Contacts of the helix formed by residues 741 - 748 (chain J) in PDB entry 1O1F
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 LYS 741 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506J GLU* 5.9 0.6 + - - -
717J TYR* 3.9 44.9 - - + -
739J ASP* 2.6 14.3 + - - +
740J SER* 1.3 76.4 - - - +
742J LYS* 1.3 60.0 + - - +
743J ALA 2.7 15.3 + - - -
744J SER* 3.0 17.2 + - - -
745J GLU* 3.2 21.2 + - + +
760J PHE* 5.5 4.0 - - - -
761J GLY* 4.7 5.0 - - - +
762J HIS* 4.6 27.8 - - - +
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Residues in contact with LYS 742 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735J GLY* 3.7 1.1 - - - +
738J MET* 5.7 3.1 - - + +
739J ASP* 2.7 38.9 + - + +
741J LYS* 1.3 77.1 - - - +
743J ALA* 1.3 51.0 + - - +
745J GLU* 2.8 14.5 - - + +
746J LYS* 2.8 56.9 + - + +
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Residues in contact with ALA 743 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721J LYS* 3.9 1.6 - - + -
735J GLY* 1.9 37.0 + - - +
736J GLN* 2.0 41.3 - - + +
739J ASP 2.5 16.5 + - - +
740J SER 4.2 1.3 - - - +
741J LYS 2.7 0.4 + - - -
742J LYS* 1.3 67.5 - - - +
744J SER* 1.4 52.1 + - - +
745J GLU 2.8 3.6 - - - -
746J LYS* 2.6 9.9 + - - +
747J LEU* 2.6 32.9 + - - -
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Residues in contact with SER 744 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717J TYR* 2.9 54.0 + - - -
720J PHE* 3.3 27.3 - - - -
721J LYS 4.6 1.0 + - - -
736J GLN* 4.2 4.6 - - - +
740J SER 3.8 4.2 + - - -
741J LYS 3.0 3.7 + - - -
743J ALA* 1.4 73.4 - - - +
745J GLU* 1.3 66.5 + - - +
747J LEU* 3.6 4.2 - - - +
748J LEU* 3.1 30.7 + - - +
760J PHE* 4.5 1.3 - - - -
765J VAL* 4.9 0.9 - - - -
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Residues in contact with GLU 745 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506J GLU* 5.7 0.9 - - - +
741J LYS* 3.2 23.1 + - - +
742J LYS* 2.8 24.2 - - + +
744J SER* 1.3 82.7 - - - +
746J LYS* 1.3 68.9 + - + +
747J LEU 3.0 0.2 + - - -
748J LEU* 3.1 14.0 + - - +
749J GLY* 3.8 2.4 + - - -
760J PHE* 3.6 44.5 - - + +
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Residues in contact with LYS 746 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731J ALA* 4.4 13.9 - - + +
735J GLY* 3.9 15.0 - - - -
742J LYS* 3.5 32.4 - - + +
743J ALA 2.6 11.3 + - - +
745J GLU* 1.3 78.6 - - + +
747J LEU* 1.3 62.7 + - - +
749J GLY* 2.9 17.2 + - - -
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Residues in contact with LEU 747 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720J PHE* 4.8 8.1 - - + -
724J TYR* 3.7 6.7 - - + +
725J ARG* 3.6 4.9 - - - -
727J LEU* 4.4 6.5 - - + -
728J ASN* 4.6 0.6 - - + +
731J ALA* 4.3 2.2 + - - +
732J ILE* 0.6 137.2 - - + +
736J GLN* 3.6 5.6 - - - +
743J ALA 2.6 18.0 + - - +
744J SER* 3.6 11.7 - - - +
745J GLU 3.1 0.2 - - - -
746J LYS* 1.3 67.5 - - - +
748J LEU* 1.3 62.4 + - + +
749J GLY 2.5 17.4 + - - -
750J GLY 3.0 14.3 + - - +
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Residues in contact with LEU 748 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720J PHE* 3.6 29.6 - - + -
744J SER* 3.1 26.5 + - - +
745J GLU 3.1 9.4 + - - +
747J LEU* 1.3 81.2 - - + +
749J GLY* 1.3 62.3 + - - +
750J GLY 3.0 10.0 - - - +
753J VAL* 5.1 8.8 - - + +
755J HIS* 3.0 22.0 + - - -
758J TYR* 3.5 47.3 - - + +
760J PHE* 4.5 11.7 - - + -
765J VAL* 5.2 2.9 - - + -
767J PHE* 4.3 16.6 - - + -
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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