Contacts of the helix formed by residues 856 - 870 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768D LEU 6.1 0.9 - - - -
778D LEU* 6.3 2.2 - - + -
780D VAL* 5.1 4.0 - - + -
810D MET* 4.1 14.8 - - + -
844D VAL* 4.6 8.5 - - + -
853D GLY* 3.0 19.1 + - - +
855D SER* 1.3 76.7 + - - +
857D GLY* 1.3 63.4 + - - +
858D CYS 3.2 3.1 - - - -
859D THR* 3.0 16.5 + - - +
860D ILE* 3.0 30.4 + - + +
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Residues in contact with GLY 857 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813D SER* 4.8 7.8 + - - -
817D ALA* 3.5 6.0 - - - +
853D GLY 4.6 0.2 + - - -
854D PRO* 2.9 16.2 + - - +
855D SER 3.3 1.6 - - - -
856D ALA* 1.3 76.1 - - - +
858D CYS* 1.3 55.7 - - - +
860D ILE* 3.1 14.7 + - - +
861D VAL* 3.0 30.0 + - - +
881D GLY 3.5 1.3 + - - -
883D VAL* 3.4 20.9 - - - -
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Residues in contact with CYS 858 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855D SER 4.4 0.2 - - - -
856D ALA 3.2 0.2 - - - -
857D GLY* 1.3 74.3 - - - +
859D THR* 1.3 64.0 + - - +
861D VAL* 3.5 9.0 + - - -
862D THR* 2.6 33.3 + - - -
879D MET* 3.5 27.1 - - - +
880D THR 3.8 3.4 - - - -
881D GLY* 3.1 40.6 + - - +
883D VAL* 3.8 8.2 - - + +
889D ILE* 5.3 2.9 - - + -
911D VAL* 5.6 0.2 - - - -
939D TYR* 3.6 7.8 - - + -
942D ILE* 3.8 24.5 - - + -
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Residues in contact with THR 859 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D VAL* 3.2 37.4 - - + +
766D MET 3.7 2.0 - - - -
767D GLY* 3.7 26.4 - - - +
780D VAL* 4.3 16.2 - - + +
855D SER 4.5 0.2 + - - -
856D ALA* 3.0 16.1 + - - -
858D CYS* 1.3 80.2 - - - +
860D ILE* 1.3 58.8 + - - +
862D THR* 3.3 2.1 + - - -
863D ALA* 2.8 27.4 + - - +
879D MET* 3.3 29.3 + - + +
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Residues in contact with ILE 860 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780D VAL* 4.1 14.1 - - + -
800D LEU* 5.4 1.3 - - + -
810D MET* 5.1 6.7 - - + -
813D SER* 5.4 1.8 - - - +
814D ALA* 4.6 20.9 - - + +
817D ALA* 4.3 10.5 - - + -
842D LEU* 3.8 37.2 - - + -
844D VAL* 4.4 7.6 - - + -
856D ALA* 3.0 31.5 + - + +
857D GLY* 3.1 11.6 + - - +
859D THR* 1.3 73.8 - - - +
861D VAL* 1.3 66.3 + - - +
862D THR 2.9 1.7 + - - -
863D ALA* 3.2 7.2 + - - +
864D LEU* 2.9 44.0 + - + +
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Residues in contact with VAL 861 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817D ALA* 3.6 28.7 - - + +
820D PHE* 3.8 21.1 - - + -
821D ALA* 4.1 11.0 - - + -
857D GLY 3.0 21.2 + - - +
858D CYS* 3.7 10.3 - - - +
859D THR 3.4 0.2 - - - -
860D ILE* 1.3 74.8 - - - +
862D THR* 1.3 52.0 + - - +
864D LEU* 3.3 3.3 + - - +
865D LEU* 2.8 47.9 + - + +
883D VAL* 3.9 13.7 - - + -
939D TYR* 3.5 34.3 - - + -
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Residues in contact with THR 862 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765D VAL* 3.7 18.6 - - + -
858D CYS 2.6 21.4 + - - -
859D THR 3.6 4.5 - - - -
860D ILE 2.9 0.8 - - - -
861D VAL* 1.3 75.2 - - - +
863D ALA* 1.3 69.5 + - - +
865D LEU* 3.0 3.0 + - - -
866D SER* 2.9 22.2 + - - -
873D VAL* 4.0 4.9 - - + -
879D MET* 3.6 15.1 - - + +
939D TYR* 2.6 26.7 + - - +
942D ILE* 4.3 0.2 - - - +
946D ALA* 4.0 11.4 - - + -
947D PHE* 3.7 22.7 - - + -
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Residues in contact with ALA 863 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763D GLY* 3.6 24.2 - - - +
765D VAL* 3.9 8.6 - - + +
780D VAL* 4.3 15.5 - - + +
782D THR* 3.4 25.6 + - + +
859D THR 2.8 14.3 + - - +
860D ILE* 3.4 11.7 - - - +
862D THR* 1.3 78.2 - - - +
864D LEU* 1.3 61.5 + - - +
866D SER* 3.1 2.8 + - - -
867D LEU 3.0 18.7 + - - -
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Residues in contact with LEU 864 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D THR* 3.6 23.1 - - + -
800D LEU* 4.1 19.5 - - + -
817D ALA 4.1 2.7 - - - +
818D TYR* 3.7 40.6 - - + -
821D ALA* 3.8 18.2 - - + -
835D LEU* 4.4 8.3 - - + +
840D ILE* 4.3 22.9 - - + +
860D ILE* 2.9 34.0 + - + +
861D VAL 3.5 4.0 - - - +
863D ALA* 1.3 72.4 - - - +
865D LEU* 1.3 66.2 + - - +
867D LEU* 3.5 3.0 + - - +
868D ALA* 3.0 25.4 + - - +
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Residues in contact with LEU 865 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821D ALA* 3.9 24.9 - - + +
824D PHE* 4.1 11.9 - - + -
825D LEU* 3.9 27.6 - - + +
835D LEU* 3.9 8.7 - - + -
861D VAL* 2.8 25.5 + - + +
862D THR 3.9 2.2 - - - +
864D LEU* 1.3 77.9 - - - +
866D SER* 1.3 56.0 + - - +
868D ALA* 3.3 2.6 + - - +
869D MET* 2.9 43.3 + - + +
939D TYR* 3.5 35.2 - - + +
943D PHE* 4.0 16.4 - - + -
947D PHE* 4.3 11.2 - - + -
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Residues in contact with SER 866 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761D PRO 4.3 0.9 + - - -
762D PRO* 3.3 5.0 - - - +
763D GLY* 2.8 19.1 + - - -
764D VAL 4.3 2.0 + - - -
862D THR 2.9 12.5 + - - -
863D ALA* 3.4 10.1 - - - -
865D LEU* 1.3 78.1 - - - +
867D LEU* 1.3 63.5 + - - +
869D MET* 3.2 2.6 + - - -
870D GLY 2.9 18.7 + - - -
871D ARG 2.6 33.2 + - - -
872D PRO* 3.9 3.3 - - - +
873D VAL* 4.3 7.8 + - - +
947D PHE* 3.7 17.1 - - - -
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Residues in contact with LEU 867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762D PRO* 4.3 13.7 - - + +
763D GLY* 3.4 6.5 - - - +
782D THR* 3.1 54.1 - - - +
783D SER* 3.5 14.8 - - - +
784D LEU* 5.1 1.1 - - + +
834D TYR* 3.5 33.6 - - + +
840D ILE* 3.9 19.5 - - + -
863D ALA 3.0 7.7 + - - +
864D LEU* 3.7 4.5 - - - +
866D SER* 1.3 75.0 + - - +
868D ALA* 1.3 62.3 + - - +
870D GLY* 3.0 14.7 + - - -
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Residues in contact with ALA 868 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825D LEU* 3.5 9.9 - - + -
832D ASN* 3.2 16.6 + - - -
834D TYR* 3.6 28.9 - - + -
835D LEU* 2.9 38.8 - - + -
864D LEU 3.0 16.4 + - - +
865D LEU* 3.4 5.4 - - - +
867D LEU* 1.3 76.9 - - - +
869D MET* 1.4 59.2 + - - +
870D GLY 3.7 0.3 + - - -
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Residues in contact with MET 869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825D LEU* 4.4 16.8 - - + -
828D HIS* 4.4 18.8 - - - -
832D ASN* 4.3 8.1 - - - +
865D LEU* 2.9 19.3 + - + +
866D SER 3.9 1.8 - - - +
868D ALA* 1.4 75.5 - - - +
870D GLY* 1.3 60.3 + - - +
871D ARG* 3.6 18.8 + - + +
943D PHE* 4.0 17.3 - - + -
947D PHE* 3.7 52.7 - - + -
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Residues in contact with GLY 870 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762D PRO* 3.7 19.8 - - - +
866D SER 2.9 4.4 + - - -
867D LEU 3.0 14.0 + - - -
868D ALA 3.3 0.8 + - - -
869D MET* 1.3 77.3 - - - +
871D ARG* 1.3 57.8 + - - +
872D PRO* 4.2 1.9 - - - +
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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