Contacts of the helix formed by residues 916 - 927 (chain C) in PDB entry 3LZB
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 THR 916 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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911C GLN* 3.8 0.9 - - - +
914C ILE 3.8 0.2 + - - -
915C CYS* 1.3 74.7 - - - +
917C ILE* 1.3 67.2 + - - +
918C ASP* 3.6 16.3 + - - -
919C VAL* 3.0 21.5 + - - +
920C TYR* 3.0 11.3 + - - +
953C ARG 3.6 13.7 - - - +
954C TYR* 2.3 52.1 + - - +
956C VAL* 4.1 20.0 - - + -
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Residues in contact with ILE 917 (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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898A GLU* 5.8 3.6 - - + -
901A SER* 3.9 29.4 - - - +
902A ILE* 4.5 12.1 - - + -
905A LYS* 4.3 20.9 - - + -
911C GLN* 3.9 15.4 - - - +
916C THR* 1.3 73.1 - - - +
918C ASP* 1.3 62.8 + - - +
920C TYR* 3.3 20.8 + - + -
921C MET* 2.6 61.6 + - - +
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Residues in contact with ASP 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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905A LYS* 6.3 0.4 - - - -
916C THR* 3.6 16.6 + - - +
917C ILE* 1.3 81.9 + - - +
919C VAL* 1.3 59.3 + - - +
921C MET* 3.5 8.2 - - - +
922C ILE* 3.0 29.5 + - - +
947C MET* 3.7 18.6 - - + -
953C ARG* 4.5 9.3 + - - +
954C TYR* 3.9 19.8 - - + -
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Residues in contact with VAL 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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791C LEU* 4.8 3.6 - - + -
880C VAL* 5.3 0.2 - - + -
884C MET* 4.5 18.2 - - + -
915C CYS* 3.9 24.0 - - + -
916C THR* 3.0 9.9 + - - +
918C ASP* 1.3 73.9 - - - +
920C TYR* 1.3 68.0 + - - +
922C ILE* 2.9 19.0 + - - +
923C MET* 3.1 19.5 + - + +
944C PHE* 4.7 10.8 - - + -
947C MET* 3.9 15.9 - - + -
954C TYR* 3.2 39.5 - - + +
955C LEU* 4.6 5.4 - - + -
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Residues in contact with TYR 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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894A ILE* 5.8 8.1 - - + +
898A GLU* 4.4 11.0 - - - -
902A ILE* 6.2 2.7 - - + -
908C ARG* 4.8 2.3 - - - +
909C LEU 2.6 27.5 + - - -
910C PRO* 3.8 3.4 - - - +
911C GLN* 3.5 59.9 + - + +
912C PRO* 4.2 1.8 - - + -
915C CYS* 4.4 3.0 - - + +
916C THR 3.0 11.2 + - - +
917C ILE* 3.7 18.2 - - + +
919C VAL* 1.3 76.1 - - - +
921C MET* 1.3 55.4 + - - +
923C MET* 3.1 21.4 + - + +
924C ARG* 2.7 57.3 + - + +
927C TRP* 4.3 13.7 - + - -
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Residues in contact with MET 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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902A ILE* 4.4 8.3 - - + +
905A LYS* 3.9 28.0 - - + +
907A GLU* 2.8 54.1 - - + +
917C ILE* 2.6 46.7 + - - +
918C ASP* 3.5 11.2 - - - +
920C TYR* 1.3 73.3 - - - +
922C ILE* 1.3 58.1 + - + +
924C ARG* 3.4 8.7 + - + +
925C LYS* 3.0 27.7 + - - +
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Residues in contact with ILE 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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876C TYR* 5.8 0.2 - - + -
918C ASP 3.0 17.9 - - - +
919C VAL* 2.9 8.5 + - - +
921C MET* 1.3 73.8 - - + +
923C MET* 1.3 68.9 + - + +
925C LYS* 3.0 17.8 + - - +
926C CYS* 3.2 13.2 + - - -
935C PRO* 5.2 2.0 - - + -
940C LEU* 3.6 29.2 - - + -
943C GLU* 3.9 27.1 - - + -
944C PHE* 3.9 26.5 - - + -
947C MET* 4.1 18.6 - - + -
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Residues in contact with MET 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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877C GLY* 3.9 5.2 - - - +
880C VAL* 4.0 24.9 - - + -
881C TRP* 3.0 59.9 - - + +
884C MET* 4.8 0.4 - - - -
912C PRO* 4.3 11.4 - - + -
915C CYS* 4.5 9.0 - - - -
919C VAL* 3.7 11.0 - - + +
920C TYR* 3.1 25.1 + - + +
922C ILE* 1.3 77.3 - - + +
924C ARG* 1.3 58.8 + - - +
926C CYS* 2.9 34.9 + - - +
927C TRP* 3.5 28.9 + - + -
944C PHE* 5.8 1.6 - - + -
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Residues in contact with ARG 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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894A ILE* 5.8 5.0 - - + +
907A GLU* 4.0 31.7 + - - +
910A PRO* 6.0 3.6 - - - +
906C GLY 6.0 0.2 - - - -
908C ARG* 3.5 54.6 - - - +
920C TYR* 2.7 48.4 + - + +
921C MET* 3.5 12.1 - - + +
923C MET* 1.3 73.3 - - - +
925C LYS* 1.3 60.9 + - - +
927C TRP* 3.1 23.8 + - + +
928C MET* 3.8 21.4 + - - +
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Residues in contact with LYS 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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921C MET 3.0 14.0 + - - +
922C ILE* 3.0 12.3 + - - +
924C ARG* 1.3 75.5 - - - +
926C CYS* 1.3 58.4 + - - +
928C MET* 2.9 41.0 - - + +
933C SER 3.4 22.9 + - - +
934C ARG* 3.4 2.2 - - - +
935C PRO* 3.0 43.0 - - + +
939C GLU* 3.6 22.2 + - - -
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Residues in contact with CYS 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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873C VAL* 3.8 36.1 - - - +
874C TRP* 3.4 13.0 - - - -
876C TYR* 4.2 13.0 - - - -
877C GLY* 4.0 19.3 - - - -
922C ILE* 3.2 16.8 + - - -
923C MET* 2.9 13.2 + - - +
925C LYS* 1.3 76.6 - - - +
927C TRP* 1.3 59.4 + - + +
928C MET 3.4 0.9 - - - -
934C ARG* 3.1 21.0 + - - -
935C PRO* 4.0 15.3 - - - -
940C LEU* 4.3 7.6 - - - -
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Residues in contact with TRP 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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874C TRP* 3.2 58.7 + + + -
877C GLY* 3.5 23.9 - - - -
878C VAL* 3.6 12.2 - - + +
881C TRP* 4.4 0.4 - + - -
891C TYR* 5.5 2.7 - - - -
908C ARG* 3.0 54.5 + - + +
909C LEU* 3.9 47.8 - - + -
920C TYR* 4.3 3.8 - + - -
923C MET* 3.5 47.8 - - + -
924C ARG* 3.1 25.8 + - - +
926C CYS* 1.3 83.6 - - - +
928C MET* 1.3 62.5 + - - +
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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