Contacts of the helix formed by residues 705 - 723 (chain B) in PDB entry 5JO3
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 SER 705 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B GLY 3.7 1.6 + - - -
704B LEU* 1.3 78.6 - - - +
706B ILE* 1.3 65.9 + - - +
707B GLU* 3.7 5.5 + - - +
708B GLU* 3.2 32.0 + - - +
709B TYR* 2.9 22.0 + - - +
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Residues in contact with ILE 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704B LEU 3.9 0.2 + - - -
705B SER* 1.3 74.9 - - - +
707B GLU* 1.3 69.3 + - + +
709B TYR* 3.4 7.0 + - - +
710B LYS* 3.0 28.9 + - + +
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Residues in contact with GLU 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B SER* 3.2 5.4 + - - +
706B ILE* 1.3 84.5 - - + +
708B GLU* 1.3 67.8 + - + +
710B LYS* 3.4 21.1 + - - +
711B THR* 3.1 29.8 + - - +
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Residues in contact with GLU 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B PHE* 3.5 24.0 - - - -
641B LEU* 3.8 34.1 - - + +
704B LEU* 3.9 10.2 - - + +
705B SER* 3.2 23.3 + - - +
707B GLU* 1.3 75.8 - - + +
709B TYR* 1.3 58.5 + - - +
711B THR* 3.4 1.9 + - - -
712B THR* 2.8 38.4 + - - -
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Residues in contact with TYR 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690B LEU* 5.7 0.9 - - - +
693B LEU* 5.6 6.0 - - + +
694B ASN* 4.1 19.1 + - - -
701B LEU* 3.8 49.6 - - + -
702B SER* 6.0 0.2 - - - -
704B LEU* 3.9 13.6 - - + +
705B SER 2.9 18.2 + - - +
706B ILE* 3.7 6.3 - - - +
708B GLU* 1.3 74.9 - - - +
710B LYS* 1.3 68.1 + - - +
712B THR* 3.8 1.0 - - - -
713B LEU* 3.0 58.3 + - + +
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Residues in contact with LYS 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B ILE* 3.0 19.2 + - + +
707B GLU* 3.7 22.7 - - - +
709B TYR* 1.3 81.5 - - - +
711B THR* 1.3 62.9 + - - +
713B LEU* 3.6 4.6 + - - +
714B LYS* 3.3 25.1 + - + +
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Residues in contact with THR 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 3.8 22.1 - - + +
707B GLU* 3.1 19.5 + - - +
708B GLU 3.7 4.5 - - - -
710B LYS* 1.3 76.8 - - - +
712B THR* 1.3 64.4 + - - +
714B LYS* 3.4 9.7 + - - +
715B ILE* 3.2 42.3 + - + +
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Residues in contact with THR 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 3.5 24.9 - - - +
644B LEU* 4.0 22.8 - - + +
645B ALA* 4.1 12.1 - - + +
701B LEU* 4.3 10.8 - - + -
704B LEU* 3.6 8.6 - - - +
708B GLU 2.8 20.5 + - - -
709B TYR* 3.8 3.4 - - - -
711B THR* 1.3 75.7 - - - +
713B LEU* 1.3 57.4 + - - +
715B ILE* 3.2 11.7 + - - +
716B ILE* 2.9 45.1 + - + +
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Residues in contact with LEU 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686B PHE* 4.3 6.0 - - + -
690B LEU* 3.7 33.0 - - + -
693B LEU* 4.2 18.4 - - + -
701B LEU* 4.5 4.0 - - + -
709B TYR* 3.0 60.2 + - + +
710B LYS* 4.1 4.3 - - - +
712B THR* 1.3 75.7 - - - +
714B LYS* 1.3 58.0 + - - +
716B ILE* 3.3 12.9 + - + +
717B LYS* 2.9 28.9 + - - +
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Residues in contact with LYS 714 (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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710B LYS* 3.3 14.2 + - + +
711B THR* 3.5 11.9 - - - +
712B THR 3.2 0.2 - - - -
713B LEU* 1.3 78.8 - - - +
715B ILE* 1.3 63.9 + - + +
717B LYS* 3.4 6.9 + - - +
718B GLN* 3.1 51.3 + - + +
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Residues in contact with ILE 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.2 5.6 - - + +
642B GLU* 3.9 38.4 - - + +
645B ALA* 3.4 21.1 - - + -
646B LEU* 5.0 3.4 - - + +
711B THR* 3.3 33.9 - - + +
712B THR* 3.2 3.7 + - - +
714B LYS* 1.3 75.1 - - + +
716B ILE* 1.3 61.4 + - - +
718B GLN* 3.3 13.1 + - - +
719B ALA* 2.8 33.0 + - + +
756B LEU* 4.2 22.9 - - + -
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Residues in contact with ILE 716 (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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645B ALA* 3.7 22.9 - - + +
648B ILE* 3.8 23.6 - - + -
649B ALA* 4.6 4.5 - - + -
686B PHE* 4.2 9.0 - - + -
689B CYS* 4.0 14.6 - - - -
693B LEU* 4.4 2.5 - - + -
701B LEU* 4.3 8.5 - - + -
712B THR* 2.9 33.7 + - + +
713B LEU* 3.6 23.6 - - + +
714B LYS 3.3 0.2 - - - -
715B ILE* 1.3 75.1 - - - +
717B LYS* 1.3 64.6 + - - +
719B ALA* 3.2 5.5 + - - +
720B ILE* 2.9 44.9 + - + +
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Residues in contact with LYS 717 (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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683B HIS* 4.4 14.6 - - - -
686B PHE* 3.6 49.7 - - + -
713B LEU 2.9 14.1 + - - +
714B LYS* 3.7 6.5 - - - +
715B ILE 3.3 0.2 - - - -
716B ILE* 1.3 76.7 - - - +
718B GLN* 1.3 65.8 + - + +
720B ILE* 3.9 1.0 - - - +
721B LEU* 2.9 48.2 + - + +
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Residues in contact with GLN 718 (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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714B LYS* 3.1 50.4 + - + +
715B ILE* 3.9 14.4 - - + +
717B LYS* 1.3 79.1 - - + +
719B ALA* 1.3 57.5 + - - +
721B LEU* 3.5 7.9 + - + +
722B ALA* 2.9 29.6 + - - +
753B GLU* 3.5 45.4 + - + +
757B ALA* 5.3 0.8 - - - +
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Residues in contact with ALA 719 (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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645B ALA 5.0 0.9 - - - +
646B LEU* 4.6 9.6 - - + -
649B ALA* 3.5 24.2 - - + -
715B ILE* 2.8 20.9 + - + +
716B ILE 3.2 0.6 + - - +
718B GLN* 1.3 77.4 - - - +
720B ILE* 1.3 62.7 + - - +
722B ALA* 3.4 15.8 + - - +
723B THR* 3.6 2.9 - - - +
756B LEU* 5.6 4.0 - - + +
757B ALA* 5.7 1.3 - - - +
760B MET* 3.5 35.0 - - + +
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Residues in contact with ILE 720 (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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649B ALA* 4.0 14.1 - - + -
652B SER* 4.2 12.1 - - - +
653B HIS* 4.0 22.0 - - - +
682B GLU* 3.5 28.5 - - - +
685B HIS* 3.9 11.7 - - + -
686B PHE* 3.9 17.7 - - + +
689B CYS* 3.9 25.6 - - + -
716B ILE* 2.9 35.8 + - + +
717B LYS 4.0 2.5 - - - +
719B ALA* 1.3 72.3 - - - +
721B LEU* 1.3 65.5 + - - +
723B THR* 2.6 27.0 + - - -
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Residues in contact with LEU 721 (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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680B SER* 4.1 6.7 - - - -
682B GLU* 4.0 10.5 - - + +
683B HIS* 3.7 51.6 - - + +
686B PHE* 5.6 2.2 - - + -
717B LYS* 2.9 51.4 + - + +
718B GLN* 4.0 7.0 - - + +
720B ILE* 1.3 76.9 - - + +
722B ALA* 1.3 62.3 + - - +
723B THR 3.0 1.6 + - - -
724B ASP* 3.1 14.2 + - - +
727B LEU* 3.3 25.8 - - + +
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Residues in contact with ALA 722 (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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718B GLN 2.9 18.6 + - - +
719B ALA* 3.4 9.9 - - - +
720B ILE 3.2 0.4 - - - -
721B LEU* 1.3 75.1 - - - +
723B THR* 1.3 60.0 + - - +
724B ASP 3.2 11.3 + - - +
727B LEU* 4.8 7.6 - - - -
728B TYR* 4.4 5.5 + - - +
731B ARG* 6.0 0.2 - - - +
757B ALA* 3.6 41.3 - - + +
760B MET* 4.3 1.8 - - + -
761B THR* 3.5 16.2 + - - -
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Residues in contact with THR 723 (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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621B THR* 6.2 0.2 - - + -
653B HIS* 3.7 34.5 + - + -
682B GLU* 3.9 8.8 - - - +
719B ALA 3.6 14.6 - - - +
720B ILE 2.6 17.3 + - - +
721B LEU 3.1 0.2 - - - -
722B ALA* 1.3 74.1 - - - +
724B ASP* 1.3 63.3 + - - +
725B LEU* 3.2 6.5 + - - +
760B MET* 3.7 27.1 - - + +
761B THR* 4.9 4.5 - - - +
764B ASP* 3.6 29.4 - - - +
902B ZN 4.2 9.3 - - - -
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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
------------------------------------------------------------
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