Contacts of the helix formed by residues 736 - 740 (chain O) in PDB entry 4E45
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 TRP 736 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68N ASP* 3.8 33.4 - - + -
71N GLU* 2.9 49.8 + - + +
72N LYS* 3.1 53.8 - - + -
75N PRO* 6.3 0.7 - - + -
732O SER 4.8 3.6 - - - -
733O LEU 5.4 1.5 - - - -
734O SER 3.1 1.4 - - - +
735O GLU* 1.3 109.0 - - + +
737O ARG* 1.3 64.8 + - - +
738O LEU 3.1 3.1 - - - -
739O TRP* 2.9 45.1 + + + +
740O GLN* 3.3 17.9 + - - +
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Residues in contact with ARG 737 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ARG* 5.4 0.7 + - - -
20D HIS* 3.9 29.7 + - - -
26D ASP* 4.5 10.7 + - - -
68L ASP* 4.3 7.6 + - - +
71L GLU* 2.6 43.1 + - + +
72L LYS* 4.2 33.7 - - - +
733O LEU 5.9 0.7 - - - -
734O SER* 3.1 20.2 + - - +
735O GLU 3.3 3.9 + - - +
736O TRP* 1.3 76.7 - - - +
738O LEU* 1.3 84.0 + - + +
740O GLN* 2.9 26.3 + - - +
741O ASP* 4.5 0.9 + - - +
762O MET* 3.3 29.5 - - + +
769O ARG* 3.3 15.4 - - - +
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Residues in contact with LEU 738 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C TYR* 3.6 18.2 - - + +
17D ARG* 2.9 63.6 + - + +
20D HIS* 3.5 37.9 - - + +
21D LEU 5.4 0.2 - - - +
71L GLU* 4.6 0.2 - - - +
735O GLU 5.2 0.4 + - - -
736O TRP 3.1 1.2 + - - -
737O ARG* 1.3 111.1 - - + +
739O TRP* 1.3 70.1 + - + +
740O GLN 3.3 0.8 + - - -
741O ASP* 3.9 4.3 - - - +
769O ARG* 3.9 13.7 - - - +
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Residues in contact with TRP 739 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TYR* 3.5 44.0 - + + +
16C GLN* 5.2 7.4 - - + +
21D LEU* 3.9 30.3 - - + -
56N GLN* 3.6 27.5 - - - +
60N GLU* 5.1 2.2 - - - -
72N LYS* 3.4 31.2 - - + -
735O GLU 5.5 0.4 - - - -
736O TRP* 2.9 47.6 + + + +
738O LEU* 1.3 88.5 - - + +
740O GLN* 1.3 70.8 + - - +
741O ASP* 3.6 3.7 + - - -
742O HIS* 4.0 13.2 + - - +
744O LEU* 4.1 23.0 - - + +
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Residues in contact with GLN 740 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72N LYS 3.0 28.0 + - - +
75N PRO* 4.0 19.3 - - + +
76N GLN* 3.2 31.0 + - - +
733O LEU 5.9 0.7 - - - +
736O TRP* 3.3 22.5 + - - +
737O ARG* 2.9 24.4 + - - +
738O LEU 3.3 0.4 - - - -
739O TRP* 1.3 87.6 + - - +
741O ASP* 1.3 56.4 + - - +
742O HIS 3.2 9.1 + - - -
744O LEU* 4.2 0.8 - - - +
758O PHE* 3.8 27.1 - - + -
759O ILE* 3.7 26.7 - - - +
762O MET* 3.8 11.3 - - + +
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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
------------------------------------------------------------
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