Contacts of the helix formed by residues 42 - 48 (chain B) in PDB entry 3EXF
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 GLY 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B ASP* 2.7 17.4 + - - -
40B SER 3.4 0.4 + - - -
41B ARG* 1.3 73.7 - - - +
43B LEU* 1.3 58.8 + - - +
44B TRP 3.4 2.0 - - - +
45B LYS* 3.3 14.0 + - - +
46B LYS* 3.2 21.4 + - - +
158G ASP* 3.5 14.4 - - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASN* 3.4 26.0 - - - +
13B MET* 3.8 36.1 - - + -
14B ASP* 4.1 25.8 - - + +
17B LEU* 4.7 7.2 - - + -
25B LEU* 4.0 12.6 - - + -
40B SER* 3.2 21.7 + - - +
41B ARG 3.2 3.7 + - - +
42B GLY* 1.3 74.9 - - - +
44B TRP* 1.3 67.8 + - - +
45B LYS 3.1 0.9 - - - -
46B LYS* 3.3 5.8 + - + +
47B TYR* 3.0 36.5 + - + -
52B ILE* 3.7 12.2 - - + +
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Residues in contact with TRP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 3.2 45.2 - - + +
32B GLN* 3.8 43.7 + - + +
34B ASP* 5.7 1.3 - - - +
40B SER 4.2 2.4 + - - -
42B GLY 4.7 0.4 - - - +
43B LEU* 1.3 80.4 - - - +
45B LYS* 1.3 73.6 + - + +
48B GLY* 2.5 48.5 + - - -
49B ASP* 2.4 37.8 + - - +
52B ILE* 3.8 17.2 + - - +
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLY* 3.3 16.1 + - - +
43B LEU 3.1 0.6 - - - -
44B TRP* 1.3 91.7 - - + +
46B LYS* 1.3 65.6 + - - +
48B GLY* 4.6 1.2 + - - -
80G ASN* 4.4 11.5 + - - +
82G THR* 5.0 8.7 + - - -
83G ASP* 5.0 1.0 + - - -
157G LYS 3.1 27.9 + - - +
158G ASP* 3.3 25.2 + - + +
159G GLU* 4.2 6.9 - - - +
245G ARG* 3.3 29.3 - - - +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP* 2.6 37.7 + - - +
18B GLU* 2.6 26.6 + - - -
42B GLY 3.2 7.2 + - - +
43B LEU* 3.8 5.4 - - + +
44B TRP 3.2 0.2 - - - -
45B LYS* 1.3 83.9 - - - +
47B TYR* 1.3 81.1 + - + +
48B GLY 3.9 0.2 + - - -
158G ASP* 3.5 32.3 + - - +
242G ALA* 4.5 2.8 - - - +
245G ARG* 3.4 41.1 - - - +
246G SER* 3.7 14.0 + - - -
247G GLY* 4.3 2.9 - - - +
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ASP* 2.7 37.9 + - - -
17B LEU* 4.0 24.0 - - + -
18B GLU* 3.4 17.8 + - - +
43B LEU* 3.0 28.2 + - + +
46B LYS* 1.3 101.4 + - + +
48B GLY* 1.3 63.8 + - - +
50B LYS* 4.5 3.3 + - - +
51B ARG* 3.4 50.4 + - + +
52B ILE* 4.4 4.5 - - + -
246G SER* 3.5 35.3 - - - -
248G LYS* 6.1 0.2 - - - -
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU 4.2 0.2 + - - -
44B TRP* 2.5 33.6 + - - -
45B LYS 4.5 1.1 + - - -
46B LYS 3.7 1.0 - - - -
47B TYR* 1.3 72.2 - - - +
49B ASP* 1.3 59.3 + - - -
50B LYS 3.1 10.8 + - - -
52B ILE* 3.1 22.7 + - - +
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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