Contacts of the strand formed by residues 885 - 895 (chain B) in PDB entry 4X52
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 VAL 885 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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767B LEU 4.7 3.1 - - - +
771B PHE* 3.5 10.7 - - - +
801B ASN* 3.0 25.5 + - - +
802B PHE* 3.6 22.7 - - + -
818B ILE* 5.2 4.7 - - + -
820B PHE* 3.5 42.0 - - + -
843B ALA* 3.8 7.6 - - + -
844B GLN 3.4 9.4 - - - +
845B VAL* 4.1 4.5 - - + -
879B ILE* 3.6 21.5 - - + -
881B GLN 4.5 0.4 - - - +
882B LYS* 2.9 10.1 + - - +
883B ASP* 3.2 2.2 - - - -
884B GLN* 1.4 84.6 - - - +
886B TYR* 1.3 65.0 + - - +
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Residues in contact with TYR 886 (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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762B ILE* 3.1 18.3 + - + -
763B GLU* 3.5 3.1 - - - +
764B ASN* 3.1 39.9 + - + -
767B LEU* 3.8 9.0 - - + -
768B LEU* 3.6 44.1 - - + +
771B PHE* 3.8 22.4 - + + -
843B ALA* 3.4 0.9 - - - -
844B GLN* 2.9 42.1 + - + +
885B VAL* 1.3 78.2 - - - +
887B PRO* 1.4 88.2 - - + +
888B GLN* 3.3 33.4 + - + -
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Residues in contact with PRO 887 (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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762B ILE* 3.5 34.4 - - + +
767B LEU* 3.9 16.2 - - + -
797B ILE* 3.7 28.7 - - + +
798B CYS* 4.8 0.2 - - - -
801B ASN* 3.7 17.7 - - - +
802B PHE* 3.7 27.2 - - + -
841B PHE* 4.2 0.9 - - + -
842B VAL 4.1 4.0 - - - +
886B TYR* 1.4 104.1 - - + +
888B GLN* 1.3 59.8 + - - +
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Residues in contact with GLN 888 (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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761B LYS* 3.7 26.1 - - - +
762B ILE* 2.8 42.4 + - - -
768B LEU* 5.8 0.7 - - - +
842B VAL* 2.8 20.2 + - + +
843B ALA 4.9 0.2 - - - -
844B GLN* 4.7 18.8 - - + +
886B TYR* 3.3 28.2 + - + +
887B PRO* 1.3 74.5 - - - +
889B TYR* 1.3 86.2 + - + +
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Residues in contact with TYR 889 (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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733B ILE* 3.8 21.5 - - + -
739B GLU* 2.7 35.6 + - + +
742B ARG* 4.7 7.0 + - - -
743B VAL* 3.4 31.2 - - + +
759B ILE* 4.1 13.2 - - + -
760B LYS 3.2 15.5 - - - +
761B LYS* 3.8 13.8 - - + -
762B ILE* 3.8 2.0 - - - +
784B LEU* 5.5 4.5 - - + -
841B PHE* 3.3 9.7 - - - -
842B VAL* 2.8 54.4 + - + +
888B GLN* 1.3 101.6 - - + +
890B VAL* 1.3 64.9 + - - +
891B ILE 4.3 0.2 - - - -
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Residues in contact with VAL 890 (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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730B LEU* 3.8 19.7 - - + -
758B LYS 4.0 0.9 - - - +
759B ILE* 3.4 3.5 - - - +
760B LYS* 2.9 41.5 + - + +
762B ILE* 3.7 9.0 - - + -
794B VAL* 4.2 18.8 - - + -
798B CYS* 4.4 0.2 - - - -
839B VAL* 4.0 31.4 - - + -
840B MET 3.5 4.0 - - - +
841B PHE* 3.6 27.8 - - + +
889B TYR* 1.3 75.9 - - - +
891B ILE* 1.3 64.4 - - - +
892B GLU* 4.3 5.1 + - + +
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Residues in contact with ILE 891 (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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743B VAL* 3.7 22.9 - - + -
747B PHE* 3.7 37.9 - - + -
756B ILE* 3.9 25.4 - - + -
758B LYS 3.5 7.6 - - - +
759B ILE* 4.3 7.9 - - + -
786B PHE* 4.4 0.9 - - + -
839B VAL* 3.6 7.4 - - - +
840B MET* 2.7 47.3 + - + +
842B VAL* 3.6 28.0 - - + -
890B VAL* 1.3 77.3 - - - +
892B GLU* 1.3 73.7 + - - +
893B TYR* 3.8 3.6 - - + -
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Residues in contact with GLU 892 (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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756B ILE* 3.6 2.8 - - - -
757B GLU* 2.7 35.7 + - + -
758B LYS* 2.9 47.1 + - + +
760B LYS* 3.5 19.6 + - + +
791B ARG* 2.8 35.7 + - - +
838B VAL 5.6 0.4 - - - -
839B VAL* 4.2 8.7 - - + -
890B VAL* 4.2 6.3 - - + +
891B ILE* 1.3 72.5 - - - +
893B TYR* 1.3 56.3 + - - +
729C LYS* 4.5 13.7 + - - -
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Residues in contact with TYR 893 (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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747B PHE* 3.6 26.7 - + + -
751B MET* 3.5 19.5 - - + -
754B PHE* 3.7 20.0 - + - -
755B LYS 3.2 17.9 - - - +
756B ILE* 4.2 2.2 - - - -
757B GLU* 4.1 4.6 - - - +
791B ARG* 5.6 3.3 + - - +
828B HIS* 2.7 32.5 + + - -
835B ALA 5.0 8.1 - - - +
838B VAL* 3.2 40.0 + - + +
840B MET* 3.6 38.2 - - + +
891B ILE* 3.8 12.3 - - + -
892B GLU* 1.3 74.1 - - - +
894B THR* 1.3 70.0 + - - +
895B GLU* 6.0 0.2 - - + -
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Residues in contact with THR 894 (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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754B PHE* 3.4 6.8 - - - -
755B LYS* 2.8 38.0 + - - +
757B GLU* 2.7 32.2 + - + +
836B LYS* 6.5 0.9 - - - -
893B TYR* 1.3 79.9 - - - +
895B GLU* 1.3 64.4 + - - +
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Residues in contact with GLU 895 (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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753B ASN* 3.4 11.7 - - - +
754B PHE* 3.2 26.0 - - + -
828B HIS* 4.0 12.1 + - + -
835B ALA* 3.9 25.3 - - + +
893B TYR* 6.0 0.4 - - + -
894B THR* 1.3 78.6 + - - +
896B ASP* 1.3 70.5 + - - +
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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