Contacts of the helix formed by residues 723 - 731 (chain E) in PDB entry 1FSJ
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 THR 723 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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623E LEU 5.5 0.4 - - - +
626E ALA* 3.2 12.5 + - + -
627E GLY* 3.7 19.2 - - - +
687E THR* 4.4 5.6 - - + -
688E PRO* 5.4 2.0 - - + -
691E GLN* 2.6 46.0 + - + +
699E TYR* 4.1 12.3 - - + -
700E GLU* 5.0 0.9 - - - -
722E THR* 1.3 74.7 - - - +
724E PRO* 1.4 69.3 - - - +
725E LYS 3.7 0.3 + - - -
726E ARG* 3.2 13.3 + - - +
727E HIS* 2.8 30.6 + - - +
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Residues in contact with PRO 724 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687E THR* 3.6 12.8 - - + +
691E GLN 3.4 15.3 - - - +
692E GLN* 4.4 0.4 - - - -
693E VAL* 4.0 9.9 - - + +
696E ARG* 3.2 34.8 - - + +
697E LYS* 4.2 1.1 - - - -
698E VAL 3.3 28.7 - - - +
700E GLU* 3.7 23.5 - - - +
723E THR* 1.4 83.3 - - - +
725E LYS* 1.3 62.3 + - - +
728E ILE* 3.0 31.1 + - + +
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Residues in contact with LYS 725 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 5.2 1.6 - - - +
129B ASP* 3.0 28.3 + - - +
509D GLN* 3.8 33.4 - - + +
691E GLN* 3.0 46.7 + - - +
693E VAL* 3.6 15.9 - - + +
723E THR 3.2 0.2 - - - -
724E PRO* 1.3 76.9 - - - +
726E ARG* 1.3 63.0 + - - +
728E ILE* 4.0 2.4 - - + +
729E ASP* 2.8 56.5 + - - +
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Residues in contact with ARG 726 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626E ALA 3.7 17.0 - - - +
627E GLY 3.6 24.0 - - - +
628E LYS 4.0 6.1 - - - +
629E ASP* 2.7 46.2 + - - +
691E GLN* 4.0 0.2 + - - -
722E THR* 4.6 4.3 - - + -
723E THR* 3.2 19.7 + - - +
725E LYS* 1.3 79.7 - - - +
727E HIS* 1.3 58.4 + - - +
729E ASP* 3.2 25.3 + - - +
730E ILE* 2.9 58.8 + - + +
732E ARG* 6.0 2.2 - - - +
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Residues in contact with HIS 727 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696E ARG* 4.1 5.8 + - - +
700E GLU* 2.8 32.9 + - + +
701E LEU 3.9 12.3 - - - -
702E HIS* 3.3 16.6 + + + +
722E THR* 3.3 17.0 - - - +
723E THR 2.8 15.8 + - - +
724E PRO 4.0 1.1 - - - +
726E ARG* 1.3 73.6 - - - +
728E ILE* 1.3 63.3 + - - +
730E ILE* 3.4 7.4 + - + +
731E HIS* 3.1 31.1 + + - -
734E LYS* 4.1 0.6 - - - +
804E PO4 3.6 17.5 - - - -
904E ZN 2.1 36.2 - - - -
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Residues in contact with ILE 728 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693E VAL* 3.6 36.3 - - + -
696E ARG* 3.5 44.9 - - - +
724E PRO* 3.0 21.8 + - + +
725E LYS* 4.1 4.0 - - + +
727E HIS* 1.3 74.9 - - - +
729E ASP* 1.3 67.6 + - - +
731E HIS 3.4 0.9 + - - -
732E ARG 3.0 4.3 + - - -
733E GLY* 2.9 53.8 + - - +
734E LYS* 3.7 6.7 - - - +
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Residues in contact with ASP 729 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LYS* 2.9 31.5 + - - +
129B ASP* 4.2 2.8 - - - +
725E LYS* 2.8 51.4 + - - +
726E ARG* 3.2 23.8 + - - +
728E ILE* 1.3 79.6 - - - +
730E ILE* 1.3 65.7 + - - +
732E ARG* 3.0 31.5 + - - +
733E GLY 5.0 0.2 - - - +
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Residues in contact with ILE 730 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629E ASP 3.8 16.4 - - - +
630E SER* 4.8 3.4 - - - -
702E HIS* 3.7 43.3 - - + +
722E THR* 4.3 10.1 - - + -
726E ARG* 2.9 47.5 + - + +
727E HIS* 3.6 9.6 - - + +
729E ASP* 1.3 77.3 - - - +
731E HIS* 1.3 70.3 + - + +
732E ARG* 3.5 19.1 + - - +
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Residues in contact with HIS 731 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696E ARG* 6.2 0.2 - - - -
702E HIS* 3.5 12.7 + + - -
703E HIS 5.4 1.1 - - - -
706E PRO* 5.5 11.7 - - + -
727E HIS* 3.1 30.4 + + - +
728E ILE 3.4 0.4 + - - -
729E ASP 3.2 0.2 - - - -
730E ILE* 1.3 81.4 + - + +
732E ARG* 1.3 71.5 + - - +
733E GLY 3.3 3.2 + - - -
734E LYS* 3.4 33.9 + - + +
804E PO4 3.8 9.7 + - - -
904E ZN 2.1 36.6 - - - -
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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