Contacts of the strand formed by residues 786 - 794 (chain B) in PDB entry 5FO9
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 ILE 786 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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562A SER* 3.8 21.5 - - - +
586A GLU* 4.3 21.5 - - + -
587A GLY 3.8 7.4 - - - +
588A ASP* 4.1 12.3 - - - +
781B PRO 5.0 0.3 - - - +
782B PRO* 3.9 3.9 - - - +
783B LYS* 3.6 23.4 + - - +
784B ASN 3.2 10.7 + - - +
785B GLY* 1.3 86.2 - - - +
787B SER* 1.3 72.4 + - - +
788B THR* 3.9 8.4 + - - +
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Residues in contact with SER 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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585A ILE 3.7 0.7 - - - +
586A GLU* 3.6 2.6 - - - -
587A GLY 3.0 37.5 + - - -
589A HIS* 3.3 24.9 + - - +
778B LEU* 3.9 25.5 - - - +
780B GLU* 2.7 30.7 + - - -
781B PRO 5.1 0.7 - - - -
782B PRO* 4.2 3.5 - - - +
785B GLY 4.0 1.6 + - - -
786B ILE* 1.3 73.8 - - - +
788B THR* 1.3 62.3 + - - +
789B LYS 4.2 0.2 - - - -
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Residues in contact with THR 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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584A LYS* 3.9 30.3 - - + -
585A ILE 3.4 9.4 - - - +
586A GLU* 4.1 13.2 + - + +
780B GLU* 3.3 24.2 - - - +
786B ILE* 3.9 9.4 + - - +
787B SER* 1.3 78.5 + - - +
789B LYS* 1.3 64.8 + - - +
790B LEU* 4.1 12.0 + - + +
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Residues in contact with LYS 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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583A LEU 3.5 2.3 - - - +
584A LYS* 3.7 1.6 - - - -
585A ILE* 2.9 40.9 + - + +
776B GLU* 3.6 29.9 + - + +
777B ASP 3.1 28.0 + - - -
778B LEU* 3.7 21.9 - - + +
779B LYS* 4.7 3.6 - - - +
780B GLU* 2.8 37.4 + - - +
787B SER 4.2 0.8 - - - -
788B THR* 1.3 74.5 - - - +
790B LEU* 1.3 73.9 + - - +
791B MET* 4.0 8.9 + - + -
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Residues in contact with LEU 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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568A GLY 4.8 7.9 - - - +
582A THR* 4.2 20.4 - - + -
583A LEU 3.3 4.3 - - - -
584A LYS* 4.7 25.6 - - + -
780B GLU* 4.6 1.4 + - - -
788B THR* 5.0 10.1 - - + +
789B LYS* 1.3 83.7 - - - +
791B MET* 1.3 61.9 + - - +
792B ASN 3.9 2.2 + - - -
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Residues in contact with MET 791 (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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581A MET 3.3 3.5 - - - +
582A THR* 3.2 3.6 - - - -
583A LEU* 2.4 58.1 + - + +
585A ILE* 3.8 19.1 - - + -
595A LEU* 3.6 29.2 - - + -
772B LEU* 4.7 4.3 - - + -
774B ASN* 3.8 26.2 - - - +
776B GLU* 3.9 20.4 - - - +
789B LYS* 4.6 10.3 - - + -
790B LEU* 1.3 74.5 - - - +
792B ASN* 1.3 60.7 + - - +
793B ILE* 3.5 23.8 + - + -
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Residues in contact with ASN 792 (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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580A GLN* 2.5 53.2 + - - +
581A MET 3.9 2.2 - - - -
582A THR* 3.7 24.7 + - + +
790B LEU 3.9 2.8 + - - -
791B MET* 1.3 71.6 - - - +
793B ILE* 1.3 60.0 + - - +
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Residues in contact with ILE 793 (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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580A GLN* 3.2 31.8 - - - +
581A MET* 3.2 22.8 + - + +
583A LEU* 4.5 15.9 - - + -
771B TRP* 4.0 25.4 - - + -
772B LEU* 4.2 26.0 - - + -
791B MET* 3.7 38.1 - - + +
792B ASN* 1.3 78.6 - - - +
794B PHE* 1.3 59.8 + - - +
795B LEU* 4.0 15.9 - - + -
804B ILE* 5.1 4.5 - - + -
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Residues in contact with PHE 794 (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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578A GLY* 3.0 32.3 - - - -
580A GLN* 3.9 23.1 - - + +
771B TRP* 3.4 22.6 - - - -
793B ILE* 1.3 76.7 - - - +
795B LEU* 1.3 88.0 + - - +
796B LYS* 3.5 26.2 + - + +
797B ASP* 5.3 5.2 - - - -
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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