Contacts of the helix formed by residues 819 - 835 (chain E) in PDB entry 3T06
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 GLY 819 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818E ASP* 1.3 81.0 + - - +
820E PRO* 1.3 72.0 - - - +
822E ARG* 3.2 6.5 + - - +
823E GLU* 3.1 27.9 + - - +
912E GLN* 4.6 3.2 - - - +
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Residues in contact with PRO 820 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818E ASP 3.5 6.5 - - - +
819E GLY* 1.3 82.0 - - - +
821E ALA* 1.3 61.4 + - + +
823E GLU* 3.1 10.7 + - + +
824E GLU* 3.0 25.4 + - - +
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Residues in contact with ALA 821 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815E ALA 3.1 28.9 - - - +
816E ARG* 3.3 37.1 + - - +
818E ASP 3.1 10.7 + - - +
820E PRO* 1.3 80.0 - - - +
822E ARG* 1.3 56.7 + - - +
824E GLU* 3.7 6.3 + - - +
825E LEU* 3.1 21.3 + - - +
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Residues in contact with ARG 822 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816E ARG 3.7 5.3 + - - -
817E PHE 3.6 20.9 - - - +
818E ASP* 3.5 5.3 + - - +
819E GLY 3.2 10.0 + - - +
821E ALA* 1.3 77.0 - - - +
823E GLU* 1.3 71.8 + - - +
825E LEU* 3.7 0.2 - - - +
826E GLN* 2.4 77.7 + - - +
912E GLN* 3.2 31.1 + - - +
915E GLU* 3.3 41.6 + - - +
916E ILE* 3.4 23.9 - - + +
919E TYR* 5.1 1.2 - - - +
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Residues in contact with GLU 823 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819E GLY* 3.1 16.7 + - - +
820E PRO* 3.1 10.2 + - + +
822E ARG* 1.3 88.5 + - - +
824E GLU* 1.3 61.7 + - - +
826E GLN* 3.5 23.6 + - - +
827E GLN* 3.2 41.6 + - - +
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Residues in contact with GLU 824 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788E ILE* 4.2 21.6 - - + +
816E ARG* 3.3 26.1 + - - -
820E PRO 3.0 15.0 + - - +
821E ALA* 3.9 5.7 - - - +
823E GLU* 1.3 78.5 - - - +
825E LEU* 1.3 56.8 + - - +
827E GLN* 3.8 5.9 - - - +
828E VAL* 3.0 41.6 + - + +
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Residues in contact with LEU 825 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785E LEU* 5.6 2.0 - - + -
788E ILE* 3.7 38.1 - - + -
789E HIS* 5.1 4.7 - - + +
816E ARG* 4.0 11.0 - - - +
817E PHE* 3.5 38.4 - - + -
821E ALA 3.1 18.2 + - - +
822E ARG* 3.2 4.2 + - - +
824E GLU* 1.3 74.1 - - - +
826E GLN* 1.3 66.3 + - - +
829E ALA* 3.1 28.2 + - + +
878E GLU* 5.1 1.6 - - - +
882E LEU* 4.4 24.9 - - + -
885E TYR* 5.6 0.7 - - + -
916E ILE* 3.8 15.5 - - + -
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Residues in contact with GLN 826 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822E ARG* 2.4 69.5 + - - +
823E GLU* 3.5 24.6 + - - +
825E LEU* 1.3 73.7 - - - +
827E GLN* 1.3 63.8 + - + +
830E ALA* 3.1 26.0 + - - +
916E ILE* 3.7 23.5 - - + +
919E TYR* 3.4 51.2 - - + +
920E VAL* 4.2 4.3 - - - +
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Residues in contact with GLN 827 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823E GLU* 3.2 33.8 + - - +
824E GLU* 3.8 5.4 + - - +
826E GLN* 1.3 78.6 - - + +
828E VAL* 1.3 58.4 + - + +
830E ALA* 3.8 2.5 - - - +
831E GLN* 3.1 28.8 + - - +
919E TYR* 4.0 23.0 + - + +
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Residues in contact with VAL 828 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781E ASN* 3.3 20.2 + - - +
784E GLU* 4.4 14.6 - - + -
785E LEU* 3.5 35.7 - - + +
788E ILE* 3.8 23.3 - - + -
824E GLU* 3.0 28.3 + - + +
825E LEU* 4.1 0.7 - - + +
827E GLN* 1.3 76.4 - - + +
829E ALA* 1.3 64.6 + - - +
831E GLN* 4.6 0.2 - - - -
832E PHE* 3.2 18.7 + - - +
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Residues in contact with ALA 829 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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785E LEU* 4.5 5.2 - - + -
825E LEU* 3.1 20.1 + - + +
828E VAL* 1.3 75.8 - - - +
830E ALA* 1.3 60.3 + - - +
832E PHE* 3.4 4.9 + - - +
833E CYS* 2.9 36.3 + - - +
878E GLU* 4.9 13.7 - - + +
882E LEU* 3.7 30.1 - - + -
920E VAL* 3.9 11.0 - - + -
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Residues in contact with ALA 830 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826E GLN 3.1 21.7 + - - +
827E GLN* 3.8 3.8 - - - +
829E ALA* 1.3 73.7 - - - +
831E GLN* 1.3 61.6 - - - +
834E SER* 2.8 36.9 + - - -
919E TYR* 4.0 13.7 - - + -
920E VAL* 4.1 14.7 - - + +
923E ALA* 3.6 25.1 - - + -
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Residues in contact with GLN 831 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780E PRO* 3.5 30.8 + - - +
781E ASN* 2.5 37.9 + - - +
827E GLN 3.1 14.4 + - - +
828E VAL* 4.6 0.2 - - - -
829E ALA 3.3 0.2 - - - -
830E ALA* 1.3 82.4 - - - +
832E PHE* 1.3 61.3 + - - +
834E SER* 4.0 10.8 + - - +
835E TYR* 4.8 4.3 + - - +
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Residues in contact with PHE 832 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753E LEU* 5.7 0.7 - - + -
756E LEU* 4.6 9.9 - - + -
778E LEU 4.7 1.8 - - - +
779E PHE* 4.6 13.0 - + - -
780E PRO* 3.9 21.0 - - + +
781E ASN* 3.2 22.3 + - - +
782E LEU* 4.0 18.8 - - + -
785E LEU* 3.4 29.4 - - + -
828E VAL 3.2 12.2 + - - +
829E ALA* 3.8 4.5 - - - +
830E ALA 3.2 0.4 - - - -
831E GLN* 1.3 81.6 - - - +
833E CYS* 1.3 69.6 + - - +
835E TYR 4.9 0.3 + - - -
836E GLN* 3.5 33.4 + - - +
875E ILE* 3.6 32.1 - - + -
878E GLU* 4.0 15.7 - - + -
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Residues in contact with CYS 833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829E ALA* 2.9 21.1 + - - +
832E PHE* 1.3 93.4 - - - +
834E SER* 1.3 67.7 + - - +
835E TYR 3.1 3.5 + - - -
836E GLN* 3.2 24.8 + - + +
837E SER 4.7 1.2 + - - -
878E GLU* 4.7 4.3 - - - -
879E MET* 4.0 34.5 - - + -
882E LEU* 6.2 0.7 - - - -
920E VAL* 4.1 20.4 - - + -
924E VAL* 4.0 11.9 - - + +
69F LEU* 6.0 0.4 - - + -
72F LEU* 5.2 7.6 - - + +
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Residues in contact with SER 834 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830E ALA* 2.8 21.0 + - - +
831E GLN* 4.0 7.6 + - - -
832E PHE 3.6 0.8 - - - -
833E CYS* 1.3 78.7 - - - +
835E TYR* 1.3 66.0 + - - +
837E SER* 5.2 0.7 + - - -
838E ILE* 5.3 0.3 - - - +
923E ALA* 4.1 16.4 - - - -
924E VAL* 4.0 19.6 - - - +
927E THR* 3.1 39.5 + - - +
928E GLU* 4.5 7.1 - - - +
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Residues in contact with TYR 835 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777E ARG* 3.8 55.9 + - + +
780E PRO* 6.1 2.0 - - + -
831E GLN 4.8 4.7 + - - +
832E PHE 4.9 0.4 + - - -
834E SER* 1.3 84.4 + - - +
836E GLN* 1.3 59.7 + - - +
837E SER* 3.4 2.0 - - - -
838E ILE* 2.9 57.8 + - + +
839E ALA* 3.1 12.5 + - - -
842E LEU* 4.3 13.9 - - + +
927E THR* 4.0 15.0 - - + -
931E HIS* 5.1 10.5 + + + -
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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