Contacts of the helix formed by residues 998 - 1019 (chain C) in PDB entry 4AY6
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 ASN 998 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C ILE* 4.1 1.8 - - - -
992C ILE 5.6 2.9 + - - +
994C SER 4.6 4.4 + - - +
995C PRO* 3.2 23.5 + - + +
996C LEU 3.3 1.0 + - - -
997C PHE* 1.3 74.3 - - - +
999C THR* 1.3 57.6 + - - +
1000C LYS* 3.2 8.5 + - - +
1001C GLN* 2.6 48.8 + - - +
1002C TYR* 2.9 29.5 + - - +
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Residues in contact with THR 999 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C LEU 4.9 2.7 - - - +
564C MET* 6.2 0.2 - - - -
566C SER* 4.4 7.9 - - - -
567C ILE* 4.6 8.5 - - + +
570C MET* 3.5 25.7 - - - +
695C ILE* 3.8 14.8 - - + -
696C GLY 3.6 24.2 - - - +
697C ASP* 4.1 16.4 - - - +
699C ALA* 6.0 2.7 - - + +
700C ASN* 6.2 0.2 - - - +
997C PHE 3.6 3.3 + - - +
998C ASN* 1.3 74.0 - - - +
1000C LYS* 1.3 58.1 + - - +
1002C TYR* 3.7 6.8 - - - +
1003C THR* 2.8 33.8 + - - -
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Residues in contact with LYS1000 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B ASP* 3.6 41.5 + - + +
733B ALA* 6.1 2.9 - - + -
791B GLY 5.9 0.6 + - - -
792B PHE* 4.9 10.3 - - + +
793B SER* 4.9 12.1 + - - +
815B ARG 4.2 16.0 + - - -
570C MET* 3.3 45.6 + - + +
571C HIS 5.4 0.4 + - - -
572C ASN* 5.6 1.6 - - - +
998C ASN* 3.2 6.8 + - - +
999C THR* 1.3 78.0 + - - +
1001C GLN* 1.3 66.8 + - - +
1003C THR* 3.3 2.5 + - - -
1004C MET* 3.1 50.4 + - + +
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Residues in contact with GLN1001 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691C HIS* 4.4 14.1 + - - -
995C PRO* 3.4 38.8 - - + +
998C ASN* 2.6 31.7 + - + +
1000C LYS* 1.3 70.9 - - - +
1002C TYR* 1.3 68.5 + - - +
1004C MET* 3.1 20.3 + - + +
1005C GLU* 3.1 24.7 + - + +
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Residues in contact with TYR1002 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C ILE* 4.0 17.7 - - + -
652C TRP* 3.0 35.8 + + - -
689C MET* 3.5 29.2 - - + +
692C THR* 3.7 8.3 - - + -
693C PHE* 2.5 25.6 + - - +
694C PHE 3.3 26.7 - - - -
695C ILE* 3.7 23.1 - - + -
995C PRO 5.4 2.9 + - - +
998C ASN 2.9 18.7 + - - +
999C THR* 3.7 4.5 - - - +
1001C GLN* 1.3 75.8 - - - +
1003C THR* 1.3 67.1 + - - +
1005C GLU* 3.0 18.3 + - - +
1006C LEU* 3.0 21.4 + - + +
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Residues in contact with THR1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567C ILE* 3.4 25.4 - - + +
570C MET* 3.7 34.6 - - - +
571C HIS* 3.8 28.5 - - + +
999C THR 2.8 23.9 + - - -
1000C LYS 3.6 5.2 - - - -
1002C TYR* 1.3 79.8 - - - +
1004C MET* 1.3 64.8 + - + +
1005C GLU 3.0 0.7 + - - -
1006C LEU* 3.0 7.7 + - + +
1007C GLU* 2.9 25.7 + - - +
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Residues in contact with MET1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B ASN 3.5 24.5 - - - +
791B GLY* 3.6 24.7 - - - +
792B PHE* 3.6 31.9 - - + -
570C MET 5.9 0.2 - - - +
1000C LYS* 3.1 38.5 + - + +
1001C GLN* 3.1 11.9 + - + +
1003C THR* 1.3 78.1 - - - +
1005C GLU* 1.3 60.7 + - + +
1007C GLU* 3.3 20.0 + - - +
1008C ARG* 3.1 27.6 + - - +
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Residues in contact with GLU1005 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689C MET* 3.7 17.6 - - + +
690C PRO* 3.5 34.5 - - + +
691C HIS* 5.8 0.9 - - - +
1001C GLN* 3.1 24.1 + - + +
1002C TYR* 3.0 10.1 + - - +
1004C MET* 1.3 75.8 - - + +
1006C LEU* 1.3 66.9 + - - +
1007C GLU 3.0 1.1 - - - -
1008C ARG* 3.0 33.6 + - - +
1009C LEU* 2.9 23.4 + - - +
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Residues in contact with LEU1006 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550C TYR* 3.7 12.6 - - - +
567C ILE* 4.5 11.9 - - + -
571C HIS* 4.7 3.4 - - + -
652C TRP* 4.3 31.9 - - + +
668C ILE* 4.2 18.2 - - + -
689C MET* 3.8 18.4 - - - +
1002C TYR* 3.0 21.4 + - + +
1003C THR* 3.3 10.8 - - - +
1005C GLU* 1.3 76.5 - - - +
1007C GLU* 1.3 55.3 + - - +
1009C LEU* 3.4 5.3 + - + +
1010C TYR* 2.9 70.3 + - + +
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Residues in contact with GLU1007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B GLY 4.9 3.5 - - - +
570C MET 5.1 0.7 - - - +
571C HIS* 2.8 29.8 + - + +
572C ASN* 2.7 36.8 + - - +
576C PHE* 3.3 33.1 - - + -
1003C THR* 2.9 15.2 + - - +
1004C MET* 3.4 28.7 + - - +
1005C GLU 3.0 0.2 - - - -
1006C LEU* 1.3 74.5 - - - +
1008C ARG* 1.3 69.8 + - - +
1010C TYR* 3.1 6.2 + - - +
1011C LEU* 3.1 26.3 + - + +
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Residues in contact with ARG1008 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004C MET 3.1 16.0 + - - +
1005C GLU* 3.0 35.2 + - - +
1007C GLU* 1.3 76.3 - - - +
1009C LEU* 1.3 64.7 + - - +
1011C LEU* 2.8 22.2 + - - +
1012C GLN* 2.9 27.9 + - + +
1028C LYS* 4.8 17.8 - - - +
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Residues in contact with LEU1009 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668C ILE* 4.1 29.8 - - + -
687C ALA* 3.8 33.2 - - + -
688C TYR 3.5 29.2 - - - +
689C MET* 4.2 10.3 - - - -
1005C GLU 2.9 14.2 + - - +
1006C LEU* 3.7 7.6 - - + +
1008C ARG* 1.3 77.5 - - - +
1010C TYR* 1.3 61.4 + - + +
1012C GLN* 3.5 15.2 + - - +
1013C MET* 3.1 33.5 + - + +
1026C MET* 4.3 13.9 - - + +
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Residues in contact with TYR1010 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546C LEU* 3.9 10.5 - - + -
548C VAL* 4.0 22.4 - - + -
550C TYR* 2.9 41.1 + - - -
571C HIS* 4.0 9.2 - + - -
576C PHE* 4.1 6.3 - + + -
625C ILE* 3.7 31.6 - - + +
627C VAL* 3.6 15.2 - - + +
650C ALA* 5.8 0.2 - - + -
652C TRP* 5.1 0.9 - - - -
668C ILE* 4.4 13.3 - - + +
1006C LEU* 2.9 49.8 + - + +
1007C GLU* 3.4 11.4 - - - +
1008C ARG 3.1 0.4 - - - -
1009C LEU* 1.3 77.7 - - + +
1011C LEU* 1.3 61.9 + - - +
1013C MET* 3.2 15.6 + - + +
1014C TRP* 3.0 21.8 + - - +
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Residues in contact with LEU1011 (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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539C LEU* 5.6 7.0 - - + -
546C LEU* 4.3 16.8 - - + -
575C LYS* 5.4 13.0 - - + +
576C PHE* 3.6 25.1 - - + -
1007C GLU* 3.1 18.0 + - + +
1008C ARG* 2.8 9.2 + - + +
1010C TYR* 1.3 76.1 - - - +
1012C GLN* 1.3 66.2 + - - +
1014C TRP* 3.7 10.6 - - + +
1015C GLU* 3.0 42.5 + - + +
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Residues in contact with GLN1012 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008C ARG* 2.9 26.7 + - + +
1009C LEU* 3.6 20.2 - - - +
1010C TYR 3.2 0.2 - - - -
1011C LEU* 1.3 77.8 - - - +
1013C MET* 1.3 63.1 + - - +
1014C TRP 3.2 0.9 + - - -
1015C GLU* 3.4 6.2 + - - +
1016C HIS* 3.2 23.6 + - - +
1026C MET* 3.7 36.0 - - - +
1028C LYS* 3.9 29.8 + - - +
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Residues in contact with MET1013 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C ILE* 4.6 6.3 - - + -
648C ILE* 3.5 25.5 - - + +
650C ALA* 4.6 4.9 - - + -
666C TYR* 3.7 44.1 + - + -
668C ILE* 4.2 14.6 - - + -
687C ALA* 3.4 32.1 - - + -
1009C LEU* 3.1 21.5 + - + +
1010C TYR* 3.2 25.7 + - - +
1012C GLN* 1.3 75.6 - - - +
1014C TRP* 1.3 61.5 + - - +
1016C HIS* 3.7 3.1 - - - +
1017C TYR* 3.1 17.3 + - - +
1026C MET* 4.1 16.4 - - + -
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Residues in contact with TRP1014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C PRO 3.8 10.1 - - - -
537C LYS 3.9 7.9 - - - -
538C ASP* 3.8 19.8 - - - +
539C LEU* 3.6 39.6 - - + +
546C LEU* 4.2 16.8 - - + -
624C HIS* 3.7 30.3 - + + -
625C ILE* 5.1 0.4 - - + -
647C PRO* 4.1 11.0 - - + -
648C ILE* 3.9 13.5 - - + -
1010C TYR 3.0 15.2 + - - +
1011C LEU* 3.7 11.7 - - + +
1013C MET* 1.3 74.9 - - - +
1015C GLU* 1.3 84.3 + - - +
1017C TYR* 2.9 40.9 + + - -
1018C ALA* 2.7 34.4 + - + +
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Residues in contact with GLU1015 (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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1011C LEU* 3.0 32.8 + - + +
1012C GLN* 3.8 6.3 - - - +
1014C TRP* 1.3 89.1 + - - +
1016C HIS* 1.3 53.2 + - - +
1018C ALA* 3.1 6.0 + - - +
1019C ALA* 2.7 36.8 + - - +
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Residues in contact with HIS1016 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666C TYR* 4.0 7.9 - - - -
1012C GLN 3.2 14.0 + - - +
1013C MET 3.7 4.7 - - - +
1014C TRP 3.2 0.2 - - - -
1015C GLU* 1.3 81.8 - - - +
1017C TYR* 1.3 60.6 + - + +
1019C ALA* 3.4 5.9 - - - +
1021C ASN* 3.1 55.0 + - + +
1022C LYS 2.9 28.8 + - - -
1023C PRO* 4.2 0.4 - - + -
1024C ASP* 3.7 17.5 + - + +
1026C MET* 3.7 25.1 - - + +
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Residues in contact with TYR1017 (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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535C HIS* 3.9 11.6 + - - +
536C PRO 3.4 15.6 + - - -
537C LYS* 4.4 14.0 - - + +
647C PRO* 3.6 30.4 - - + +
648C ILE* 3.9 14.1 - - + -
1013C MET 3.1 13.7 + - - +
1014C TRP* 2.9 45.6 + + - +
1016C HIS* 1.3 74.3 - - + +
1018C ALA* 1.3 65.6 + - - +
1020C GLY* 2.9 20.1 + - - -
1021C ASN 3.5 17.6 + - - +
1022C LYS* 6.1 0.2 - - - -
1023C PRO* 6.4 1.3 - - + -
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Residues in contact with ALA1018 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C LYS 4.1 14.4 - - - +
538C ASP* 5.8 0.2 - - - -
1014C TRP* 2.7 47.3 + - + +
1015C GLU* 3.6 8.3 - - - +
1017C TYR* 1.3 78.7 - - - +
1019C ALA* 1.3 61.3 + - - +
1020C GLY* 3.1 2.1 + - - -
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Residues in contact with ALA1019 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015C GLU 2.7 17.4 + - - +
1016C HIS* 3.4 3.1 - - - +
1017C TYR 3.1 0.2 - - - -
1018C ALA* 1.3 77.2 - - - +
1020C GLY* 1.3 56.9 + - - +
1021C ASN* 3.4 24.7 + - - +
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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
------------------------------------------------------------
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