Contacts of the helix formed by residues 718 - 726 (chain A) in PDB entry 1FO4
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 ASP 718 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717A GLY* 1.3 73.0 - - - +
719A LEU* 1.3 57.8 + - - +
720A LYS* 3.3 11.4 + - - +
721A LYS* 3.0 53.8 + - - +
722A GLY 2.9 22.5 + - - -
893A ASN* 2.7 19.0 + - - +
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Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A GLU* 3.8 11.7 + - + +
716A LYS 5.5 0.7 - - - +
717A GLY 4.1 1.6 + - - -
718A ASP* 1.3 69.1 + - - +
720A LYS* 1.3 67.2 + - - +
722A GLY* 3.0 0.9 + - - -
723A PHE* 2.8 39.8 + - + -
858A ALA* 4.4 0.2 - - + -
859A LEU 3.5 24.2 - - - +
860A GLU* 3.2 30.3 - - + +
893A ASN* 3.9 9.2 - - + +
894A ILE* 3.9 19.5 - - - +
895A ARG* 3.2 42.6 - - + +
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Residues in contact with LYS 720 (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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718A ASP* 3.3 7.9 + - - +
719A LEU* 1.3 77.7 - - - +
721A LYS* 1.3 64.3 + - - +
723A PHE* 3.5 5.4 + - - +
724A SER* 3.1 23.4 + - - -
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Residues in contact with LYS 721 (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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717A GLY* 6.0 0.2 - - - -
718A ASP* 3.0 43.3 + - + +
720A LYS* 1.3 77.0 - - - +
722A GLY* 1.3 63.7 + - - +
724A SER* 3.1 8.5 + - - -
725A GLU* 3.0 58.3 + - + +
893A ASN* 4.5 9.2 + - - +
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Residues in contact with GLY 722 (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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718A ASP 2.9 11.4 + - - -
719A LEU 3.0 3.3 + - - -
721A LYS* 1.3 78.4 - - - +
723A PHE* 1.3 61.1 + - - +
725A GLU* 3.4 1.7 + - - -
726A ALA* 3.2 13.0 + - - +
857A VAL* 3.2 24.1 - - - +
858A ALA* 3.7 11.0 - - - -
893A ASN* 3.5 24.0 - - - -
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Residues in contact with PHE 723 (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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719A LEU* 2.8 32.7 + - + +
720A LYS* 4.1 4.3 - - - +
722A GLY* 1.3 72.8 - - - +
724A SER* 1.3 62.6 + - - +
726A ALA* 3.4 18.4 + - - +
729A VAL* 3.9 23.8 - - + +
847A LYS* 3.5 58.6 - - + +
848A VAL 3.8 1.8 - - - -
849A GLY* 3.5 23.1 - - - -
858A ALA* 3.8 18.4 - - + -
860A GLU* 3.3 35.4 - - + -
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Residues in contact with SER 724 (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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720A LYS* 3.1 15.0 + - - -
721A LYS* 3.1 13.8 + - - -
723A PHE* 1.3 80.1 - - - +
725A GLU* 1.3 63.6 + - - +
726A ALA 3.4 5.4 + - - +
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Residues in contact with GLU 725 (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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721A LYS* 3.0 45.2 + - + +
722A GLY* 4.0 3.8 - - - +
724A SER* 1.3 77.9 - - - +
726A ALA* 1.3 63.6 + - - +
727A ASP* 3.6 2.3 + - - +
851A MET* 3.3 24.4 - - + +
857A VAL* 3.8 19.5 - - + +
893A ASN* 4.5 2.9 + - - -
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Residues in contact with ALA 726 (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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722A GLY 3.2 14.2 + - - +
723A PHE* 3.5 18.7 - - - +
724A SER 3.2 5.7 - - - +
725A GLU* 1.3 78.4 - - - +
727A ASP* 1.3 64.0 + - - +
728A ASN 3.5 18.5 - - - +
729A VAL* 4.4 3.0 - - + +
849A GLY* 3.7 9.9 - - - -
850A PHE* 3.7 13.9 - - - +
851A MET* 3.9 8.5 - - - -
857A VAL* 4.6 1.8 - - + +
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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