Contacts of the helix formed by residues 856 - 869 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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778F LEU* 5.9 3.4 - - + -
780F VAL* 5.3 5.2 - - + -
810F MET* 4.0 27.1 - - + -
813F SER* 4.7 0.4 - - - +
844F VAL* 5.0 4.5 - - + -
852F ASP* 4.7 0.4 + - - -
853F GLY 3.7 3.5 + - - +
854F PRO 3.1 1.2 + - - -
855F SER* 1.3 75.9 - - - +
857F GLY* 1.3 64.1 + - - +
858F CYS 3.5 0.7 - - - -
859F THR* 3.2 13.8 + - - +
860F ILE* 3.0 42.7 + - + +
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Residues in contact with GLY 857 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813F SER* 3.9 11.8 + - - -
817F ALA* 3.8 4.5 - - - +
854F PRO 3.2 11.4 + - - -
855F SER 3.1 3.8 - - - -
856F ALA* 1.3 80.4 - - - +
858F CYS* 1.3 62.5 + - - +
860F ILE* 4.4 4.3 - - - -
861F VAL* 3.1 26.0 + - - +
881F GLY 3.5 4.2 + - - -
883F VAL* 4.0 17.7 - - - -
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Residues in contact with CYS 858 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855F SER 4.1 0.7 - - - -
857F GLY* 1.3 73.3 - - - +
859F THR* 1.3 66.1 + - - +
861F VAL* 3.6 5.3 + - - -
862F THR* 2.5 34.5 + - - -
879F MET* 3.7 9.8 - - - +
880F THR* 3.1 49.6 - - - -
881F GLY* 2.8 19.4 + - - +
883F VAL* 4.3 4.8 - - - +
889F ILE* 4.8 4.7 - - + -
939F TYR* 3.8 5.3 - - - -
942F ILE* 3.5 28.7 - - + -
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Residues in contact with THR 859 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765F VAL* 3.8 17.5 - - + +
766F MET 4.3 0.9 - - - -
767F GLY* 3.9 22.3 - - - +
780F VAL* 3.8 31.4 - - + -
855F SER 4.6 0.2 + - - -
856F ALA* 3.4 18.2 + - - -
857F GLY 3.2 0.6 - - - -
858F CYS* 1.3 79.5 - - - +
860F ILE* 1.3 57.5 + - - +
862F THR* 3.4 6.8 - - - -
863F ALA* 3.1 20.4 + - - +
879F MET* 3.6 31.7 + - + +
880F THR* 4.6 0.2 - - - -
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Residues in contact with ILE 860 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780F VAL* 4.2 15.5 - - + -
782F THR* 5.8 0.2 - - + -
800F LEU* 6.1 0.2 - - + -
810F MET* 5.0 5.6 - - - -
813F SER* 4.7 2.7 - - - +
814F ALA* 4.4 24.0 - - + +
817F ALA* 3.8 14.6 - - + -
842F LEU* 3.8 24.0 - - + -
844F VAL* 4.2 18.8 - - + -
856F ALA* 3.0 34.3 + - + +
857F GLY* 3.8 6.3 - - - +
859F THR* 1.3 73.6 - - - +
861F VAL* 1.3 69.8 + - - +
862F THR 3.1 0.9 - - - -
863F ALA* 3.0 14.8 + - + +
864F LEU* 3.1 23.6 + - + +
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Residues in contact with VAL 861 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817F ALA* 3.6 24.9 - - + +
820F PHE* 3.8 29.2 - - + -
821F ALA* 3.9 16.5 - - + +
824F PHE* 5.6 0.4 - - + -
857F GLY 3.1 18.1 + - - +
858F CYS* 3.8 2.9 - - - +
860F ILE* 1.3 79.3 - - - +
862F THR* 1.3 62.3 + - - +
864F LEU* 3.4 3.7 + - - +
865F LEU* 3.1 24.7 + - + +
883F VAL* 4.0 11.9 - - + -
939F TYR* 3.4 37.0 - - + -
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Residues in contact with THR 862 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765F VAL* 4.0 17.9 - - + -
858F CYS 2.5 21.8 + - - -
859F THR 3.4 8.7 - - - -
861F VAL* 1.3 77.8 - - - +
863F ALA* 1.3 57.1 + - - +
865F LEU* 4.5 2.2 - - - +
866F SER* 2.9 31.5 + - - -
873F VAL* 4.3 3.4 - - + -
879F MET* 3.7 11.7 - - + +
939F TYR* 2.8 25.3 + - - +
946F ALA* 4.1 15.3 - - + -
947F PHE* 3.8 21.9 - - + -
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Residues in contact with ALA 863 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763F GLY* 3.4 21.0 - - - +
765F VAL* 3.6 18.8 - - + -
780F VAL* 4.0 19.7 - - + +
782F THR* 3.2 21.9 + - + -
859F THR 3.1 9.4 + - - +
860F ILE* 3.0 8.0 + - - +
862F THR* 1.3 75.2 - - - +
864F LEU* 1.3 62.4 + - - +
866F SER* 4.3 1.8 - - - -
867F LEU 3.0 18.2 + - - -
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Residues in contact with LEU 864 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782F THR* 4.1 14.6 - - + -
800F LEU* 4.2 12.3 - - + -
817F ALA 4.3 0.9 - - - +
818F TYR* 3.8 41.3 - - + +
821F ALA* 4.3 9.2 - - + -
835F LEU* 3.6 19.6 - - + +
840F ILE* 3.9 39.0 - - + -
842F LEU* 5.7 0.7 - - + -
860F ILE* 3.1 24.4 + - + +
861F VAL 3.8 4.7 - - - +
863F ALA* 1.3 77.4 - - - +
865F LEU* 1.3 52.3 + - - +
867F LEU* 3.4 2.0 + - - +
868F ALA* 2.6 36.4 + - - +
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Residues in contact with LEU 865 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821F ALA* 3.7 27.8 - - + +
824F PHE* 3.9 14.1 - - + -
825F LEU* 3.8 24.7 - - + -
835F LEU* 4.1 4.9 - - + -
861F VAL* 3.1 18.2 + - + +
862F THR 4.0 2.5 - - - +
863F ALA 3.3 0.2 - - - -
864F LEU* 1.3 72.7 - - - +
866F SER* 1.3 60.1 + - - +
868F ALA* 4.2 3.6 - - - -
869F MET* 2.9 45.8 + - + +
939F TYR* 3.6 26.9 - - + +
943F PHE* 3.4 34.1 - - + -
947F PHE* 4.5 1.6 - - + -
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Residues in contact with SER 866 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761F PRO 4.3 0.2 + - - -
762F PRO* 3.5 4.7 - - - +
763F GLY* 2.7 26.8 + - - -
862F THR 2.9 23.3 + - - -
863F ALA* 3.7 2.7 - - - -
865F LEU* 1.3 70.3 - - - +
867F LEU* 1.3 63.8 + - - +
869F MET* 4.7 0.9 - - - -
870F GLY* 3.2 3.3 + - - -
871F ARG 2.8 47.8 + - - -
872F PRO* 3.6 5.9 - - - +
873F VAL* 3.8 10.9 - - - +
947F PHE* 3.8 14.5 - - - -
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Residues in contact with LEU 867 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762F PRO* 4.3 13.6 - - + +
763F GLY* 3.6 7.1 - - - +
782F THR* 3.4 50.9 - - - +
783F SER* 3.9 14.4 - - - -
784F LEU* 4.1 2.7 - - + +
834F TYR* 3.3 30.6 - - + +
840F ILE* 3.7 26.5 - - + -
863F ALA 3.0 9.5 + - - +
864F LEU* 3.6 3.4 - - + +
866F SER* 1.3 75.5 - - - +
868F ALA* 1.3 64.5 + - - +
869F MET 2.9 1.4 + - - -
870F GLY* 3.0 12.5 + - - -
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Residues in contact with ALA 868 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825F LEU* 4.0 15.3 - - + -
832F ASN* 3.1 17.7 + - - +
834F TYR* 3.3 26.8 - - + +
835F LEU* 3.7 27.4 - - + -
864F LEU 2.6 22.4 + - - +
865F LEU* 3.6 5.6 - - - +
867F LEU* 1.3 73.8 - - - +
869F MET* 1.3 61.2 + - + +
870F GLY 3.4 0.6 + - - -
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Residues in contact with MET 869 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825F LEU* 4.5 20.9 - - + -
829F ALA* 6.1 2.5 - - + -
832F ASN* 4.3 7.2 - - - +
865F LEU* 2.9 23.4 + - - +
868F ALA* 1.3 78.3 - - - +
870F GLY* 1.3 63.6 + - - +
871F ARG* 3.2 25.2 + - + +
943F PHE* 3.8 24.0 - - + -
947F PHE* 3.8 45.3 - - + -
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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