Contacts of the strand formed by residues 852 - 860 (chain B) in PDB entry 5J67
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 HIS 852 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B GLY* 3.4 5.0 - - - -
730B TYR* 2.8 39.7 + - + +
732B ASN* 3.6 28.3 + - + -
851B SER* 1.3 105.0 + - - +
853B TYR* 1.3 58.1 + - - +
959B VAL* 3.8 33.9 - - + +
960B VAL 3.2 10.8 - - - +
961B PRO* 3.4 37.0 - - + +
962B LEU* 3.6 12.2 - - - +
979B LEU* 5.2 9.2 - - + -
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Residues in contact with TYR 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B MET 4.9 2.0 - - - +
727B LEU 6.5 0.2 - - - -
729B GLY* 4.2 9.9 - - - -
730B TYR 4.5 0.2 - - - +
742B VAL* 4.6 3.8 - - + -
743B PHE* 3.6 35.0 - + + -
817B LEU* 4.3 13.0 - - + -
852B HIS* 1.3 75.7 - - - +
854B ILE* 1.3 73.3 + - - +
855B ALA* 4.5 4.3 - - + -
959B VAL* 3.5 2.9 - - - -
960B VAL* 2.9 75.8 + - + +
961B PRO 4.3 1.6 - - - -
962B LEU* 4.0 14.4 - - + -
964B THR* 4.8 4.3 - - - +
965B LEU* 3.4 33.4 - - + +
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Residues in contact with ILE 854 (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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725B GLU* 3.9 25.6 - - + +
726B MET* 3.6 39.0 + - - +
729B GLY* 5.1 2.0 - - - +
730B TYR* 3.9 20.0 - - + -
737B VAL* 4.1 16.2 - - + -
817B LEU* 3.2 17.8 - - - +
853B TYR* 1.3 74.4 - - - +
855B ALA* 1.3 60.0 + - - +
856B GLU 3.6 20.4 - - - +
857B ALA* 3.9 6.7 - - + -
953B LEU* 4.8 3.4 - - + -
956B ILE* 3.7 38.8 - - + -
958B ARG 3.8 3.6 - - - -
959B VAL* 4.6 1.1 - - - -
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Residues in contact with ALA 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B MET* 3.5 2.6 - - - +
816B LYS* 3.4 23.0 - - - +
817B LEU* 3.4 18.4 + - + +
853B TYR* 3.5 6.8 + - + -
854B ILE* 1.3 73.3 - - - +
856B GLU* 1.3 58.5 + - - +
958B ARG* 2.9 46.0 + - + +
960B VAL* 4.0 20.4 - - + -
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Residues in contact with GLU 856 (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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814B ARG* 3.6 31.3 + - - +
815B VAL 3.5 4.9 - - - -
816B LYS* 3.4 33.4 - - + -
854B ILE* 3.6 4.2 - - - +
855B ALA* 1.3 77.9 - - - +
857B ALA* 1.3 67.0 + - - +
957B ASN* 2.9 38.6 + - + +
958B ARG* 3.1 40.3 + - + +
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Residues in contact with ALA 857 (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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726B MET* 3.7 23.6 - - - -
814B ARG* 3.6 3.3 - - - -
815B VAL* 2.7 39.4 + - - +
854B ILE* 3.9 6.7 - - + -
856B GLU* 1.3 77.9 - - - +
858B LEU* 1.3 58.8 + - - +
859B TYR* 3.9 4.7 - - + -
953B LEU* 3.8 17.3 - - + -
955B GLU 3.4 14.1 - - - +
956B ILE* 4.5 0.4 - - - -
957B ASN* 3.4 8.7 - - - -
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Residues in contact with LEU 858 (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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768B LEU* 3.7 32.1 - - + -
809B ARG* 3.4 24.5 - - - +
812B LEU* 4.1 13.9 - - + -
813B TYR 3.6 14.8 - - - +
814B ARG* 3.9 15.3 - - - +
857B ALA* 1.3 72.4 - - - +
859B TYR* 1.3 68.6 + - - +
953B LEU* 3.9 2.4 - - - +
954B LEU* 2.9 27.3 + - + +
955B GLU* 2.9 45.9 + - + +
957B ASN* 3.4 8.6 + - - +
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Residues in contact with TYR 859 (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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722B LEU* 5.8 0.9 - - + -
723B PHE* 3.6 42.1 - + + -
725B GLU* 2.6 44.7 + - - +
726B MET* 3.9 10.4 - - - +
812B LEU* 3.2 10.0 - - - +
813B TYR* 2.8 34.9 + - + +
815B VAL* 3.5 27.6 - - + -
854B ILE* 5.9 0.2 - - - +
857B ALA* 3.9 20.9 - - + -
858B LEU* 1.3 78.1 - - - +
860B GLY* 1.3 58.4 + - - +
951B PRO* 3.9 12.1 - - + -
952B VAL* 3.2 7.0 - - - +
953B LEU* 3.3 35.0 - - + +
954B LEU* 3.8 4.0 - - - -
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Residues in contact with GLY 860 (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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811B ASN* 3.2 23.3 - - - -
812B LEU* 4.1 1.1 - - - -
859B TYR* 1.3 76.9 - - - +
861B SER* 1.3 64.2 + - - -
929B LYS 4.0 0.2 - - - +
930B GLY* 4.3 0.3 - - - -
951B PRO* 3.7 6.3 - - - +
952B VAL* 2.8 36.0 + - - +
954B LEU* 3.7 11.5 - - - +
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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