Contacts of the helix formed by residues 819 - 835 (chain E) in PDB entry 6V3O
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 TRP 819 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE* 4.3 2.2 - - - -
615E TRP* 3.6 31.0 - + - -
618E TYR* 4.5 8.8 + + - -
706E PRO* 6.1 0.4 - - + +
707E VAL* 4.4 12.7 + - + -
709E PRO* 3.5 35.8 - - + +
713E TRP* 3.5 48.0 - + + -
717E MET* 3.8 22.4 - - + -
815E MET* 2.8 28.2 + - - +
817E ASN 3.9 0.6 - - - -
818E GLU* 1.3 71.6 - - - +
820E PRO* 1.3 76.0 - - + +
821E PHE* 3.6 35.4 - + + +
822E PHE* 3.0 16.5 + - + -
823E ARG* 3.0 18.7 + - - +
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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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131E PHE* 3.8 37.0 - - + -
654E LEU* 4.6 5.8 - - + -
657E LEU* 5.0 1.1 - - + +
658E SER* 3.4 26.0 - - - +
706E PRO* 3.9 20.2 - - + -
707E VAL* 4.0 10.3 - - + +
818E GLU 3.5 10.1 - - - +
819E TRP* 1.3 91.2 - - + +
821E PHE* 1.3 62.1 + - - +
823E ARG* 3.1 1.9 + - + +
824E VAL* 3.0 28.5 + - + +
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Residues in contact with PHE 821 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611E LEU* 5.9 1.3 - - + -
614E ALA* 3.6 35.7 - - + -
615E TRP* 3.9 24.7 - + - -
618E TYR* 3.9 29.6 - + + -
658E SER* 3.7 18.1 + - - +
717E MET* 3.9 18.6 - - + -
819E TRP* 3.3 37.4 - + - +
820E PRO* 1.3 80.0 - - - +
822E PHE* 1.3 78.3 + + - +
824E VAL* 3.3 3.2 + - + +
825E THR* 3.0 48.0 + - + +
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Residues in contact with PHE 822 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611E LEU* 5.2 5.2 - - + -
717E MET* 3.9 25.8 - - + -
720E MET* 4.4 4.5 - - + -
798E PHE* 4.3 17.0 - + - -
812E LEU* 3.9 21.3 - - + -
815E MET* 3.7 31.0 - - + +
816E TYR* 3.6 22.0 - - + -
819E TRP* 3.0 25.4 + + + +
821E PHE* 1.3 85.4 - + - +
823E ARG* 1.3 62.6 + - - +
825E THR* 3.4 4.7 + - - -
826E LEU* 3.1 66.7 + - + +
874E ILE* 4.3 6.1 - - + -
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Residues in contact with ARG 823 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LYS* 5.2 5.1 - - - +
131E PHE* 4.4 10.1 - - + -
132E ALA* 3.5 33.5 + - - +
654E LEU* 4.3 17.9 - - + -
816E TYR* 3.3 63.8 + - - +
817E ASN* 4.3 14.9 + - - +
819E TRP 3.0 10.3 + - - +
820E PRO* 3.5 12.6 - - + +
822E PHE* 1.3 76.7 - - - +
824E VAL* 1.3 64.1 + - + +
826E LEU* 3.3 2.8 + - - +
827E ASP* 2.7 51.3 + - - +
877E HIS* 5.7 2.2 + - - -
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Residues in contact with VAL 824 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644E THR* 3.8 25.8 - - + +
647E ARG* 5.1 2.1 + - - -
651E PRO 5.6 0.4 - - - +
654E LEU* 3.6 34.1 - - + -
655E ALA* 4.0 12.3 - - + +
658E SER* 3.7 24.2 - - - +
820E PRO 3.0 13.0 + - - +
821E PHE* 3.3 12.1 - - + +
823E ARG* 1.3 75.3 - - - +
825E THR* 1.3 72.9 + - + +
827E ASP* 3.5 4.9 + - - +
828E LEU* 3.2 22.9 + - - +
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Residues in contact with THR 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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611E LEU* 5.0 9.0 - - - +
614E ALA* 4.5 13.7 - - + -
644E THR* 4.5 10.3 - - + -
821E PHE* 3.0 46.7 + - + +
822E PHE* 3.4 12.1 + - - -
824E VAL* 1.3 83.1 - - + +
826E LEU* 1.3 74.4 + - - +
828E LEU* 3.6 3.7 + - - +
829E LEU* 3.4 27.8 + - - +
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Residues in contact with LEU 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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611E LEU* 5.7 3.6 - - + -
798E PHE* 4.3 20.0 - - + -
816E TYR* 3.7 26.5 - - + -
822E PHE* 3.1 65.6 + - + +
823E ARG 3.9 2.5 - - - +
825E THR* 1.3 89.8 + - - +
827E ASP* 1.3 59.7 + - - +
829E LEU* 3.1 16.8 + - + +
830E GLU* 2.9 26.1 + - - +
871E LEU* 4.0 18.2 - - + +
874E ILE* 4.3 15.9 - - + -
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Residues in contact with ASP 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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647E ARG* 4.0 11.5 + - - +
816E TYR* 3.1 21.3 + - - -
823E ARG* 2.7 52.3 + - - +
824E VAL* 4.3 4.4 - - - +
826E LEU* 1.3 73.0 - - - +
828E LEU* 1.3 65.0 + - - +
830E GLU* 3.5 16.4 - - - +
831E MET* 3.0 23.4 + - - +
877E HIS* 4.7 1.6 - - - -
881E LEU* 5.2 6.0 - - + +
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Residues in contact with LEU 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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610E ARG* 3.6 34.8 - - - +
642E GLY 4.3 5.2 - - - +
643E GLY 5.0 1.1 - - - +
644E THR* 3.8 24.0 - - + -
647E ARG* 4.1 19.8 - - + +
790E VAL* 5.1 4.7 - - + -
824E VAL 3.2 13.3 + - - +
825E THR* 3.7 11.0 - - - +
826E LEU 3.3 0.2 - - - -
827E ASP* 1.3 76.0 - - - +
829E LEU* 1.3 62.9 + - + +
831E MET* 3.3 23.6 + - + +
832E VAL* 3.0 30.2 + - + +
968E ASN* 5.4 0.7 - - - +
969E THR 3.5 23.6 - - - +
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Residues in contact with LEU 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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610E ARG* 4.5 10.5 - - + -
611E LEU* 6.2 3.1 - - + -
790E VAL* 3.1 43.1 - - + +
791E TRP* 4.0 11.2 - - + -
794E VAL* 4.8 18.6 - - + -
798E PHE* 5.8 3.1 - - + -
825E THR* 3.4 20.4 - - - +
826E LEU* 3.1 19.4 + - + +
828E LEU* 1.3 74.1 - - + +
830E GLU* 1.3 66.6 + - - +
832E VAL* 3.1 7.2 + - - +
833E PHE* 2.9 33.2 + - + -
871E LEU* 3.6 17.0 - - + -
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Residues in contact with GLU 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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816E TYR* 3.8 3.3 + - - -
826E LEU 2.9 15.7 + - - +
827E ASP* 3.5 19.4 - - - +
829E LEU* 1.3 76.3 - - - +
831E MET* 1.3 62.4 + - - +
833E PHE* 3.3 3.9 + - - +
834E ALA* 3.0 18.9 + - - +
871E LEU* 4.0 23.9 - - + +
872E LEU* 4.0 2.6 - - - +
875E ALA* 4.6 0.9 - - - +
877E HIS* 2.8 36.8 + - - -
880E ILE* 3.7 18.8 - - + +
881E LEU* 2.7 45.2 + - + +
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Residues in contact with MET 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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647E ARG* 3.6 27.1 - - - +
827E ASP 3.0 17.8 + - - +
828E LEU* 3.6 28.7 - - + +
829E LEU 3.2 0.2 - - - -
830E GLU* 1.3 76.7 - - - +
832E VAL* 1.3 67.5 + - + +
834E ALA* 3.3 8.7 + - - +
835E LYS* 3.2 51.0 + - - +
881E LEU* 4.5 6.9 - - + +
887E LEU* 4.2 16.8 - - + -
891E LEU* 4.5 4.7 - - + -
968E ASN* 3.6 31.0 - - - +
1004E FLC 4.3 4.9 - - - +
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Residues in contact with VAL 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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787E HIS* 3.5 42.2 + - + -
790E VAL* 3.9 30.1 - - + -
791E TRP* 5.2 4.7 - - + -
828E LEU* 3.0 16.2 + - + +
829E LEU* 3.1 6.7 + - - +
831E MET* 1.3 83.0 - - - +
833E PHE* 1.3 58.9 + - + +
835E LYS* 2.9 21.3 + - - +
836E GLY 3.1 8.5 + - - -
969E THR* 3.9 29.4 - - - +
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Residues in contact with PHE 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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791E TRP* 3.7 25.6 - + + -
794E VAL* 5.7 0.2 - - + -
829E LEU* 2.9 27.2 + - + +
830E GLU* 3.7 4.9 - - - +
832E VAL* 1.3 77.3 - - + +
834E ALA* 1.3 57.3 + - - +
836E GLY 3.0 21.8 + - - +
864E TYR* 3.5 56.3 + + - -
867E THR* 3.5 33.2 - - + -
868E GLN* 3.7 29.6 - - + +
871E LEU* 3.9 23.8 - - + -
880E ILE* 3.8 16.6 - - + +
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Residues in contact with ALA 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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785E ARG* 5.7 0.3 + - - -
830E GLU 3.0 10.4 + - - +
831E MET 3.5 9.9 - - - +
832E VAL 3.3 0.2 - - - -
833E PHE* 1.3 75.0 - - - +
835E LYS* 1.3 60.3 + - - +
836E GLY 3.4 2.6 + - - +
880E ILE* 3.9 22.5 - - + +
881E LEU* 3.6 29.2 - - + -
888E LYS* 5.6 3.4 - - + -
891E LEU* 4.2 13.8 - - + +
895E ASN* 4.8 10.7 + - - +
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Residues in contact with LYS 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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785E ARG* 3.2 23.1 + - - +
787E HIS* 3.1 11.9 - - + -
831E MET* 3.2 25.5 + - - +
832E VAL* 2.9 13.0 + - + +
834E ALA* 1.3 75.6 - - - +
836E GLY* 1.3 57.2 + - - +
891E LEU* 3.8 28.5 - - + -
894E ARG* 4.5 2.7 - - - +
895E ASN* 5.8 2.5 - - - -
965E GLY 5.1 0.4 - - - +
966E MET* 2.8 55.7 + - + +
968E ASN* 2.8 21.2 + - - +
969E THR* 4.5 2.7 - - + -
1004E FLC 2.8 30.9 + - - -
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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