Contacts of the helix formed by residues 741 - 748 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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717D TYR* 3.9 45.3 - - + +
739D ASP* 2.6 14.4 + - - +
740D SER* 1.3 77.2 - - - +
742D LYS* 1.3 59.4 - - - +
743D ALA 2.7 15.2 + - - -
744D SER* 3.0 16.3 + - - -
745D GLU* 3.2 22.3 + - + +
760D PHE* 5.5 3.6 - - - -
761D GLY* 4.7 5.0 - - - +
762D HIS* 4.6 28.0 - - - +
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Residues in contact with LYS 742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735D GLY* 4.7 0.4 - - - -
738D MET* 5.7 3.6 - - + +
739D ASP* 2.7 39.3 + - + +
741D LYS* 1.3 76.6 - - + +
743D ALA* 1.3 49.3 + - - +
745D GLU* 2.8 14.8 - - + +
746D LYS* 2.8 57.4 + - + +
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Residues in contact with ALA 743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721D LYS* 3.9 1.6 - - + -
735D GLY* 1.9 37.7 + - - +
736D GLN* 2.0 41.3 - - + +
739D ASP 2.5 15.5 + - - +
740D SER 4.2 1.6 - - - +
741D LYS 2.7 0.4 + - - -
742D LYS* 1.3 66.7 - - - +
744D SER* 1.3 51.8 - - - +
745D GLU 2.8 3.8 - - - -
746D LYS* 2.6 8.8 + - - +
747D LEU* 2.6 33.8 + - - +
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Residues in contact with SER 744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717D TYR* 2.9 54.3 + - - -
720D PHE* 3.3 27.3 - - - -
721D LYS 4.6 1.2 + - - -
736D GLN* 4.2 3.6 - - - +
740D SER 3.8 4.3 + - - -
741D LYS 3.0 3.5 + - - -
743D ALA* 1.3 73.0 - - - +
745D GLU* 1.3 67.6 + - - +
747D LEU* 3.6 4.7 - - - +
748D LEU* 3.1 30.1 + - - +
760D PHE* 4.5 1.3 - - - -
765D VAL* 4.9 0.9 - - - -
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Residues in contact with GLU 745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717D TYR* 5.1 0.4 - - - +
741D LYS* 3.2 20.2 + - - +
742D LYS* 2.8 25.8 - - + +
743D ALA 2.8 0.2 + - - -
744D SER* 1.3 82.8 - - - +
746D LYS* 1.3 67.5 + - + +
747D LEU 3.0 0.2 + - - -
748D LEU* 3.0 14.0 + - - +
749D GLY 3.8 2.3 + - - -
760D PHE* 3.6 44.2 - - + +
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Residues in contact with LYS 746 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731D ALA* 4.4 14.6 - - + +
735D GLY* 3.9 15.9 - - - +
742D LYS* 2.8 32.2 + - + +
743D ALA 2.6 10.8 + - - +
745D GLU* 1.3 76.5 - - + +
747D LEU* 1.3 63.2 + - - +
749D GLY* 2.9 17.5 + - - -
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Residues in contact with LEU 747 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720D PHE* 4.8 8.3 - - + -
724D TYR* 3.7 6.7 - - + +
725D ARG* 3.6 4.7 - - - -
727D LEU* 4.5 5.6 - - + -
728D ASN* 4.6 0.2 - - + -
731D ALA* 4.3 2.8 + - - +
732D ILE* 0.6 136.4 - - + +
736D GLN* 3.6 5.2 - - - +
743D ALA 2.6 19.3 + - - +
744D SER* 3.6 11.7 - - - +
745D GLU 3.0 0.2 + - - -
746D LYS* 1.3 67.3 - - - +
748D LEU* 1.3 61.5 + - + +
749D GLY 2.5 18.0 + - - -
750D GLY 3.0 15.5 + - - +
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Residues in contact with LEU 748 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720D PHE* 3.6 29.2 - - + -
744D SER* 3.1 26.2 + - - +
745D GLU 3.0 9.2 + - - +
747D LEU* 1.3 81.6 - - + +
749D GLY* 1.3 61.9 + - - +
750D GLY 3.0 10.3 - - - +
753D VAL* 5.1 9.5 - - + +
755D HIS* 3.0 21.4 + - - -
758D TYR* 3.5 47.7 + - + +
760D PHE* 4.5 12.1 - - + -
765D VAL* 5.2 3.1 - - + -
767D 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