Contacts of the helix formed by residues 856 - 870 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A VAL* 5.4 4.3 - - + -
810A MET* 4.5 5.4 - - + -
844A VAL* 5.2 8.3 - - + -
852A ASP 5.5 0.2 - - - +
853A GLY 3.3 13.5 + - - +
854A PRO 3.1 1.8 - - - -
855A SER* 1.3 79.6 + - - +
857A GLY* 1.3 62.9 + - - +
858A CYS 3.5 1.1 - - - -
859A THR* 3.3 15.2 + - - -
860A ILE* 3.0 36.4 + - + +
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Residues in contact with GLY 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A SER* 5.3 5.8 + - - -
817A ALA* 4.0 6.5 - - - +
854A PRO 3.1 12.5 + - - -
855A SER 3.0 4.8 - - - -
856A ALA* 1.3 77.9 - - - +
858A CYS* 1.3 61.7 + - - +
860A ILE* 3.2 11.2 + - - +
861A VAL* 3.1 24.5 + - - +
881A GLY 3.6 2.9 + - - -
883A VAL* 3.6 14.6 - - - -
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Residues in contact with CYS 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A SER 4.6 0.4 - - - -
857A GLY* 1.3 69.5 - - - +
859A THR* 1.3 63.2 + - - +
861A VAL* 3.6 1.4 - - - +
862A THR* 2.4 40.0 + - - -
879A MET* 3.6 25.6 - - - -
880A THR 3.8 19.5 - - - -
881A GLY* 3.3 17.8 + - - +
883A VAL* 3.4 16.4 - - + +
889A ILE* 5.3 0.2 - - + -
939A TYR* 3.8 12.1 - - + -
942A ILE* 3.8 27.8 - - + -
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Residues in contact with THR 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765A VAL* 3.6 23.9 - - + +
767A GLY* 3.8 23.5 - - - -
780A VAL* 3.6 25.8 - - + -
855A SER 4.6 0.7 + - - -
856A ALA* 3.4 18.1 + - - -
858A CYS* 1.3 83.7 - - - +
860A ILE* 1.3 57.6 + - - +
862A THR* 3.5 2.1 - - - -
863A ALA* 2.9 27.7 + - - +
879A MET* 3.3 28.3 + - - +
880A THR* 4.8 0.2 - - - -
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Residues in contact with ILE 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A VAL* 4.2 20.0 - - + -
810A MET* 4.7 8.5 - - + -
813A SER* 5.2 2.0 - - - +
814A ALA* 4.4 20.4 - - + +
817A ALA* 3.7 17.9 - - + -
842A LEU* 3.8 26.7 - - + -
844A VAL* 4.1 19.5 - - + -
856A ALA* 3.0 26.1 + - + +
857A GLY* 3.7 8.7 - - - +
859A THR* 1.3 78.5 - - - +
861A VAL* 1.3 54.3 + - - +
863A ALA* 3.6 6.6 - - - +
864A LEU* 3.0 41.1 + - + +
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Residues in contact with VAL 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ALA* 3.8 25.8 - - + +
820A PHE* 3.9 24.5 - - + -
821A ALA* 4.1 13.2 - - + +
857A GLY 3.1 19.6 + - - +
858A CYS* 3.6 2.5 - - - +
860A ILE* 1.3 71.2 - - - +
862A THR* 1.4 61.8 + - - +
864A LEU* 3.2 7.4 + - - +
865A LEU* 3.2 33.8 + - + +
883A VAL* 4.4 8.7 - - + -
939A TYR* 3.3 38.4 - - + -
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Residues in contact with THR 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A VAL* 4.0 5.2 - - + -
858A CYS 2.4 25.1 + - - -
859A THR 3.5 4.7 - - - -
861A VAL* 1.4 73.6 - - - +
863A ALA* 1.3 55.6 + - - +
865A LEU* 3.4 3.3 + - - +
866A SER* 2.8 35.7 + - - -
873A VAL* 3.8 17.5 - - + -
879A MET* 3.4 20.9 - - + +
939A TYR* 2.8 17.6 + - - -
942A ILE* 4.4 1.2 - - - +
946A ALA* 4.0 11.7 - - + -
947A PHE* 3.6 26.9 - - + -
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Residues in contact with ALA 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763A GLY* 3.4 13.0 - - - +
765A VAL* 3.4 17.2 - - + +
780A VAL* 3.7 18.4 - - + -
782A THR* 3.2 31.4 + - + -
859A THR 2.9 17.3 + - - +
860A ILE 3.6 5.4 - - - +
862A THR* 1.3 73.7 - - - +
864A LEU* 1.3 55.8 + - - +
866A SER* 3.5 0.9 + - - -
867A LEU 3.0 23.0 + - - -
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Residues in contact with LEU 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782A THR* 4.0 17.7 - - + -
800A LEU* 4.3 24.2 - - + -
817A ALA 4.0 0.9 - - - +
818A TYR* 3.8 38.4 - - + +
821A ALA* 4.0 17.7 - - + -
835A LEU* 3.8 12.3 - - + +
840A ILE* 4.5 15.3 - - + -
842A LEU* 5.2 1.3 - - + -
860A ILE* 3.0 37.2 + - + +
861A VAL 3.2 6.0 + - - +
863A ALA* 1.3 72.2 - - - +
865A LEU* 1.3 55.8 + - - +
867A LEU* 3.2 5.2 + - - +
868A ALA* 2.8 35.9 + - - +
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Residues in contact with LEU 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821A ALA* 3.9 24.7 - - + +
824A PHE* 3.6 34.3 - - + -
825A LEU* 4.0 23.8 - - + -
835A LEU* 4.6 1.6 - - + -
861A VAL* 3.2 35.6 + - + +
862A THR* 3.7 4.9 - - - +
864A LEU* 1.3 74.5 - - - +
866A SER* 1.3 60.1 + - - +
868A ALA* 4.2 2.9 - - - -
869A MET* 2.8 44.9 + - + +
939A TYR* 3.7 15.9 - - + +
943A PHE* 4.3 6.1 - - + -
947A PHE* 4.6 7.0 - - + -
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Residues in contact with SER 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761A PRO 4.7 0.2 + - - -
762A PRO* 3.6 5.9 - - - +
763A GLY* 3.2 17.2 + - - -
764A VAL 4.7 0.8 + - - -
862A THR 2.8 19.8 + - - -
863A ALA* 3.6 6.7 - - - -
865A LEU* 1.3 76.3 - - - +
867A LEU* 1.3 62.3 + - - +
869A MET* 4.6 0.4 - - - -
870A GLY* 3.1 19.1 + - - -
871A ARG 2.5 33.8 + - - -
872A PRO* 3.8 3.5 - - - +
873A VAL* 4.2 8.0 + - - +
947A PHE* 3.7 13.3 - - - -
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Residues in contact with LEU 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A PRO* 4.7 7.0 - - + -
763A GLY* 3.6 8.6 - - - +
782A THR* 3.3 29.4 - - - +
783A SER* 3.8 19.7 - - - +
784A LEU* 5.3 3.6 - - + +
834A TYR* 3.0 33.7 - - - +
840A ILE* 3.6 38.1 - - + -
863A ALA 3.0 7.7 + - - +
864A LEU 3.5 7.4 - - - +
866A SER* 1.3 73.5 - - - +
868A ALA* 1.3 63.7 + - - +
870A GLY* 3.2 12.8 + - - -
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Residues in contact with ALA 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A LEU* 3.5 28.7 - - + -
832A ASN* 3.1 16.5 + - - +
834A TYR* 3.3 29.7 - - + +
835A LEU* 3.6 15.9 - - + -
864A LEU 2.8 18.1 + - - +
865A LEU* 3.7 4.7 - - - +
867A LEU* 1.3 78.4 - - - +
869A MET* 1.3 58.8 + - - +
870A GLY 3.7 0.3 + - - -
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Residues in contact with MET 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A LEU* 4.1 20.2 - - + -
828A HIS* 4.0 12.6 - - - -
829A ALA* 5.5 2.7 - - + -
832A ASN* 3.9 10.1 - - - +
865A LEU* 2.8 26.6 + - - +
866A SER 4.6 0.2 - - - +
868A ALA* 1.3 71.9 - - - +
870A GLY* 1.3 61.3 + - - +
871A ARG* 3.2 16.2 + - + +
943A PHE* 4.0 20.2 - - + -
947A PHE* 3.7 38.6 - - + -
950A GLU* 3.9 26.4 - - + +
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Residues in contact with GLY 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762A PRO* 4.4 15.2 - - - +
866A SER 3.1 10.7 + - - -
867A LEU 3.2 11.2 + - - -
868A ALA 3.4 1.4 + - - -
869A MET* 1.3 75.7 - - - +
871A ARG* 1.3 59.0 + - - +
872A PRO* 4.1 4.9 - - - +
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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
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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