Contacts of the helix formed by residues 741 - 748 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A MLY 2.8 56.1 + - + +
506A GLU* 3.4 18.6 - - - +
717A TYR* 3.9 36.8 - - + -
739A ASP* 2.6 14.8 + - - +
740A SER* 1.3 76.1 - - - +
742A LYS* 1.3 60.2 + - - +
743A ALA 2.7 14.7 + - - -
744A SER* 3.0 16.5 + - - -
745A GLU* 3.2 17.8 + - + +
762A HIS 4.8 1.6 - - - +
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Residues in contact with LYS 742 (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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735A GLY* 3.7 1.1 - - - +
738A MET* 5.7 3.6 - - + +
739A ASP* 2.7 38.5 + - + +
741A LYS* 1.3 77.1 - - - +
743A ALA* 1.3 49.7 + - - +
745A GLU* 2.8 14.7 - - + +
746A LYS* 2.8 58.9 + - + +
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Residues in contact with ALA 743 (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* 3.9 1.8 - - + -
735A GLY* 1.9 36.9 + - - +
736A GLN* 2.0 41.7 - - + +
739A ASP 2.5 15.9 + - - +
740A SER 4.2 1.3 - - - +
741A LYS 2.7 0.4 + - - -
742A LYS* 1.3 67.3 - - - +
744A SER* 1.3 51.9 + - - +
745A GLU 2.8 3.6 - - - -
746A LYS* 2.6 9.5 + - - +
747A LEU 2.6 33.3 + - - -
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Residues in contact with SER 744 (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 TYR* 2.9 54.2 + - - -
720A PHE* 3.3 27.1 - - - -
721A LYS 4.6 1.2 + - - -
736A GLN* 4.2 4.3 - - - +
740A SER 3.8 4.3 + - - -
741A LYS 3.0 3.3 + - - -
743A ALA* 1.3 73.4 - - - +
745A GLU* 1.3 66.5 + - - +
747A LEU* 3.2 4.6 + - - +
748A LEU* 3.1 30.5 + - - +
760A PHE* 4.5 0.9 - - - -
765A VAL* 4.9 1.1 - - - -
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Residues in contact with GLU 745 (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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505A MLY 5.6 0.9 - - - +
506A GLU* 4.4 11.3 - - - +
741A LYS* 3.2 17.0 + - - +
742A LYS* 2.8 25.6 - - + +
743A ALA 2.8 0.2 + - - -
744A SER* 1.3 81.6 - - - +
746A LYS* 1.3 66.7 + - + +
747A LEU 3.0 0.2 + - - -
748A LEU* 3.0 13.7 + - - +
749A GLY* 3.8 2.4 + - - -
760A PHE* 3.6 43.6 - - + -
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Residues in contact with LYS 746 (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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731A ALA* 4.4 14.4 - - + +
735A GLY* 3.9 15.3 - - - +
742A LYS* 2.8 32.1 + - + +
743A ALA 2.6 11.1 + - - +
745A GLU* 1.3 77.3 - - + +
747A LEU* 1.3 63.0 + - - +
749A GLY* 2.9 17.5 + - - -
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Residues in contact with LEU 747 (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 PHE* 4.8 8.3 - - + -
724A TYR* 3.7 6.7 - - + +
725A ARG* 3.6 4.5 - - - -
727A LEU* 4.4 5.6 - - + -
728A ASN* 4.6 0.2 - - + -
731A ALA* 4.3 2.6 + - - +
732A ILE* 0.6 136.6 - - + +
736A GLN* 3.6 5.8 - - - +
743A ALA 2.6 18.6 + - - +
744A SER* 3.6 12.1 - - - +
745A GLU 3.0 0.4 + - - -
746A LYS* 1.3 67.5 - - - +
748A LEU* 1.3 61.3 + - + +
749A GLY 2.5 17.8 + - - -
750A GLY 3.0 15.3 + - - +
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Residues in contact with LEU 748 (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 PHE* 3.6 29.4 - - + -
744A SER* 3.1 26.2 + - - +
745A GLU 3.0 8.8 + - - +
747A LEU* 1.3 81.5 - - + +
749A GLY* 1.3 62.3 + - - +
750A GLY 3.0 10.4 - - - +
753A VAL* 5.1 9.3 - - + +
755A HIS* 3.0 21.3 + - - -
758A TYR* 3.5 48.4 + - + +
760A PHE* 4.5 13.0 - - + -
765A VAL* 5.2 2.9 - - + -
767A PHE* 4.3 16.2 - - + -
775A LEU* 6.4 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