Contacts of the helix formed by residues 63 - 71 (chain E) in PDB entry 3KDO
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 GLU 63 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E TYR* 1.3 71.8 - - - +
64E GLN* 1.3 68.4 + - - +
65E GLU* 3.1 13.6 - - + +
66E ARG* 3.0 46.6 + - - +
67E TRP* 3.2 11.4 + - - +
22H LYS* 2.9 23.5 + - - -
355H LYS* 2.9 31.6 + - - +
357H TYR* 2.6 27.6 + - - -
167I GLY 4.5 0.3 - - - +
172I GLU* 3.0 13.6 + - - +
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Residues in contact with GLN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E PRO* 5.3 7.8 - - - +
62E TYR* 3.0 34.0 + - - +
63E GLU* 1.3 71.3 - - - +
65E GLU* 1.3 63.2 + - - +
67E TRP* 3.1 36.0 + - + +
68E ALA* 3.0 25.2 + - + +
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLU* 3.1 17.5 - - + +
64E GLN* 1.3 79.6 - - - +
66E ARG* 1.3 61.7 + - - +
68E ALA* 3.5 5.3 + - - +
69E ASP* 3.1 24.1 + - - +
21H LYS* 6.0 7.2 - - + -
22H LYS* 3.9 13.4 - - + +
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Residues in contact with ARG 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLU* 3.0 34.5 + - - +
65E GLU* 1.3 76.0 - - - +
67E TRP* 1.3 67.3 + - - +
69E ASP* 3.3 9.7 + - + +
70E LEU* 3.3 31.4 - - + +
22H LYS* 3.6 14.4 - - + +
130H GLU* 2.8 41.9 + - - +
355H LYS* 5.6 0.2 - - - +
357H TYR* 3.8 14.8 - - - -
167I GLY* 3.2 29.0 + - - +
168I TYR* 4.4 0.9 - - - +
169I SER* 3.6 20.3 - - - +
172I GLU* 3.0 33.7 + - - -
198I TRP* 4.6 7.6 - - + -
199I TYR* 4.2 19.7 - - - +
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Residues in contact with TRP 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 5.5 8.1 - - + -
11E TYR* 3.5 48.5 - + + -
12E TYR* 3.5 19.6 + + - -
52E THR* 3.2 27.2 + - + +
53E GLY* 5.3 0.2 - - - -
58E LEU* 5.9 1.2 - - + +
62E TYR* 3.8 31.1 + + + -
63E GLU 3.2 2.6 + - - -
64E GLN* 3.1 39.9 - - - +
66E ARG* 1.3 79.0 - - - +
68E ALA* 1.3 77.2 + - + +
70E LEU* 3.0 12.3 + - - +
71E SER* 3.0 19.6 + - - -
164I PRO* 3.5 32.1 - - + +
166I VAL 4.3 0.9 - - - -
167I GLY* 4.1 13.6 + - - +
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Residues in contact with ALA 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E TYR* 3.4 25.2 + - - +
64E GLN* 3.0 18.3 + - + +
65E GLU* 3.9 5.8 - - - +
67E TRP* 1.3 83.8 - - + +
69E ASP* 1.3 63.2 + - - +
70E LEU 3.1 1.0 + - - -
71E SER* 3.3 17.0 + - - +
73E LYS* 4.9 8.8 + - - -
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Residues in contact with ASP 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E GLU 3.1 17.5 + - - +
66E ARG* 3.6 6.4 - - - +
67E TRP 3.2 0.4 - - - -
68E ALA* 1.3 76.1 - - - +
70E LEU* 1.3 60.6 + - - +
71E SER 4.8 1.1 - - - +
92E PRO* 3.7 8.0 - - - +
94E HIS* 2.6 27.4 + - - -
20H SER* 4.3 3.3 + - - -
22H LYS* 3.6 30.8 - - + +
23H ARG* 2.5 50.2 + - - +
198I TRP* 5.3 1.7 - - - -
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Residues in contact with LEU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E SER* 4.4 4.7 - - - -
52E THR* 4.1 15.7 - - + +
66E ARG* 3.3 26.7 - - + +
67E TRP* 3.0 5.1 + - - +
69E ASP* 1.3 81.0 - - - +
71E SER* 1.3 67.0 + - - +
72E ALA* 3.7 1.4 + - - +
91E TYR* 6.0 0.2 - - - -
92E PRO* 3.9 13.9 - - + +
94E HIS* 3.4 46.4 - - + +
95E ALA* 4.1 18.1 - - + +
166I VAL* 5.2 2.4 - - + +
167I GLY* 3.9 20.2 - - - +
198I TRP* 4.6 4.3 - - + -
199I TYR* 3.7 33.2 - - + +
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Residues in contact with SER 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E TYR* 4.0 14.3 - - - -
12E TYR* 3.6 12.5 - - - -
52E THR* 2.6 29.4 + - - -
67E TRP* 3.0 27.3 + - - -
68E ALA 3.3 10.8 + - - +
69E ASP 4.8 1.0 - - - +
70E LEU* 1.3 81.2 - - - +
72E ALA* 1.3 63.5 + - - +
73E LYS* 3.6 17.1 - - - +
92E PRO* 4.1 7.0 - - - +
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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