Contacts of the helix formed by residues 831 - 846 (chain H) in PDB entry 5YWB
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 SER 831 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830H LEU* 1.3 76.4 - - - +
832H GLY* 1.3 68.3 + - - +
833H GLY* 3.5 3.3 + - - -
834H GLN* 3.1 44.1 + - - +
835H ARG* 3.2 27.6 + - - +
837H ARG* 5.1 0.5 + - - -
2502H ADP 5.5 13.6 + - - -
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Residues in contact with GLY 832 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831H SER* 1.3 80.2 + - - +
833H GLY* 1.3 61.1 + - - +
834H GLN 3.4 0.3 + - - -
835H ARG* 3.7 18.0 + - - +
836H GLN* 3.7 17.5 + - - +
859H ALA* 3.9 9.3 - - - +
1427H GLN* 5.6 6.3 - - - -
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Residues in contact with GLY 833 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831H SER* 3.5 4.7 + - - -
832H GLY* 1.3 73.5 - - - +
834H GLN* 1.3 59.6 + - - +
835H ARG 3.4 0.2 - - - -
836H GLN* 3.3 2.7 + - - +
837H ARG* 2.9 47.6 + - - +
859H ALA* 3.3 30.4 + - - +
860H LEU* 4.5 0.4 - - - +
1427H GLN* 5.8 0.2 - - - +
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Residues in contact with GLN 834 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808H LEU* 4.4 3.7 - - + +
811H ASP* 3.0 40.5 + - - +
815H LEU* 4.7 9.0 - - - +
829H ASN 4.8 0.9 - - - +
830H LEU* 3.6 21.2 - - + +
831H SER* 3.1 42.9 + - - +
832H GLY 3.3 1.0 - - - -
833H GLY* 1.3 76.3 - - - +
835H ARG* 1.3 57.7 + - - +
837H ARG* 3.3 22.6 + - - +
838H ILE* 2.9 36.4 + - + +
2502H ADP 5.3 8.5 + - - -
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Residues in contact with ARG 835 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777H PRO* 4.2 17.0 - - + +
778H TRP* 6.5 0.2 - - - +
779H LEU* 3.6 28.2 - - + +
826H ARG 3.4 23.7 + - - -
827H GLY 2.4 30.7 + - - -
828H ILE* 4.5 1.2 + - - +
830H LEU* 2.8 32.8 + - + -
831H SER 3.2 20.9 + - - +
832H GLY* 3.7 10.9 + - - +
833H GLY 3.4 0.4 - - - -
834H GLN* 1.3 76.3 - - - +
836H GLN* 1.3 58.4 + - - +
838H ILE* 3.2 6.4 + - - +
839H SER* 2.9 29.6 + - - -
1428H ASP* 4.5 14.3 + - - -
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Residues in contact with GLN 836 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775H GLN 5.0 4.8 + - - -
777H PRO* 4.1 22.6 - - + +
832H GLY 3.7 13.0 + - - +
833H GLY 3.3 7.7 + - - +
834H GLN 3.3 0.4 - - - -
835H ARG* 1.3 77.2 - - - +
837H ARG* 1.3 62.2 + - - +
839H SER* 2.8 24.0 + - - -
840H VAL* 2.9 16.7 + - + +
855H ASP 4.1 3.8 + - - +
856H PRO* 4.0 14.6 - - + +
858H SER* 2.5 35.3 + - - -
859H ALA* 3.4 22.6 + - + +
860H LEU* 4.3 9.2 - - + +
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Residues in contact with ARG 837 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806H CYS* 3.1 31.9 - - + +
807H SER* 3.3 20.9 + - - -
808H LEU* 3.5 19.2 - - + +
811H ASP* 4.7 9.1 - - - +
831H SER* 5.1 0.8 + - - -
833H GLY* 2.9 28.6 + - - +
834H GLN* 3.6 32.3 - - - +
836H GLN* 1.3 76.0 - - - +
838H ILE* 1.3 57.6 + - - +
840H VAL* 3.4 6.5 + - - +
841H ALA* 2.9 29.1 + - - +
859H ALA 4.9 1.2 + - - -
860H LEU* 4.2 30.5 - - + +
861H ASP* 5.3 0.6 + - - -
864H LEU* 3.3 25.9 - - - +
868H LEU* 5.4 4.9 - - + -
1381H THR* 5.0 8.1 + - - -
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Residues in contact with ILE 838 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779H LEU* 3.9 17.5 - - + -
784H VAL* 4.2 18.2 - - + -
787H ASN* 4.4 20.9 - - + -
788H ILE* 4.7 8.7 - - + +
808H LEU* 3.6 21.8 - - + -
812H ILE* 5.0 5.2 - - + -
823H ILE* 4.1 11.9 - - + -
830H LEU* 3.6 29.8 - - + -
834H GLN* 2.9 19.4 + - + +
835H ARG* 3.7 5.4 - - - +
837H ARG* 1.3 73.1 - - - +
839H SER* 1.3 61.4 + - - +
841H ALA* 3.3 7.7 + - - +
842H ARG* 2.9 29.1 + - - +
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Residues in contact with SER 839 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773H ALA* 4.0 14.0 - - - +
774H SER 5.2 3.4 + - - -
777H PRO* 3.7 22.7 - - - +
778H TRP* 5.1 2.5 - - - -
779H LEU* 5.4 0.4 - - - -
835H ARG 2.9 13.4 + - - -
836H GLN* 2.8 24.8 + - - +
838H ILE* 1.3 77.7 - - - +
840H VAL* 1.3 60.5 + - - +
842H ARG* 3.2 26.6 + - - +
843H ALA* 3.0 28.1 + - - +
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Residues in contact with VAL 840 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773H ALA* 4.5 12.6 - - + -
806H CYS* 4.9 1.8 - - - -
836H GLN* 2.9 18.8 + - + +
837H ARG* 3.8 7.0 - - - +
839H SER* 1.3 84.0 + - - +
841H ALA* 1.3 58.1 + - - +
843H ALA* 3.4 2.2 + - + +
844H LEU* 2.9 42.5 + - + +
853H LEU* 4.3 19.7 - - + -
856H PRO* 3.5 33.9 - - + +
868H LEU* 4.5 27.8 - - + -
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Residues in contact with ALA 841 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788H ILE* 4.0 26.0 - - + -
802H VAL* 3.6 7.8 - - + +
803H ILE* 5.6 1.3 - - + -
806H CYS* 3.5 26.0 - - + -
808H LEU* 4.8 3.1 - - + -
837H ARG 2.9 18.3 + - - +
838H ILE* 3.5 6.5 - - - +
839H SER 3.2 0.2 - - - -
840H VAL* 1.3 75.1 - - - +
842H ARG* 1.3 60.2 + - - +
844H LEU* 4.4 0.4 - - - -
845H TYR* 2.9 34.1 + - - +
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Residues in contact with ARG 842 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772H TYR 6.0 0.9 - - - -
773H ALA* 6.3 0.6 - - - +
778H TRP* 3.1 33.1 + - - +
779H LEU* 4.1 6.7 - - - +
780H LEU* 4.0 7.3 - - - +
787H ASN* 3.2 48.5 + - - +
788H ILE* 4.2 11.9 - - - +
790H PHE* 3.5 41.6 - - + -
838H ILE* 2.9 12.1 + - - +
839H SER* 3.2 38.1 + - - +
841H ALA* 1.3 78.9 - - - +
843H ALA* 1.3 63.8 + - - +
844H LEU 3.2 0.2 + - - -
845H TYR* 3.4 7.4 + - - +
846H GLN* 3.5 16.9 + - + +
1213H THR* 5.0 5.5 - - - +
1217H PHE* 4.8 14.1 - - + -
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Residues in contact with ALA 843 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771H ALA* 3.5 24.9 - - + +
772H TYR* 4.0 13.0 - - - +
773H ALA* 3.8 31.4 - - + +
839H SER 3.0 14.9 + - - +
840H VAL* 4.0 3.4 - - - +
842H ARG* 1.3 77.8 - - - +
844H LEU* 1.3 59.0 + - - +
846H GLN 4.3 4.8 + - - +
851H VAL* 4.1 11.6 - - + +
852H PHE 5.2 1.6 - - - +
853H LEU* 5.3 8.1 - - + -
882H ARG* 5.7 0.2 + - - -
1217H PHE* 4.8 3.6 - - - -
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Residues in contact with LEU 844 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798H ARG* 4.0 8.8 + - - -
802H VAL* 4.6 7.5 - - + +
805H ALA* 5.4 2.0 - - + -
806H CYS* 4.5 18.4 - - - -
840H VAL* 2.9 26.5 + - + +
841H ALA* 3.9 4.3 - - - +
842H ARG 3.2 0.2 - - - -
843H ALA* 1.3 77.6 - - - +
845H TYR* 1.3 60.7 + - - +
846H GLN 3.4 3.0 - - - +
851H VAL* 5.8 0.4 - - - -
853H LEU* 6.5 0.4 - - + -
868H LEU* 5.0 4.9 - - + -
872H GLY* 4.1 26.0 - - - +
873H ILE* 6.0 1.6 - - + -
876H LEU* 4.5 19.9 - - + +
877H LEU* 3.5 42.4 - - + -
882H ARG* 5.0 4.0 + - - -
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Residues in contact with TYR 845 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788H ILE* 3.1 31.4 - - + +
789H THR* 3.8 26.8 - - + +
792H SER* 4.2 13.2 - - - -
793H PRO 2.9 24.9 + - - -
794H PHE* 3.9 9.7 - - - -
795H ASN* 4.0 6.5 + - - -
798H ARG* 2.9 44.6 + - + +
799H TYR* 3.9 23.6 - + + +
802H VAL* 3.8 30.3 - - + +
841H ALA 2.9 16.6 + - - +
842H ARG 3.4 1.1 + - - +
844H LEU* 1.3 78.3 - - - +
846H GLN* 1.3 63.7 + - + +
847H GLN* 3.7 1.9 + - - +
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Residues in contact with GLN 846 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771H ALA* 4.5 9.6 - - + -
789H THR 2.8 28.0 + - - +
790H PHE* 3.1 22.8 + - + +
792H SER* 3.5 16.1 + - - -
798H ARG* 3.5 0.2 + - - -
842H ARG 3.5 13.9 + - - +
843H ALA 4.3 2.5 + - - +
844H LEU 3.4 3.9 - - - +
845H TYR* 1.3 84.2 - - + +
847H GLN* 1.3 74.6 + - - +
848H THR* 3.6 3.8 + - + +
882H ARG* 2.9 20.0 + - - -
1217H PHE* 3.6 31.1 - - + -
1219H TYR* 3.4 16.4 + - - -
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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
------------------------------------------------------------
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