contacts of the helix formed by residues 917 - 929 (chain C) in PDB entry 4YOC
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 CYS 917 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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915C HIS 5.1 0.9 - - - -
916C GLY* 1.3 78.8 - - - -
918C VAL* 1.3 67.2 - - - +
919C ARG* 3.1 26.2 - - + +
920C ASP* 3.0 18.8 + - - +
921C LEU 3.5 2.1 + - - -
955C GLU 3.7 13.0 - - - +
956C ASP* 3.7 15.3 - - - +
957C GLU 3.3 12.1 - - - +
958C LEU* 4.1 14.8 - - - -
959C LEU* 3.3 18.9 - - - +
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Residues in contact with VAL 918 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917C CYS* 1.3 71.3 - - - +
919C ARG* 1.3 64.1 + - - +
921C LEU* 3.0 5.1 + - - +
922C LEU* 2.9 37.2 + - + +
941C LEU* 3.7 36.1 - - + -
953C HIS* 4.2 10.5 - - + +
954C GLN 3.9 1.8 - - - +
955C GLU* 3.6 22.4 + - - +
957C GLU* 2.8 36.2 + - + +
959C LEU* 3.9 8.2 - - + +
962C LEU* 4.2 15.5 - - + -
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Residues in contact with ARG 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917C CYS* 3.9 21.8 - - + +
918C VAL* 1.3 75.6 - - - +
920C ASP* 1.3 71.1 + - - +
922C LEU* 3.4 8.6 + - - +
923C GLU* 2.9 31.2 + - + +
955C GLU* 2.9 41.1 + - + +
956C ASP* 2.3 35.2 + - - +
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Residues in contact with ASP 920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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912C PRO* 4.2 14.8 - - + -
913C ASP* 5.2 4.8 - - + +
916C GLY* 3.2 12.5 - - - -
917C CYS* 3.0 30.4 + - - +
919C ARG* 1.3 90.4 + - - +
921C LEU* 1.3 60.6 + - - +
923C GLU* 3.2 8.8 + - - +
924C GLU* 2.9 32.3 + - + +
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Residues in contact with LEU 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894C PHE* 3.8 46.4 - - + -
896C CYS* 4.8 0.2 - - - -
910C LEU* 4.0 17.6 - - + +
912C PRO* 3.8 31.0 - - + +
917C CYS 3.5 2.0 + - - -
918C VAL 3.0 8.4 + - - +
920C ASP* 1.3 78.7 - - - +
922C LEU* 1.3 63.0 + - + +
924C GLU* 3.1 5.6 + - - +
925C CYS* 2.9 21.8 + - - +
941C LEU* 4.1 24.5 - - + -
959C LEU* 4.0 17.9 - - + -
972C ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918C VAL* 2.9 29.8 + - + +
919C ARG* 3.6 7.9 - - - +
921C LEU* 1.3 76.9 - - + +
923C GLU* 1.3 57.1 + - - +
925C CYS* 3.4 3.9 + - - +
926C LYS* 2.9 24.4 + - - +
939C LEU* 3.4 38.7 - - + +
940C ARG* 3.8 23.1 - - - +
941C LEU* 4.0 12.6 - - + +
953C HIS 5.8 0.7 - - - +
955C GLU* 4.6 17.5 - - + +
972C ILE* 3.7 31.6 - - + -
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Residues in contact with GLU 923 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919C ARG* 2.9 18.9 + - + +
920C ASP* 3.4 14.1 - - - +
921C LEU 3.1 0.2 - - - -
922C LEU* 1.3 75.2 - - - +
924C GLU* 1.3 58.7 + - - +
926C LYS* 3.2 38.5 + - - +
927C LYS* 2.9 45.3 + - + +
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Residues in contact with GLU 924 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910C LEU* 4.0 21.4 - - + +
911C TYR* 4.3 17.1 + - - +
912C PRO* 4.1 23.4 - - + +
920C ASP* 2.9 16.7 + - + +
921C LEU* 3.4 7.6 - - - +
923C GLU* 1.3 76.1 - - - +
925C CYS* 1.3 62.0 + - - +
927C LYS* 3.0 38.7 + - - +
928C ALA* 3.0 22.2 + - - +
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Residues in contact with CYS 925 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C TRP* 3.6 30.7 - - - -
908C ILE* 4.8 4.7 - - - -
910C LEU* 3.6 25.3 - - + +
921C LEU 2.9 6.4 + - - +
922C LEU 3.7 7.4 - - - +
923C GLU 3.3 0.2 - - - -
924C GLU* 1.3 76.0 - - - +
926C LYS* 1.3 62.3 + - - +
928C ALA* 3.2 8.9 + - - +
929C VAL* 3.2 25.6 + - - +
939C LEU* 4.4 1.6 - - + -
972C ILE* 3.6 40.8 - - + -
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Residues in contact with LYS 926 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922C LEU 2.9 17.4 + - - +
923C GLU* 3.3 38.0 + - - +
925C CYS* 1.3 75.8 - - - +
927C LYS* 1.3 64.7 + - + +
928C ALA 3.3 0.5 + - - -
929C VAL* 3.5 20.7 - - - +
931C LEU* 5.0 14.5 - - + +
937C GLY 4.4 18.5 + - - +
939C LEU* 3.6 19.7 - - + +
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Residues in contact with LYS 927 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923C GLU* 2.9 28.4 + - + +
924C GLU* 3.0 48.8 + - - +
926C LYS* 1.3 77.1 - - - +
928C ALA* 1.3 58.7 + - - +
929C VAL 4.8 1.1 - - - +
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Residues in contact with ALA 928 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908C ILE* 4.0 25.6 - - + -
910C LEU* 4.2 7.2 - - + -
924C GLU 3.0 13.6 + - - +
925C CYS 3.6 5.6 - - - +
926C LYS 3.1 0.8 - - - -
927C LYS* 1.3 80.2 - - - +
929C VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 929 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898C TRP* 3.5 62.4 - - + +
908C ILE* 4.6 6.7 - - + -
925C CYS* 3.2 22.4 + - - +
926C LYS* 3.5 14.3 + - - +
927C LYS 4.8 1.2 - - - +
928C ALA* 1.3 90.3 - - + +
930C GLU* 1.3 63.4 + - - +
931C LEU* 4.0 11.6 - - + +
939C LEU* 5.5 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