Contacts of the strand formed by residues 647 - 654 (chain A) in PDB entry 2BDP
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 TRP 647 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A PRO* 3.2 22.9 - - + +
643A SER* 4.6 0.9 - - - -
644A GLU* 3.4 58.8 + - + +
645A SER 3.2 21.9 + - - -
646A ASP* 1.3 83.9 + - - +
648A LEU* 1.3 73.6 + - - +
821A GLN* 3.7 39.8 - - + +
823A HIS* 3.6 27.1 - + - -
835A GLU* 3.8 25.6 - - + -
836A ALA* 3.0 25.4 - - - +
837A PRO* 3.7 22.5 - - + +
870A SER* 5.2 0.2 - - - -
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642A PRO* 3.8 3.8 - - - -
646A ASP 5.5 0.7 - - - -
647A TRP* 1.3 83.9 - - - +
649A ILE* 1.3 67.2 + - - +
650A PHE 3.9 0.3 + - - -
835A GLU* 3.1 5.2 - - - +
836A ALA 2.7 29.4 + - - +
838A LYS* 3.9 20.2 - - + -
841A MET* 3.6 38.7 - - + +
868A TYR* 3.9 16.4 - - + -
869A GLY* 3.4 17.7 - - - +
870A SER* 3.9 17.3 - - - +
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Residues in contact with ILE 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493A VAL* 6.1 1.3 - - + -
640A PHE 4.4 2.9 - - - +
641A VAL* 4.0 5.4 - - - +
642A PRO* 3.8 33.4 - - + -
648A LEU* 1.3 71.6 - - - +
650A PHE* 1.3 62.1 + - - +
825A LEU* 4.4 9.0 - - + -
833A ILE* 3.8 21.3 - - + -
834A LEU 3.5 7.4 - - - +
835A GLU* 4.0 14.8 - - + -
868A TYR* 3.0 8.1 - - - +
869A GLY 2.9 33.4 + - - +
871A THR* 3.8 28.3 - - - +
872A TRP* 3.9 20.4 - - + +
875A ALA* 4.0 9.7 - - + +
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Residues in contact with PHE 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A LEU 3.9 0.4 + - - -
649A ILE* 1.3 75.6 - - - +
651A ALA* 1.3 61.5 + - - +
652A ALA* 4.0 15.9 - - + -
832A LEU 3.8 0.5 - - - +
833A ILE* 3.5 1.4 - - - -
834A LEU* 2.7 55.2 + - + +
841A MET* 4.1 13.7 - - + -
844A LEU* 3.5 39.3 - - + -
845A CYS* 3.8 33.7 - - - -
848A VAL* 3.8 29.4 - - + -
849A PRO* 4.6 0.9 - - + -
866A TYR* 3.8 24.0 - + + -
867A HIS 3.6 3.1 - - - -
868A TYR* 3.9 17.3 - + + -
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Residues in contact with ALA 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ILE 4.2 0.4 - - - -
650A PHE* 1.3 75.9 - - - +
652A ALA* 1.3 60.7 + - - +
653A ASP* 5.0 1.0 - - - +
831A GLU* 6.1 4.3 - - + -
832A LEU 3.5 3.8 - - - -
833A ILE* 4.3 18.8 - - + +
866A TYR* 3.2 3.1 - - - -
867A HIS* 2.8 42.0 + - + +
872A TRP* 5.1 4.9 - - - +
875A ALA* 4.0 26.9 - - + +
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Residues in contact with ALA 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A PHE* 4.0 8.9 - - + -
651A ALA* 1.3 74.8 - - - +
653A ASP* 1.3 60.0 + - - +
831A GLU* 3.1 3.2 - - - +
832A LEU 2.8 38.6 + - - +
848A VAL* 3.7 19.1 - - + -
849A PRO 5.2 0.7 - - - -
852A MET* 3.7 26.8 - - - +
864A VAL* 3.9 6.1 - - + -
865A ASP 3.3 9.4 - - - +
866A TYR* 4.2 2.9 - - + -
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Residues in contact with ASP 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ALA 5.0 0.5 - - - +
652A ALA* 1.3 75.7 - - - +
654A TYR* 1.3 64.1 + - - +
655A SER* 4.8 1.2 - - - -
830A ASP 3.4 5.2 - - - +
831A GLU* 3.6 23.6 - - + +
852A MET* 4.5 0.2 - - - -
864A VAL* 3.3 6.0 - - - -
865A ASP* 2.9 58.1 + - - +
867A HIS* 4.7 10.6 + - - -
950A MG 2.8 24.7 - - - -
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Residues in contact with TYR 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A ASP* 1.3 70.4 - - - +
655A SER* 1.3 60.5 + - - +
656A GLN 3.6 1.2 + - - -
657A ILE* 3.7 36.3 + - + -
803A ILE* 3.6 14.3 - - + +
804A ILE* 4.0 23.3 - - + -
807A ALA* 3.5 13.7 - - - +
830A ASP* 2.8 36.2 + - + +
852A MET* 2.7 54.9 + - + +
862A LEU* 3.9 26.2 - - + -
863A LYS 3.5 5.8 - - - -
864A VAL* 3.5 18.8 - - + -
950A MG 2.8 23.2 - - - -
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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