Contacts of the strand formed by residues 783 - 790 (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 LYS 783 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781B GLU 5.3 0.7 - - - +
782B GLY* 1.3 73.3 - - - -
784B LEU* 1.3 63.8 + - - +
785B LEU* 3.3 20.7 + - + +
843B ALA 3.3 4.7 - - - +
844B GLN* 3.5 3.3 - - - -
845B VAL* 2.8 44.2 + - - +
847B VAL* 4.0 36.5 - - + +
850B PHE* 4.6 9.5 - - - -
877B PHE* 4.4 16.3 - - + -
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Residues in contact with LEU 784 (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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742B ARG* 5.6 4.7 - - + -
743B VAL* 5.5 5.6 - - + -
746B HIS* 3.8 54.7 - - + +
782B GLY 4.3 0.8 + - - -
783B LYS* 1.3 71.4 - - - +
785B LEU* 1.3 67.3 + - - +
786B PHE* 4.0 15.0 - - + -
822B LYS 4.8 5.2 - - - +
842B VAL* 3.5 31.0 - - + -
843B ALA 3.5 5.4 - - - -
844B GLN* 3.6 17.0 + - - +
889B TYR* 5.5 7.6 - - + -
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Residues in contact with LEU 785 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783B LYS* 3.3 19.5 + - + +
784B LEU* 1.3 83.6 - - - +
786B PHE* 1.4 65.2 + - - +
820B PHE* 3.7 28.3 - - + -
821B ALA 3.6 15.5 - - - +
822B LYS* 3.8 17.5 - - + -
842B VAL* 3.5 6.1 - - - +
843B ALA* 2.8 35.0 + - - +
845B VAL* 3.8 27.8 - - + -
847B VAL* 4.0 8.7 - - + -
877B PHE* 3.7 29.6 - - + -
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Residues in contact with PHE 786 (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 5.4 0.2 - - - -
746B HIS* 3.8 39.5 - + + -
747B PHE* 3.9 9.4 - - - -
784B LEU* 4.0 15.3 - - + -
785B LEU* 1.4 76.0 - - - +
787B TYR* 1.3 60.4 - - - +
820B PHE* 3.3 9.3 - - - -
821B ALA 2.9 33.5 + - - +
822B LYS 3.6 21.3 - - - -
823B ASP* 4.5 1.1 - - - -
824B ALA* 3.3 36.3 - - + -
827B SER* 3.8 9.3 + - - -
840B MET* 3.6 29.4 - - + -
841B PHE 3.5 6.5 - - - -
842B VAL* 3.8 21.5 - - + -
891B ILE* 4.4 6.1 - - + -
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Residues in contact with TYR 787 (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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786B PHE* 1.3 75.7 - - - +
788B ALA* 1.4 61.8 + - - +
789B THR* 3.6 28.2 + - + -
797B ILE* 3.9 7.8 - - + +
802B PHE* 3.4 40.8 - + + -
803B ASP 4.3 8.1 + - - -
806B LEU* 4.0 34.9 + - - +
808B GLU* 6.4 2.0 - - + -
818B ILE* 3.7 24.7 - - + -
819B TYR* 3.3 23.8 - - + -
820B PHE* 3.9 9.9 - + + -
827B SER* 3.4 3.8 - - - -
840B MET* 3.9 2.0 - - - -
841B PHE* 2.8 38.9 + + + +
843B ALA* 5.7 0.7 - - + -
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Residues in contact with ALA 788 (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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787B TYR* 1.4 79.0 - - - +
789B THR* 1.3 64.2 + - - +
827B SER* 2.7 39.9 + - - +
828B HIS* 3.9 2.5 - - - +
831B CYS* 3.9 17.6 - - + +
838B VAL* 4.0 8.1 - - + -
839B VAL 3.4 9.2 - - - +
840B MET* 3.8 16.8 - - + -
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Residues in contact with THR 789 (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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787B TYR* 3.6 15.4 + - + -
788B ALA* 1.3 75.3 - - - +
790B SER* 1.3 76.9 + - - +
793B TYR* 3.5 19.6 - - + +
797B ILE* 3.8 13.0 - - + -
806B LEU* 4.3 5.5 - - - +
831B CYS* 4.0 9.5 - - - -
833B TYR* 3.9 12.3 - - - -
838B VAL* 3.3 4.7 - - - -
839B VAL* 2.9 33.9 + - + +
841B PHE* 3.7 34.5 - - + -
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Residues in contact with SER 790 (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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789B THR* 1.3 92.0 + - - +
791B ARG* 1.4 64.9 + - - +
792B ALA* 3.1 15.6 + - - +
793B TYR* 3.1 28.5 + - - +
794B VAL 3.9 1.7 + - - -
833B TYR* 3.4 22.9 - - - -
837B ASN* 3.4 13.4 + - - +
839B VAL* 4.0 2.0 - - - +
800D ASN* 4.9 0.7 + - - -
901D GOL 3.4 24.2 + - - -
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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