Contacts of the helix formed by residues 856 - 870 (chain E) in PDB entry 2X36
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 ALA 856 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768E LEU 5.9 3.6 - - - +
780E VAL* 5.3 4.5 - - + -
810E MET* 4.4 24.0 - - + -
813E SER* 4.7 0.7 - - - +
844E VAL* 4.8 7.9 - - + -
852E ASP 4.7 1.2 + - - +
853E GLY 4.3 1.2 + - - -
854E PRO 3.3 1.4 - - - -
855E SER* 1.3 77.8 - - - +
857E GLY* 1.3 62.9 + - - +
858E CYS 3.3 1.5 + - - -
859E THR* 3.4 14.4 + - - +
860E ILE* 3.0 39.4 + - + +
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Residues in contact with GLY 857 (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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813E SER* 3.9 17.3 + - - -
817E ALA* 3.5 8.9 - - - +
854E PRO 3.4 6.5 + - - -
855E SER 3.3 4.2 - - - -
856E ALA* 1.3 78.6 - - - +
858E CYS* 1.3 60.5 + - - +
860E ILE* 3.4 4.5 + - - -
861E VAL* 3.2 24.1 + - - +
881E GLY 3.8 4.5 - - - -
883E VAL* 3.4 15.3 - - - -
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Residues in contact with CYS 858 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857E GLY* 1.3 72.8 - - - +
859E THR* 1.3 56.2 - - - +
861E VAL* 3.4 6.2 + - - +
862E THR* 2.3 41.5 + - - -
879E MET* 3.7 14.6 - - - -
880E THR* 3.5 29.6 - - - -
881E GLY* 3.1 24.2 + - - +
883E VAL* 3.3 15.0 - - + +
889E ILE* 4.0 3.1 - - + -
911E VAL* 5.7 0.2 - - - -
939E TYR* 3.7 2.2 - - + -
942E ILE* 3.4 30.7 - - + -
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Residues in contact with THR 859 (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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765E VAL* 3.8 15.8 - - + +
766E MET 3.9 2.2 - - - +
767E GLY* 3.7 24.2 - - - +
780E VAL* 3.3 32.1 - - + -
856E ALA* 3.5 18.9 + - - +
858E CYS* 1.3 77.9 - - - +
860E ILE* 1.3 62.9 + - - -
862E THR* 3.2 3.2 + - - -
863E ALA* 3.0 22.7 + - - +
879E MET* 3.6 30.7 + - + +
880E THR* 4.5 1.4 - - - -
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Residues in contact with ILE 860 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780E VAL* 4.1 13.7 - - + -
782E THR* 4.8 0.2 - - - +
800E LEU* 5.9 0.4 - - + -
810E MET* 5.2 4.9 - - - -
813E SER* 4.7 2.9 - - - +
814E ALA* 4.2 24.0 - - + +
817E ALA* 3.7 15.5 - - + -
842E LEU* 3.6 37.9 - - + -
844E VAL* 4.1 17.0 - - + -
856E ALA* 3.0 34.7 + - + +
857E GLY* 3.4 9.2 + - - +
859E THR* 1.3 69.1 - - - +
861E VAL* 1.3 66.9 + - - +
862E THR 2.9 2.1 + - - -
863E ALA* 3.1 3.4 + - - +
864E LEU* 3.1 34.8 + - + +
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Residues in contact with VAL 861 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817E ALA* 3.3 39.0 - - + +
820E PHE* 4.0 21.3 - - + -
821E ALA* 4.0 10.1 - - + -
857E GLY 3.2 9.4 + - - +
858E CYS 3.5 8.1 - - - +
860E ILE* 1.3 78.0 - - - +
862E THR* 1.3 64.6 - - - +
864E LEU* 3.4 5.7 + - - +
865E LEU* 3.2 30.2 + - + +
883E VAL* 4.3 11.9 - - + -
939E TYR* 3.6 30.7 - - + -
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Residues in contact with THR 862 (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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765E VAL* 3.8 6.1 - - + -
858E CYS 2.3 25.0 + - - -
859E THR 3.6 6.3 - - - -
860E ILE 2.9 0.4 - - - -
861E VAL* 1.3 79.2 - - - +
863E ALA* 1.3 58.3 + - - +
865E LEU* 3.4 2.4 + - - +
866E SER* 3.0 28.1 + - - -
873E VAL* 3.7 24.0 - - + -
879E MET* 3.4 27.4 - - + +
939E TYR* 3.0 25.2 + - - +
942E ILE* 3.7 0.2 - - - +
946E ALA* 4.2 11.0 - - + -
947E PHE* 4.0 4.9 - - + -
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Residues in contact with ALA 863 (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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763E GLY* 3.4 20.5 - - - +
765E VAL* 3.5 14.8 - - + +
780E VAL* 4.3 16.4 - - + +
782E THR* 2.9 27.3 + - + +
859E THR 3.0 15.1 + - - +
860E ILE 3.1 3.8 + - - +
862E THR* 1.3 75.9 - - - +
864E LEU* 1.4 63.1 + - - +
865E LEU 3.3 0.2 + - - -
866E SER* 3.4 5.1 - - - -
867E LEU* 3.0 17.5 + - - +
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Residues in contact with LEU 864 (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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782E THR* 3.5 21.8 - - + -
800E LEU* 4.4 13.0 - - + -
817E ALA 4.1 6.3 - - - +
818E TYR* 3.6 45.8 - - + +
821E ALA* 4.1 11.0 - - + -
835E LEU* 3.4 19.6 - - + +
840E ILE* 4.3 23.3 - - + -
842E LEU* 5.4 0.4 - - + -
860E ILE* 3.1 27.2 + - + +
861E VAL 3.7 6.5 - - - +
863E ALA* 1.4 75.2 - - - +
865E LEU* 1.3 59.4 + - - +
867E LEU* 3.7 3.6 + - - +
868E ALA 3.0 19.8 + - - -
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Residues in contact with LEU 865 (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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821E ALA* 3.6 16.6 - - + +
824E PHE* 3.7 27.4 - - + -
825E LEU* 3.9 19.1 - - + +
835E LEU* 3.5 26.9 - - + -
861E VAL* 3.2 22.3 + - + +
862E THR 3.9 3.8 - - - +
863E ALA 3.2 0.2 - - - -
864E LEU* 1.3 74.7 - - - +
866E SER* 1.3 55.2 - - - +
868E ALA* 3.0 2.1 + - - +
869E MET* 2.8 47.5 + - + +
939E TYR* 3.7 25.4 - - + +
943E PHE* 4.3 6.5 - - + -
947E PHE* 4.4 10.3 - - + -
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Residues in contact with SER 866 (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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762E PRO* 3.4 2.3 - - - +
763E GLY* 2.5 29.9 + - - -
764E VAL 4.2 0.9 + - - -
862E THR 3.0 18.3 + - - -
863E ALA* 3.4 5.4 - - - -
865E LEU* 1.3 73.5 - - - +
867E LEU* 1.3 51.6 + - - -
869E MET* 3.3 1.6 + - - -
870E GLY 2.8 14.4 + - - -
871E ARG 2.7 49.2 + - - -
872E PRO* 3.8 3.8 - - - +
873E VAL* 3.8 10.3 + - - +
947E PHE* 3.7 14.8 - - - -
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Residues in contact with LEU 867 (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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762E PRO* 4.5 10.5 - - + +
763E GLY* 3.9 7.9 - - - +
782E THR* 3.3 54.1 - - - +
783E SER* 3.8 12.8 - - - +
784E LEU* 4.9 3.8 - - + +
834E TYR* 3.2 36.7 - - + +
840E ILE* 4.3 11.2 - - + -
863E ALA 3.0 7.9 + - - +
864E LEU* 3.8 5.2 - - - +
866E SER* 1.3 75.7 - - - +
868E ALA* 1.3 60.6 + - - +
870E GLY* 3.2 11.7 + - - +
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Residues in contact with ALA 868 (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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825E LEU* 3.5 30.3 - - + -
832E ASN* 2.7 26.2 + - - +
834E TYR* 3.6 21.0 - - + +
835E LEU* 3.5 14.6 - - + -
864E LEU 3.0 17.8 + - - +
865E LEU* 3.0 7.1 + - - +
867E LEU* 1.3 77.8 - - - +
869E MET* 1.3 54.3 + - - +
870E GLY 3.3 1.3 + - - -
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Residues in contact with MET 869 (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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825E LEU* 4.6 18.2 - - + -
832E ASN* 4.4 5.4 - - - +
865E LEU* 2.8 17.8 + - - +
868E ALA* 1.3 75.7 - - - +
870E GLY* 1.3 64.1 + - - +
871E ARG* 3.2 23.9 + - + +
943E PHE* 3.6 25.6 - - + -
947E PHE* 3.5 53.2 - - + -
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Residues in contact with GLY 870 (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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762E PRO* 4.0 19.5 - - - +
866E SER 2.8 6.3 + - - -
867E LEU* 3.2 13.4 + - - -
868E ALA 3.3 1.0 - - - -
869E MET* 1.3 76.1 - - - +
871E ARG* 1.3 58.9 + - - +
872E PRO* 4.1 3.1 - - - +
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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