Contacts of the helix formed by residues 39 - 44 (chain F) in PDB entry 2BM8
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 39 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C SER 5.8 0.2 - - - -
205C GLY* 4.2 9.4 - - - -
208C ARG* 3.8 37.0 - - - +
37F PRO* 3.5 20.3 - - - +
38F LEU* 1.3 76.6 - - - +
40F ARG* 1.3 69.8 + - - +
41F TRP 3.6 0.4 - - - -
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Residues in contact with ARG 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TRP* 2.7 31.3 + - + +
37F PRO* 3.2 22.6 + - + +
39F ASP* 1.3 94.7 + - - +
41F TRP* 1.3 58.2 + - - +
42F ALA 3.3 3.4 - - - -
43F GLU* 3.1 46.1 + - + +
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Residues in contact with TRP 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ILE* 3.4 22.4 - - + +
193C TYR* 3.6 42.6 - + + -
200C PHE* 3.7 20.0 - + - -
201C SER* 5.5 3.1 - - - -
204C LEU* 3.4 25.4 - - + +
213C MET* 3.7 25.6 - - + +
226C ARG* 3.3 57.4 + - + +
229C LEU* 5.6 2.0 - - + +
36F TRP* 4.2 5.8 - - - -
37F PRO 3.5 5.1 + - - -
38F LEU* 3.4 23.3 + - + +
39F ASP 3.6 1.0 - - - -
40F ARG* 1.3 76.7 - - - +
42F ALA* 1.3 87.6 + - + +
44F ALA* 3.2 21.1 + - - +
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TYR* 3.7 28.0 + - + +
201C SER* 5.3 4.9 - - - +
40F ARG 3.3 0.8 - - - -
41F TRP* 1.3 99.2 - - + +
43F GLU* 1.3 62.5 + - + +
44F ALA 3.3 3.7 + - - +
46F ARG* 6.2 0.2 - - - -
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F TRP* 3.9 11.8 - - + -
40F ARG* 3.1 60.7 + - + +
42F ALA* 1.3 78.5 - - + +
44F ALA* 1.3 63.6 + - - +
45F PRO* 3.7 2.6 - - - +
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Residues in contact with ALA 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C MET* 3.6 22.0 - - + -
215C MET* 4.2 5.4 - - + -
226C ARG* 6.6 0.2 - - - -
36F TRP* 3.4 25.6 - - + +
40F ARG 3.8 0.4 + - - -
41F TRP 3.2 17.4 + - - +
42F ALA 3.3 3.5 - - - +
43F GLU* 1.3 79.4 - - - +
45F PRO* 1.3 74.1 - - + +
46F ARG* 3.5 15.2 + - - +
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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