Contacts of the helix formed by residues 904 - 920 (chain C) in PDB entry 1ZYC
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 GLU 904 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827C HIS* 3.4 47.2 - - + +
831C ILE 4.9 0.4 - - - +
832C ILE* 3.5 25.5 - - + +
903C ASN* 1.3 81.1 - - - +
905C LYS* 1.3 83.8 + - + +
906C ILE 2.7 13.2 + - - -
907C ASP* 2.8 21.9 + - - +
908C MET* 3.6 2.7 + - + -
971C GLY* 5.5 3.5 - - - -
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Residues in contact with LYS 905 (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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903C ASN* 2.6 27.2 + - - +
904C GLU* 1.3 102.4 - - - +
906C ILE* 1.3 59.1 + - - -
907C ASP 3.3 0.4 - - - -
908C MET* 3.6 19.8 + - + +
909C TYR 3.3 10.9 + - - -
966C PRO* 2.6 41.6 + - + +
967C ASN* 4.0 10.7 - - - +
969C ARG* 2.8 57.8 + - + +
970C PRO 4.4 2.5 - - - +
971C GLY* 4.4 8.5 - - - -
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Residues in contact with ILE 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832C ILE* 3.8 13.2 - - + -
834C ARG* 4.0 19.1 - - + +
890C TYR 4.8 1.0 - - - +
892C ALA* 3.9 9.2 + - + +
894C GLU* 3.1 25.1 - - - +
895C VAL* 3.5 26.9 - - + -
902C TYR* 3.5 36.1 - - + -
903C ASN 2.9 16.0 + - - +
904C GLU 2.7 4.6 + - - -
905C LYS* 1.3 73.6 - - - +
907C ASP* 1.3 71.0 + - - +
908C MET 3.2 0.2 - - - -
909C TYR* 3.3 3.6 + - - +
910C SER* 3.0 27.0 + - - -
969C ARG* 3.8 4.7 - - - +
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Residues in contact with ASP 907 (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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823C LEU* 3.9 14.8 - - + +
827C HIS* 3.2 26.0 + - + +
832C ILE* 3.5 9.5 - - - +
833C HIS* 2.8 37.4 + - - +
834C ARG* 3.2 21.3 + - - -
835C ASP 4.8 0.2 + - - -
836C LEU* 3.8 8.6 - - + +
904C GLU 2.8 8.5 + - - +
906C ILE* 1.3 78.4 - - - +
908C MET* 1.3 62.2 + - - +
910C SER* 3.3 8.1 + - - -
911C LEU* 2.8 30.1 + - - +
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Residues in contact with MET 908 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C LEU* 4.2 12.8 - - + -
823C LEU* 3.8 20.4 - - - -
827C HIS* 4.1 12.6 - - + +
904C GLU* 4.2 3.1 - - + +
905C LYS* 3.7 30.3 - - + +
906C ILE 3.2 0.2 - - - -
907C ASP* 1.3 78.4 - - - +
909C TYR* 1.3 61.9 + - - +
911C LEU* 3.2 8.0 + - + +
912C GLY 3.1 16.1 + - - -
961C LEU* 3.4 28.6 - - + +
969C ARG* 4.9 3.8 - - + -
970C PRO 3.4 19.1 - - - +
971C GLY* 3.2 10.8 - - - +
972C ALA* 3.2 39.9 - - + +
975C LEU* 4.7 1.3 - - + -
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Residues in contact with TYR 909 (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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890C TYR 3.6 8.3 - - - -
891C VAL 3.2 19.5 - - - -
892C ALA* 3.2 23.8 - - + -
893C THR* 4.6 13.1 + - - -
905C LYS 3.3 3.0 + - - -
906C ILE 3.5 5.6 - - - +
907C ASP 3.2 0.4 - - - -
908C MET* 1.3 79.5 - - - +
910C SER* 1.3 61.2 + - - +
912C GLY* 2.8 22.5 + - - -
913C ILE* 3.4 15.7 + - + +
936C ARG* 3.1 44.6 + - - +
961C LEU 3.0 12.8 + - - -
962C ILE* 3.4 46.6 - - + +
963C ASP 4.4 1.3 - - - -
964C HIS* 5.0 0.8 - - - -
969C ARG* 3.4 32.3 - - - +
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Residues in contact with SER 910 (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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836C LEU* 2.4 44.9 + - - +
890C TYR* 3.5 26.1 - - - +
906C ILE 3.0 16.5 + - - -
907C ASP* 3.5 6.7 - - - -
909C TYR* 1.3 78.9 - - - +
911C LEU* 1.3 61.7 + - - +
912C GLY 3.2 0.3 + - - -
913C ILE* 3.2 6.6 + - - +
914C ILE* 3.1 25.4 + - - +
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Residues in contact with LEU 911 (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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816C PHE* 3.4 31.6 - - + -
819C ILE* 3.8 27.4 - - + -
820C LEU* 3.4 33.9 - - + -
823C LEU* 3.9 15.3 - - + -
836C LEU* 4.1 3.4 - - + -
907C ASP 2.8 20.3 + - - +
908C MET* 3.5 14.1 - - + +
909C TYR 3.2 0.2 - - - -
910C SER* 1.3 72.7 - - - +
912C GLY* 1.3 58.1 + - - +
914C ILE* 3.9 17.4 - - + +
915C PHE* 2.9 28.1 + - - +
961C LEU* 4.3 6.1 - - + -
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Residues in contact with GLY 912 (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 MET 3.1 5.7 + - - -
909C TYR 2.8 10.8 + - - -
911C LEU* 1.3 77.8 - - - +
913C ILE* 1.3 61.4 + - - +
915C PHE* 3.5 2.9 + - - +
916C PHE* 3.3 17.7 + - - +
958C ILE* 3.8 14.1 - - - +
961C LEU* 3.6 19.7 - - - +
962C ILE* 3.5 19.3 - - - -
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Residues in contact with ILE 913 (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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889C MET 3.5 17.7 - - - +
890C TYR* 3.3 31.4 - - + -
909C TYR* 3.4 21.6 + - + +
910C SER 3.2 7.5 + - - +
912C GLY* 1.3 75.3 - - - +
914C ILE* 1.3 62.6 + - - +
916C PHE* 3.3 7.5 - - - +
917C GLU* 3.3 22.5 + - - +
932C LEU* 4.4 24.9 - - + -
935C LEU* 5.0 14.6 - - + -
936C ARG* 4.1 23.8 - - + -
958C ILE* 5.8 0.2 - - - -
962C ILE* 3.8 15.0 - - + +
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Residues in contact with ILE 914 (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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796C LEU* 4.0 27.1 - - + -
800C ILE* 5.2 0.2 - - + -
819C ILE* 4.9 0.7 - - + -
836C LEU* 3.3 51.6 - - + +
837C LYS* 4.1 4.7 - - - +
838C PRO* 4.1 11.2 - - + -
841C ILE* 4.7 8.3 - - + -
890C TYR* 4.0 15.7 - - + -
910C SER 3.1 17.1 + - - +
911C LEU* 3.5 12.8 - - + +
912C GLY 3.2 0.2 - - - -
913C ILE* 1.3 73.4 - - - +
915C PHE* 1.3 68.4 + - - +
917C GLU* 3.2 12.5 + - - +
918C MET* 3.2 25.9 + - + +
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Residues in contact with PHE 915 (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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812C TYR* 3.4 24.0 - + - -
813C TRP* 3.9 35.0 - + - -
816C PHE* 3.3 35.7 - + + -
911C LEU* 2.9 20.6 + - - +
912C GLY* 3.8 5.8 - - - +
913C ILE 3.4 0.2 - - - -
914C ILE* 1.3 72.0 - - - +
916C PHE* 1.3 67.6 + - - +
918C MET* 2.6 32.8 + - - +
919C ILE* 2.9 26.6 + - + +
954C GLU* 4.0 24.9 - - + -
957C ILE* 5.0 7.0 - - + -
958C ILE* 3.7 23.3 - - + -
961C LEU* 5.5 1.3 - - + -
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Residues in contact with PHE 916 (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 GLY 3.3 10.1 + - - +
913C ILE* 3.3 11.4 - - - +
915C PHE* 1.3 77.6 - - - +
917C GLU* 1.3 55.8 + - - +
918C MET 2.6 12.5 + - - -
919C ILE* 2.7 19.4 + - + -
920C TYR* 2.7 37.7 + + + -
922C PHE* 3.3 33.0 - + - -
931C ILE* 3.8 10.5 - - + -
932C LEU* 4.0 5.6 - - + -
935C LEU* 3.6 30.3 - - + -
942C PHE* 4.1 10.5 - + - -
943C PRO* 3.7 21.3 - - + -
946C PHE* 4.0 22.2 - + - -
958C ILE* 4.1 21.0 - - + +
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Residues in contact with GLU 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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797C TYR* 5.7 1.7 - - - -
800C ILE* 2.9 34.1 - - + +
801C HIS* 5.0 8.5 + - - +
806C ASN* 5.2 1.2 - - - +
838C PRO* 3.2 19.4 - - - +
890C TYR* 2.6 40.2 + - - -
913C ILE* 3.3 11.0 + - + +
914C ILE* 3.2 11.0 + - - +
916C PHE* 1.3 77.9 - - - +
918C MET* 1.3 59.9 + - - +
920C TYR 3.8 10.0 - - - +
921C PRO* 5.5 0.2 - - - +
922C PHE* 4.0 23.8 - - + -
928C ARG* 2.7 34.7 + - - +
932C LEU* 4.8 2.2 - - + -
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Residues in contact with MET 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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796C LEU* 3.9 26.9 - - + -
800C ILE* 3.9 23.0 - - + +
805C LEU* 3.3 15.9 - - + +
806C ASN* 3.0 28.8 + - - +
812C TYR* 4.2 19.1 - - + -
815C LEU* 3.9 26.2 - - + -
816C PHE* 4.4 11.7 - - - +
819C ILE* 4.7 6.1 - - + -
914C ILE* 3.2 21.3 - - - +
915C PHE* 2.6 37.3 + - + +
916C PHE 2.6 4.9 + - - -
917C GLU* 1.3 73.8 - - - +
919C ILE* 1.3 56.0 + - - +
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Residues in contact with ILE 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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806C ASN* 3.8 8.9 - - - +
812C TYR* 3.8 30.3 - - + +
915C PHE* 3.5 37.7 - - + +
916C PHE* 2.7 17.6 + - + +
918C MET* 1.3 74.1 - - - +
920C TYR* 1.3 61.6 + - + +
921C PRO* 3.6 9.6 - - - +
946C PHE* 4.2 16.4 - - + -
951C MET* 3.9 20.7 - - + +
954C GLU* 3.4 39.7 - - + +
958C ILE* 3.5 14.8 - - + -
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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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806C ASN* 4.2 2.7 - - - -
916C PHE* 2.7 48.5 + + + +
917C GLU 3.8 7.5 - - - +
918C MET 3.4 1.0 - - - -
919C ILE* 1.3 76.9 - - + +
921C PRO* 1.3 83.4 - - + +
922C PHE* 3.2 37.7 - + - -
927C GLU* 5.6 0.9 - - - -
931C ILE* 4.8 6.2 - - + +
943C PRO* 3.5 26.6 - - + +
945C ASP* 3.2 36.3 + - - -
946C PHE* 3.9 25.4 - + + -
947C ASP 5.7 0.4 - - - -
951C MET* 5.9 1.8 - - - -
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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
------------------------------------------------------------
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