Contacts of the helix formed by residues 67 - 75 (chain A) in PDB entry 2KE0
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 ILE 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A VAL* 1.3 85.0 - - - +
68A LYS* 1.3 67.7 + - - +
69A GLY 3.2 2.9 - - - +
70A TRP* 2.8 54.6 + - + +
71A ASP* 3.0 12.0 + - - +
87A ILE* 3.7 25.1 - - + -
91A LEU 4.5 15.9 - - - +
92A GLY* 5.7 4.0 - - - +
110A PHE* 5.9 2.7 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 5.2 1.1 - - - +
11A GLU* 5.8 3.0 - - - +
12A SER* 2.9 38.4 + - - +
14A LEU* 3.7 11.4 - - + -
67A ILE* 1.3 71.9 - - - +
69A GLY* 1.3 57.9 + - - +
71A ASP* 3.1 11.2 + - + +
72A GLU* 2.8 42.6 + - - +
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.0 38.8 - - - +
16A TYR* 5.2 0.2 - - - -
67A ILE* 3.2 6.2 - - - +
68A LYS* 1.3 74.3 - - - +
70A TRP* 1.3 61.6 + - - +
72A GLU* 3.8 4.6 - - - +
73A GLY 3.0 14.7 + - - -
85A LEU* 2.9 27.9 - - - +
87A ILE* 5.7 1.6 - - - -
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Residues in contact with TRP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.9 7.6 - - + -
37A TYR* 3.5 47.6 - + + -
57A PHE* 3.8 31.9 - + + -
59A PHE* 4.5 8.3 - + - -
65A MET 5.3 0.7 - - - -
66A VAL* 3.3 37.0 - - + -
67A ILE* 2.8 45.1 + - + +
69A GLY* 1.3 69.4 - - - +
71A ASP* 1.3 59.8 + - - +
73A GLY* 3.1 2.3 + - - -
74A VAL* 2.8 38.3 + - + +
85A LEU* 3.6 25.0 - - + +
87A ILE* 4.9 2.5 - - + +
110A PHE* 4.4 24.5 - + - +
112A VAL* 4.4 10.9 - - + +
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Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 5.7 0.9 - - + -
61A LEU* 3.5 24.7 - - + +
62A GLY* 4.3 12.9 + - - +
66A VAL* 4.1 11.1 - - + +
67A ILE 3.0 9.9 + - - +
68A LYS* 3.7 12.9 - - + +
70A TRP* 1.3 76.1 - - - +
72A GLU* 1.3 72.5 + - - +
74A VAL* 3.1 2.8 + - - -
75A GLN* 2.9 38.4 + - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A THR* 4.1 25.3 + - + +
16A TYR* 4.2 23.8 - - + +
68A LYS* 2.8 29.7 + - - +
69A GLY* 3.8 6.1 - - - +
71A ASP* 1.3 77.8 + - - +
73A GLY* 1.3 61.5 + - - +
75A GLN* 3.0 47.0 + - - +
76A GLY* 4.1 1.2 + - - -
83A ARG* 5.5 1.4 + - - -
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TYR* 5.7 1.0 - - - -
69A GLY 3.0 15.6 + - - -
70A TRP* 3.6 3.4 - - - -
72A GLU* 1.3 76.4 - - - +
74A VAL* 1.3 57.5 + - - +
76A GLY* 4.1 0.2 - - - -
77A MET* 2.9 45.1 + - - +
83A ARG* 4.5 17.3 - - - -
85A LEU* 5.0 7.0 - - - -
112A VAL* 6.2 3.4 - - - -
114A LEU* 5.9 0.4 - - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 2.9 39.8 - - + +
33A VAL* 4.4 13.5 - - + -
35A VAL* 5.4 9.0 - - + -
59A PHE* 3.6 28.7 - - + -
61A LEU* 3.2 39.7 - - + +
70A TRP* 2.8 28.7 + - + +
71A ASP* 4.4 0.4 - - - -
73A GLY* 1.3 73.1 - - - +
75A GLN* 1.3 58.7 + - - +
76A GLY 3.0 8.9 + - - -
77A MET* 4.0 5.1 + - - +
112A VAL* 5.6 7.6 - - + -
114A LEU* 5.6 5.2 - - + -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 4.5 6.0 - - - +
27A ALA 4.6 3.1 - - - -
29A ALA* 6.2 0.7 - - + -
61A LEU* 3.4 21.8 - - + -
71A ASP* 2.9 26.6 + - - +
72A GLU* 3.0 46.0 + - - +
74A VAL* 1.3 74.7 - - - +
76A GLY* 1.3 54.7 + - - +
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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