Contacts of the helix formed by residues 831 - 846 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830B LEU* 1.3 75.0 - - - +
832B GLY* 1.3 68.0 + - - +
833B GLY* 3.5 3.6 + - - -
834B GLN* 3.1 43.4 + - - +
835B ARG* 3.2 28.7 + - - +
837B ARG* 5.1 0.7 + - - -
2502B ADP 5.5 14.1 - - - -
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Residues in contact with GLY 832 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B SER* 1.3 81.2 + - - +
833B GLY* 1.3 60.3 + - - +
834B GLN 3.4 0.2 + - - -
835B ARG* 3.7 18.3 + - - +
836B GLN* 3.7 18.0 + - - +
859B ALA* 3.9 9.0 - - - +
1427B GLN* 5.6 5.8 - - - -
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Residues in contact with GLY 833 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831B SER* 3.5 4.2 + - - -
832B GLY* 1.3 74.4 - - - +
834B GLN* 1.3 58.6 + - - +
836B GLN* 3.3 2.8 + - - +
837B ARG* 2.9 47.4 + - - +
859B ALA* 3.3 30.8 + - - +
860B LEU* 4.5 0.6 - - - +
1427B GLN* 5.8 0.2 - - - +
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Residues in contact with GLN 834 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808B LEU* 4.4 4.0 - - + +
811B ASP* 3.0 40.2 + - - +
815B LEU* 4.7 9.2 - - - +
829B ASN 4.8 1.0 - - - +
830B LEU* 3.6 20.7 - - + +
831B SER* 3.1 43.1 + - - +
832B GLY 3.3 1.0 - - - -
833B GLY* 1.3 77.5 - - - +
835B ARG* 1.3 58.5 + - - +
837B ARG* 3.3 22.1 + - - +
838B ILE* 2.9 35.6 + - + +
2502B ADP 5.3 9.1 + - - -
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Residues in contact with ARG 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777B PRO* 4.2 17.6 - - + +
779B LEU* 3.6 28.0 - - + +
826B ARG 3.4 24.1 + - - -
827B GLY 2.4 31.3 + - - -
828B ILE* 4.5 1.6 + - - +
830B LEU* 2.8 32.0 + - + -
831B SER 3.2 20.7 + - - +
832B GLY* 4.2 10.6 + - - +
833B GLY 3.4 0.4 - - - -
834B GLN* 1.3 76.4 - - - +
836B GLN* 1.3 57.8 + - - +
838B ILE* 3.2 7.0 + - - +
839B SER* 2.9 29.3 + - - -
1428B ASP* 4.5 14.5 + - - -
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Residues in contact with GLN 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B GLN 5.0 5.0 + - - -
777B PRO* 4.1 22.4 - - + +
832B GLY 3.7 13.4 + - - +
833B GLY 3.3 7.1 + - - +
834B GLN 3.3 0.4 - - - -
835B ARG* 1.3 77.4 - - - +
837B ARG* 1.3 62.4 + - - +
839B SER* 2.8 23.6 + - - -
840B VAL* 2.9 16.3 + - + +
855B ASP 4.1 3.7 - - - +
856B PRO* 4.0 14.3 - - + +
858B SER* 2.5 36.2 + - - -
859B ALA* 3.4 22.9 + - + +
860B LEU* 4.3 9.9 - - + +
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Residues in contact with ARG 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B CYS* 3.1 32.1 - - - +
807B SER* 3.3 21.7 + - - -
808B LEU* 3.5 20.0 - - + +
811B ASP* 4.7 9.1 - - - +
831B SER* 5.1 0.6 + - - -
833B GLY* 2.9 28.8 + - - +
834B GLN* 3.6 31.6 - - - +
836B GLN* 1.3 75.5 - - - +
838B ILE* 1.3 57.2 + - - +
840B VAL* 3.4 6.9 + - - +
841B ALA* 2.9 29.7 + - - +
859B ALA 4.9 1.4 + - - -
860B LEU* 4.2 30.5 - - + +
861B ASP* 5.3 0.4 + - - -
864B LEU* 3.3 24.9 - - - +
868B LEU* 5.4 4.9 - - + -
1381B THR* 5.0 7.7 + - - -
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Residues in contact with ILE 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B LEU* 3.9 17.7 - - + -
784B VAL* 4.2 18.4 - - + -
787B ASN* 4.4 20.2 - - + +
788B ILE* 4.7 8.7 - - + +
808B LEU* 3.6 22.4 - - + -
812B ILE* 5.0 5.2 - - + -
823B ILE* 4.1 11.4 - - + -
830B LEU* 3.6 30.7 - - + -
834B GLN* 2.9 17.9 + - + +
835B ARG* 3.7 4.7 - - - +
836B GLN 3.2 0.4 - - - -
837B ARG* 1.3 75.0 - - - +
839B SER* 1.3 60.9 + - - +
841B ALA* 3.3 6.6 + - - +
842B ARG* 2.9 29.0 + - - +
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Residues in contact with SER 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B ALA* 4.0 14.7 - - - +
774B SER 5.2 3.0 + - - -
777B PRO* 3.7 22.0 - - - +
778B TRP 5.1 2.7 - - - -
779B LEU* 5.4 0.7 - - - -
835B ARG 2.9 12.5 + - - -
836B GLN* 2.8 24.4 + - - -
838B ILE* 1.3 77.6 - - - +
840B VAL* 1.3 60.5 + - - +
842B ARG* 3.2 24.8 + - - +
843B ALA* 3.0 28.6 + - - +
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Residues in contact with VAL 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B ALA* 4.5 12.8 - - + -
806B CYS* 4.9 1.6 - - - -
836B GLN* 2.9 19.9 + - + +
837B ARG* 3.8 6.5 - - - +
839B SER* 1.3 83.8 + - - +
841B ALA* 1.3 58.9 + - - +
843B ALA* 3.4 1.5 + - - +
844B LEU* 2.9 42.7 + - + +
853B LEU* 4.3 20.0 - - + -
856B PRO* 3.5 32.1 - - + +
868B LEU* 4.5 27.6 - - + -
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Residues in contact with ALA 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B ILE* 4.0 25.6 - - + -
802B VAL* 3.6 8.8 - - + +
803B ILE* 5.6 0.7 - - + -
806B CYS* 3.5 25.1 - - + -
808B LEU* 4.8 3.1 - - + -
837B ARG 2.9 18.2 + - - +
838B ILE* 3.5 7.6 - - - +
839B SER 3.2 0.2 - - - -
840B VAL* 1.3 74.9 - - - +
842B ARG* 1.3 60.1 + - - +
844B LEU* 4.4 0.4 - - - -
845B TYR* 2.9 34.3 + - - +
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Residues in contact with ARG 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772B TYR 6.0 1.1 - - - -
773B ALA* 6.2 0.8 - - - +
778B TRP* 3.1 32.5 + - - +
779B LEU* 4.1 7.5 - - - +
780B LEU* 4.0 6.7 - - - +
787B ASN* 3.2 48.6 + - - +
788B ILE* 4.2 10.8 - - - +
790B PHE* 3.5 42.2 - - + -
838B ILE* 2.9 11.1 + - - +
839B SER* 3.2 37.0 + - - +
841B ALA* 1.3 79.9 - - - +
843B ALA* 1.3 63.5 + - - +
844B LEU 3.2 0.3 + - - -
845B TYR* 3.4 7.3 + - - +
846B GLN* 3.5 17.2 + - + +
1213B THR* 5.0 5.5 - - - +
1217B PHE* 4.8 14.8 - - + -
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Residues in contact with ALA 843 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B ALA* 3.5 23.8 - - + +
772B TYR* 4.0 13.0 - - - +
773B ALA* 3.8 30.7 - - + +
839B SER 3.0 15.8 + - - +
840B VAL* 4.0 3.8 - - - +
842B ARG* 1.3 79.5 - - - +
844B LEU* 1.3 58.4 + - - +
846B GLN 4.3 4.8 + - - +
851B VAL* 4.1 11.8 - - + +
852B PHE 5.2 1.6 - - - +
853B LEU* 5.3 8.5 - - + -
1217B PHE* 4.8 3.8 - - + -
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Residues in contact with LEU 844 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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798B ARG* 4.0 9.4 + - - -
802B VAL* 4.6 7.8 - - + +
805B ALA* 5.4 2.0 - - + -
806B CYS* 4.5 18.4 - - - -
840B VAL* 2.9 26.4 + - + +
841B ALA* 3.9 4.0 - - - +
842B ARG 3.2 0.2 - - - -
843B ALA* 1.3 78.6 - - - +
845B TYR* 1.3 61.5 + - - +
846B GLN 3.4 3.4 - - - +
851B VAL* 5.8 0.7 - - - -
853B LEU* 6.5 0.9 - - + -
868B LEU* 5.0 5.2 - - + -
872B GLY* 4.1 26.0 - - - +
873B ILE* 6.0 1.8 - - + -
876B LEU* 4.5 21.0 - - + +
877B LEU* 3.5 42.0 - - + -
882B ARG* 5.0 3.9 + - - +
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Residues in contact with TYR 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788B ILE* 3.1 30.5 - - + +
789B THR* 3.8 26.9 - - + +
792B SER* 4.2 13.4 + - - -
793B PRO 2.9 24.1 + - - -
794B PHE* 3.9 9.4 - - - -
795B ASN* 4.0 7.1 + - - -
798B ARG* 2.9 45.2 + - + +
799B TYR* 3.9 23.7 - + + +
802B VAL* 3.8 31.0 - - + -
841B ALA 2.9 18.3 + - - +
842B ARG 3.4 1.1 + - - +
844B LEU* 1.3 77.2 - - - +
846B GLN* 1.3 64.0 + - + +
847B GLN* 3.7 1.7 + - - +
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Residues in contact with GLN 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771B ALA* 4.5 10.5 - - + -
789B THR 2.8 28.6 + - - +
790B PHE* 3.1 22.0 + - + +
792B SER* 3.5 14.3 + - - -
798B ARG* 3.5 0.3 + - - -
842B ARG 3.5 13.1 + - - +
843B ALA 4.3 2.5 + - - +
844B LEU 3.4 4.1 - - - +
845B TYR* 1.3 85.2 - - + +
847B GLN* 1.3 73.2 + - - +
848B THR* 3.6 4.5 + - - +
882B ARG* 2.9 20.7 + - - -
1217B PHE* 3.6 31.0 - - + -
1219B TYR* 3.4 17.8 + - - -
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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