Contacts of the helix formed by residues 896 - 910 (chain C) in PDB entry 4YZ9
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 896 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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863C GLU* 2.7 24.6 + - - -
870C VAL* 5.2 0.7 - - - -
874C TRP* 2.9 27.5 + - - -
893C LYS* 3.3 20.4 + - - -
894C GLY 3.4 0.2 - - - -
895C GLY* 1.3 78.1 - - - +
897C VAL* 1.3 61.2 + - - +
898C ARG* 3.8 1.7 - - - +
899C ASP* 2.9 33.5 + - - -
900C LEU 3.4 2.8 + - - -
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Residues in contact with VAL 897 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862C LEU* 3.8 37.9 - - + +
863C GLU* 2.9 8.6 + - - +
866C GLY* 3.4 40.2 - - - +
869C VAL* 4.5 10.1 - - + -
870C VAL* 5.0 4.3 - - + -
896C SER* 1.3 71.2 - - - +
898C ARG* 1.3 66.8 + - - +
899C ASP 3.2 0.2 - - - -
900C LEU* 2.9 9.3 + - + +
901C LEU* 2.9 24.5 + - + +
940C LEU* 4.0 24.9 - - + -
943C HIS* 4.6 5.6 - - + +
944C THR* 4.7 0.2 - - - +
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Residues in contact with ARG 898 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849C ILE* 3.0 44.4 + - + +
850C GLU* 3.3 40.2 + - - +
852C GLU 4.4 1.8 + - - -
854C LEU* 3.5 27.8 - - - +
859C VAL* 4.0 26.4 - - + +
862C LEU* 4.0 14.2 - - + +
863C GLU* 3.0 14.9 + - - +
896C SER* 3.8 1.6 - - - +
897C VAL* 1.3 77.8 - - - +
899C ASP* 1.3 62.6 + - - +
901C LEU* 3.4 3.5 + - - +
902C ARG* 2.8 55.2 + - + +
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Residues in contact with ASP 899 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C TRP* 3.7 7.0 - - + -
891C THR 3.1 9.7 - - - +
892C TYR* 3.8 5.7 - - + -
893C LYS* 2.8 51.1 + - - +
896C SER* 2.9 18.0 + - - +
898C ARG* 1.3 83.9 + - - +
900C LEU* 1.3 61.3 + - - +
902C ARG* 3.0 30.9 + - - +
903C ALA* 2.8 29.6 + - - +
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Residues in contact with LEU 900 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869C VAL* 6.1 0.7 - - + -
870C VAL* 5.2 5.2 - - + -
874C TRP* 3.8 45.7 - - + +
878C ILE* 5.8 0.4 - - + -
896C SER 3.4 6.3 + - - +
897C VAL* 2.9 12.1 + - + +
899C ASP* 1.3 75.3 - - - +
901C LEU* 1.3 60.8 + - - +
903C ALA* 3.2 3.5 + - + +
904C MET* 2.9 38.2 + - - +
933C PHE* 4.0 27.4 - - + -
937C PHE* 4.3 28.5 - - + -
940C LEU* 4.0 30.3 - - + -
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Residues in contact with LEU 901 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842C PHE* 3.4 39.4 - - + +
845C VAL* 3.7 30.1 - - + -
846C SER* 3.4 21.7 + - - -
849C ILE* 4.8 1.6 - - + -
862C LEU* 4.1 17.7 - - + -
897C VAL* 2.9 16.9 + - + +
898C ARG* 3.9 6.7 - - - +
900C LEU* 1.3 75.8 - - - +
902C ARG* 1.3 57.2 + - - +
904C MET* 3.9 18.0 - - - +
905C ARG* 3.1 22.9 + - - +
940C LEU* 4.0 11.4 - - + -
944C THR* 3.8 19.1 - - + +
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Residues in contact with ARG 902 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846C SER* 3.5 12.8 + - - +
850C GLU* 2.9 36.1 + - - +
891C THR* 3.0 51.4 + - - +
892C TYR* 4.2 5.8 - - + -
898C ARG* 2.8 42.6 + - - +
899C ASP* 3.0 30.7 + - - +
900C LEU 3.1 0.2 - - - -
901C LEU* 1.3 75.5 - - - +
903C ALA* 1.3 60.3 + - - +
905C ARG* 3.3 2.0 + - - +
906C ASN* 2.9 51.9 + - - +
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Residues in contact with ALA 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C TRP* 3.9 19.5 - - + -
886C LEU* 4.3 12.6 - - + -
892C TYR* 3.3 27.9 - - + -
899C ASP 2.8 20.8 + - - +
900C LEU* 3.2 5.8 + - + +
902C ARG* 1.3 73.1 - - - +
904C MET* 1.3 63.1 - - + +
906C ASN* 4.1 0.2 - - - -
907C LYS* 3.1 30.0 + - - +
933C PHE* 5.6 4.0 - - + -
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Residues in contact with MET 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C LEU* 4.6 12.3 - - + +
842C PHE* 3.5 40.6 - - + -
900C LEU* 2.9 24.3 + - - +
901C LEU* 3.9 13.7 - - - +
903C ALA* 1.3 77.5 - - - +
905C ARG* 1.3 62.1 + - - +
908C LYS* 3.1 24.3 + - - +
929C PHE* 3.5 14.9 - - + -
930C VAL* 5.2 1.8 - - + -
933C PHE* 3.6 57.4 - - + -
940C LEU* 3.8 21.5 - - + -
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Residues in contact with ARG 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842C PHE 5.7 0.2 - - - -
843C GLN* 4.0 31.2 - - + +
846C SER* 3.5 22.4 - - - +
847C ASP* 3.2 27.0 + - - +
850C GLU* 5.9 2.1 + - - -
901C LEU 3.1 19.6 + - - +
902C ARG* 3.3 2.9 + - - +
904C MET* 1.3 78.4 - - - +
906C ASN* 1.3 90.7 + - - +
908C LYS* 3.2 7.9 + - - +
909C HIS* 3.0 62.6 + - - +
910C HIS* 5.9 0.2 + - - -
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Residues in contact with ASN 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850C GLU* 5.7 0.5 - - - +
891C THR* 6.0 0.8 - - - +
892C TYR* 2.8 28.9 + - - +
902C ARG* 2.9 35.2 + - - +
903C ALA 4.1 0.4 - - - +
905C ARG* 1.3 107.6 + - - +
907C LYS* 1.3 61.0 + - + +
909C HIS* 3.0 15.8 + - - +
910C HIS* 3.0 34.5 + - + -
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Residues in contact with LYS 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882C LEU* 4.3 20.9 - - + -
885C ASP* 3.1 23.5 + - - +
886C LEU* 3.5 17.3 - - + +
889C PHE* 3.3 32.3 - - - -
892C TYR* 4.6 5.8 + - - +
903C ALA 3.1 20.1 + - - +
904C MET* 5.0 0.2 - - - -
906C ASN* 1.3 79.2 - - + +
908C LYS* 1.3 57.2 + - - +
910C HIS* 3.2 29.3 + - - +
911C TYR* 3.2 25.1 - - - +
914C LEU* 3.7 23.0 - - + +
922C LEU* 5.2 2.2 - - + -
929C PHE* 3.9 19.0 - - + -
933C PHE* 6.2 1.8 - - + -
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Residues in contact with LYS 908 (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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839C LEU* 3.7 36.8 - - + -
840C GLN* 4.4 12.3 + - - +
843C GLN* 2.7 35.7 + - + +
904C MET 3.1 17.9 + - - +
905C ARG* 3.6 6.1 - - - +
907C LYS* 1.3 77.9 - - - +
909C HIS* 1.3 67.5 + - - +
910C HIS 3.5 0.2 - - - -
911C TYR* 3.4 16.2 - - - +
925C LEU* 4.0 15.1 - - + +
926C PRO* 5.7 1.8 - - - -
929C PHE* 3.8 11.8 - - + -
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Residues in contact with HIS 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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843C GLN* 5.2 16.6 + - - -
905C ARG* 3.0 49.0 + - - +
906C ASN 3.0 8.9 + - - +
908C LYS* 1.3 81.7 + - - +
910C HIS* 1.3 62.7 + - + +
911C TYR 3.5 0.3 + - - -
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Residues in contact with HIS 910 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889C PHE* 6.1 0.7 - + - -
905C ARG* 5.9 0.4 + - - -
906C ASN* 3.0 35.8 + - + -
907C LYS* 3.2 33.0 + - - +
909C HIS* 1.3 78.8 - - + +
911C TYR* 1.3 53.4 + - - +
912C ARG* 3.2 2.9 - - - -
913C GLU* 2.6 49.3 + - + +
914C LEU* 3.6 21.3 + - + -
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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