Contacts of the helix formed by residues 831 - 846 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830F LEU* 1.3 74.7 - - - +
832F GLY* 1.3 67.3 + - - +
833F GLY* 3.5 3.1 + - - -
834F GLN* 3.1 44.8 + - - +
835F ARG* 3.2 28.8 + - - +
837F ARG* 5.1 0.5 + - - -
2502F ADP 5.5 14.5 + - - -
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Residues in contact with GLY 832 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831F SER* 1.3 80.2 + - - +
833F GLY* 1.3 61.1 + - - +
835F ARG* 3.7 18.1 + - - +
836F GLN* 3.7 18.2 + - - +
859F ALA* 3.9 9.5 - - - +
1427F GLN* 5.6 6.3 - - - -
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Residues in contact with GLY 833 (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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831F SER* 3.5 4.0 + - - -
832F GLY* 1.3 74.5 - - - +
834F GLN* 1.3 58.9 + - - +
836F GLN* 3.3 3.5 + - - +
837F ARG* 2.9 46.9 + - - +
859F ALA* 3.3 30.8 + - - +
860F LEU* 4.8 0.4 - - - -
1427F GLN* 5.8 0.2 - - - +
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Residues in contact with GLN 834 (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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808F LEU* 4.4 5.0 - - + +
811F ASP* 3.0 40.3 + - - +
815F LEU* 4.7 8.4 - - - +
829F ASN 4.8 0.7 - - - +
830F LEU* 3.6 22.0 - - + +
831F SER* 3.1 43.8 + - - +
832F GLY 3.3 1.0 - - - -
833F GLY* 1.3 77.7 - - - +
835F ARG* 1.3 56.5 + - - +
837F ARG* 3.3 22.7 + - - +
838F ILE* 2.9 35.8 + - + +
2502F ADP 5.3 8.5 + - - -
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Residues in contact with ARG 835 (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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777F PRO* 4.2 16.8 - - + +
779F LEU* 3.6 28.1 - - + +
826F ARG 3.4 23.1 + - - -
827F GLY 2.4 31.1 + - - -
828F ILE* 4.5 1.8 + - - +
830F LEU* 2.8 32.4 + - + -
831F SER 3.2 20.4 + - - +
832F GLY* 4.2 10.7 + - - +
833F GLY 3.4 0.2 - - - -
834F GLN* 1.3 75.4 - - - +
836F GLN* 1.3 60.0 + - + +
838F ILE* 3.2 6.9 + - - +
839F SER* 2.9 29.3 + - - -
1428F ASP* 4.5 14.6 + - - -
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Residues in contact with GLN 836 (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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775F GLN 5.0 5.2 + - - -
777F PRO* 4.1 23.0 - - + +
832F GLY 3.7 13.6 + - - +
833F GLY 3.3 7.7 + - - +
834F GLN 3.3 0.4 - - - -
835F ARG* 1.3 77.2 - - - +
837F ARG* 1.3 62.1 + - - +
839F SER* 2.8 23.5 + - - +
840F VAL* 2.9 16.7 + - + +
855F ASP 4.1 3.1 - - - +
856F PRO* 4.0 14.6 - - + +
858F SER* 2.5 36.3 + - - -
859F ALA* 3.4 22.4 + - + +
860F LEU* 4.3 8.6 - - + +
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Residues in contact with ARG 837 (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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806F CYS* 3.1 31.1 - - - +
807F SER* 3.3 22.0 + - - -
808F LEU* 3.5 19.4 - - + +
811F ASP* 4.7 8.9 - - - +
831F SER* 5.1 0.6 + - - -
833F GLY* 2.9 28.0 + - - +
834F GLN* 3.6 32.1 - - - +
836F GLN* 1.3 75.1 - - - +
838F ILE* 1.3 58.6 + - - +
840F VAL* 3.4 6.9 + - - +
841F ALA* 2.9 29.3 + - - +
859F ALA 4.9 1.0 + - - -
860F LEU* 4.2 30.7 - - + +
861F ASP* 5.3 0.6 + - - -
864F LEU* 3.3 26.1 - - - +
868F LEU* 5.4 4.3 - - + -
1381F THR* 5.0 7.9 + - - -
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Residues in contact with ILE 838 (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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779F LEU* 3.9 17.7 - - + -
784F VAL* 4.2 17.5 - - + -
787F ASN* 4.4 20.2 - - + +
788F ILE* 4.7 8.4 - - + +
808F LEU* 3.6 22.0 - - + -
812F ILE* 5.0 5.8 - - + -
823F ILE* 4.1 12.1 - - + -
830F LEU* 3.6 31.0 - - + -
834F GLN* 2.9 19.5 + - + +
835F ARG* 3.7 5.2 - - - +
836F GLN 3.2 0.2 - - - -
837F ARG* 1.3 74.3 - - - +
839F SER* 1.3 60.1 + - - +
841F ALA* 3.3 7.6 + - - +
842F ARG* 2.9 29.1 + - - +
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Residues in contact with SER 839 (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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773F ALA* 4.0 14.2 - - - +
774F SER 5.2 2.7 + - - -
777F PRO* 3.7 22.9 - - - +
778F TRP* 5.1 2.5 - - - -
779F LEU* 5.4 0.2 - - - -
835F ARG 2.9 13.2 + - - -
836F GLN* 2.8 23.9 + - - -
838F ILE* 1.3 78.2 - - - +
840F VAL* 1.3 59.7 + - - +
842F ARG* 3.2 26.0 + - - +
843F ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 840 (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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773F ALA* 4.5 12.1 - - + -
806F CYS* 4.9 1.8 - - - -
836F GLN* 2.9 19.7 + - - +
837F ARG* 3.8 6.5 - - - +
839F SER* 1.3 85.7 + - - +
841F ALA* 1.3 56.7 + - - +
843F ALA* 3.4 2.0 + - - +
844F LEU* 2.9 41.9 + - + +
853F LEU* 4.3 20.0 - - + -
856F PRO* 3.5 33.4 - - + +
868F LEU* 4.5 27.8 - - + -
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Residues in contact with ALA 841 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788F ILE* 4.0 25.8 - - + -
802F VAL* 3.6 9.1 - - + +
803F ILE* 5.6 0.7 - - + -
806F CYS* 3.5 25.9 - - + -
808F LEU* 4.8 2.7 - - + -
837F ARG 2.9 18.7 + - - +
838F ILE* 3.5 7.2 - - - +
840F VAL* 1.3 74.0 - - - +
842F ARG* 1.3 59.9 + - - +
844F LEU* 4.4 0.4 - - - -
845F TYR* 2.9 33.8 + - - +
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Residues in contact with ARG 842 (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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772F TYR 6.0 0.9 - - - -
773F ALA* 6.3 0.6 - - - +
778F TRP* 3.1 32.1 + - - +
779F LEU* 4.1 7.1 - - - +
780F LEU* 4.0 6.9 - - - +
787F ASN* 3.2 46.7 + - - +
788F ILE* 4.2 12.4 - - - +
790F PHE* 3.5 42.2 - - + -
838F ILE* 2.9 11.7 + - - +
839F SER* 3.2 37.2 + - - +
841F ALA* 1.3 79.1 - - - +
843F ALA* 1.3 63.8 + - - +
845F TYR* 3.4 8.1 + - - +
846F GLN* 3.5 16.6 + - - +
1213F THR* 5.0 6.1 - - - +
1217F PHE* 4.8 13.9 - - + -
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Residues in contact with ALA 843 (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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771F ALA* 3.5 23.4 - - + +
772F TYR* 4.0 13.5 - - - +
773F ALA* 3.8 30.7 - - + +
839F SER 3.0 15.8 + - - +
840F VAL* 4.0 3.1 - - - +
842F ARG* 1.3 78.4 - - - +
844F LEU* 1.3 59.7 + - - +
846F GLN 4.3 4.8 + - - +
851F VAL* 4.1 11.8 - - + +
852F PHE 5.2 1.6 - - - +
853F LEU* 5.3 8.1 - - + -
1217F PHE* 4.8 3.8 - - - -
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Residues in contact with LEU 844 (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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798F ARG* 4.0 9.5 + - - -
802F VAL* 4.6 7.9 - - + +
805F ALA* 5.4 1.8 - - + -
806F CYS* 4.5 18.2 - - - -
840F VAL* 2.9 26.1 + - + +
841F ALA* 3.9 3.8 - - - +
843F ALA* 1.3 77.4 - - - +
845F TYR* 1.3 61.7 + - - +
846F GLN 3.4 3.5 - - - +
851F VAL* 5.8 0.4 - - - -
853F LEU* 6.5 0.7 - - + -
868F LEU* 5.0 4.5 - - + -
872F GLY* 4.1 26.7 - - - +
873F ILE* 6.0 1.3 - - + -
876F LEU* 4.5 20.7 - - + +
877F LEU* 3.5 42.0 - - + +
882F ARG* 5.0 3.9 + - - -
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Residues in contact with TYR 845 (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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788F ILE* 3.1 30.7 - - + +
789F THR* 3.8 27.9 - - + +
792F SER* 4.2 13.1 + - - -
793F PRO 2.9 23.7 + - - -
794F PHE* 3.9 10.2 - - - -
795F ASN* 4.0 6.6 + - - -
798F ARG* 2.9 44.7 + - + +
799F TYR* 3.9 24.3 - + + +
802F VAL* 3.8 31.6 - - + +
841F ALA 2.9 17.6 + - - +
842F ARG 4.0 0.7 - - - +
844F LEU* 1.3 78.1 - - - +
846F GLN* 1.3 64.5 + - + +
847F GLN* 3.7 2.1 + - - +
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Residues in contact with GLN 846 (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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771F ALA* 4.5 9.2 - - + -
788F ILE 5.4 0.2 - - - +
789F THR 2.8 28.3 + - - +
790F PHE* 3.1 23.9 + - + +
792F SER* 3.5 15.2 + - - -
798F ARG* 3.5 0.2 + - - -
842F ARG 3.5 13.5 + - - +
843F ALA 4.3 2.3 + - - +
844F LEU 3.4 4.3 - - - +
845F TYR* 1.3 82.0 - - + +
847F GLN* 1.3 72.5 + - - +
848F THR* 3.6 3.3 + - - +
882F ARG* 2.9 20.8 + - - -
1217F PHE* 3.6 31.3 - - + -
1219F TYR* 3.4 16.8 + - - -
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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