Contacts of the helix formed by residues 64 - 76 (chain E) in PDB entry 5U07
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 ARG 64 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E THR* 3.1 16.0 + - - +
63E ARG* 1.3 83.9 - - - +
65E ILE* 1.3 62.9 + - - +
66E ILE 3.4 2.2 - - - +
67E SER* 3.7 18.0 + - - +
68E GLU* 3.7 15.6 + - - +
110E ALA 5.5 2.7 - - - +
111E PRO 5.1 0.9 - - - +
112E ALA* 4.2 22.0 - - + +
208F ASP* 2.3 36.2 + - - +
210F ILE* 3.3 28.9 + - + +
212F LYS* 3.4 37.9 - - - +
215F ASP* 3.9 17.8 + - - +
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Residues in contact with ILE 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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62E THR* 4.1 21.0 - - + +
63E ARG 3.6 2.0 + - - -
64E ARG* 1.3 74.9 - - - +
66E ILE* 1.3 70.0 + - - +
68E GLU* 3.0 6.0 + - + +
69E ILE* 2.9 38.9 + - + +
91E VAL* 4.1 13.2 - - + -
113E THR* 3.7 24.4 - - + +
117E PHE* 4.0 19.3 - - + -
119E LEU* 4.4 17.7 - - + -
124E ILE* 3.7 37.9 - - + -
127E LEU* 5.2 4.3 - - + -
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Residues in contact with ILE 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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64E ARG 3.4 0.4 - - - -
65E ILE* 1.3 78.1 - - - +
67E SER* 1.3 56.6 + - - +
69E ILE* 3.5 1.7 + - - -
70E ALA* 2.8 31.5 + - - +
84E ASP* 4.2 5.8 - - - +
87E ALA* 3.5 27.0 - - + +
88E ARG* 4.2 8.3 - - + +
91E VAL* 3.4 44.9 - - + -
102E LEU* 3.9 18.2 - - + -
110E ALA* 3.5 19.5 - - + -
111E PRO* 3.2 33.2 - - + +
113E THR* 4.3 4.7 - - + -
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Residues in contact with SER 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ARG* 3.7 24.1 + - - +
65E ILE 3.2 0.6 - - - -
66E ILE* 1.3 80.2 - - - +
68E GLU* 1.3 57.1 + - - +
70E ALA* 3.3 9.4 + - - +
71E LYS* 2.9 25.6 + - - +
74E ARG* 5.7 0.2 + - - -
109E GLU* 5.3 6.6 - - - +
110E ALA* 4.1 21.7 - - - +
111E PRO 5.1 0.4 + - - -
210F ILE* 5.6 3.5 - - - +
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Residues in contact with GLU 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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62E THR* 6.2 1.3 - - + -
64E ARG 3.7 8.6 + - - +
65E ILE* 3.0 11.3 + - + +
67E SER* 1.3 76.4 - - - +
69E ILE* 1.3 60.1 + - - +
71E LYS* 2.8 40.5 + - - +
72E ARG* 2.4 58.0 + - - +
124E ILE* 3.0 30.9 - - + +
210F ILE* 4.9 22.9 - - + +
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Residues in contact with ILE 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 ILE* 2.9 32.7 + - + +
66E ILE* 4.0 3.1 - - - +
68E GLU* 1.3 77.8 + - - +
70E ALA* 1.3 58.2 + - - +
72E ARG* 3.2 5.0 + - - +
73E LEU* 2.9 35.6 + - + +
87E ALA* 3.9 20.6 - - + +
90E VAL* 4.2 21.1 - - + -
91E VAL* 5.6 2.0 - - + -
124E ILE* 4.0 19.7 - - + +
127E LEU* 3.8 32.8 - - + -
128E ALA* 4.5 20.0 - - - +
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Residues in contact with ALA 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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66E ILE 2.8 19.5 + - - +
67E SER* 3.3 10.1 - - - +
68E GLU 3.1 0.2 - - - -
69E ILE* 1.3 76.5 - - - +
71E LYS* 1.3 57.4 + - - +
73E LEU* 3.4 0.6 + - - -
74E ARG* 2.9 41.6 + - - +
83E ALA* 3.6 31.7 - - + +
84E ASP* 4.4 11.0 - - + +
87E ALA* 4.0 1.9 - - + +
110E ALA* 5.2 2.7 - - + -
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Residues in contact with LYS 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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67E SER 2.9 12.3 + - - +
68E GLU* 2.8 35.0 + - - +
70E ALA* 1.3 77.0 - - - +
72E ARG* 1.3 70.5 + - - +
74E ARG* 3.2 18.8 + - - +
75E GLU* 2.9 26.8 + - + +
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Residues in contact with ARG 72 (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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68E GLU* 2.4 42.5 + - - +
69E ILE* 3.2 5.8 + - - +
71E LYS* 1.3 86.1 - - - +
73E LEU* 1.3 62.2 + - - +
75E GLU* 2.9 23.5 - - + +
76E ARG* 2.9 26.4 + - - +
121E VAL* 3.1 37.2 + - - +
124E ILE* 3.4 16.2 - - - +
125E ASP* 2.9 46.1 - - - +
128E ALA* 4.1 13.9 - - + -
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Residues in contact with LEU 73 (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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69E ILE* 2.9 26.4 + - + +
72E ARG* 1.3 75.8 - - - +
74E ARG* 1.3 62.4 + - - +
76E ARG* 3.1 28.1 + - - +
77E GLY 3.4 0.3 + - - -
78E TRP* 3.2 40.4 + - + +
83E ALA* 3.7 34.3 - - + +
86E GLY* 4.5 5.6 - - - -
87E ALA 4.3 9.2 - - - +
128E ALA* 3.6 28.0 - - + +
131E ALA* 4.2 19.3 - - + +
132E ASP* 4.6 7.4 - - + +
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Residues in contact with ARG 74 (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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70E ALA* 2.9 24.5 + - - +
71E LYS* 3.5 26.1 - - - +
72E ARG 3.1 0.2 - - - -
73E LEU* 1.3 77.5 - - - +
75E GLU* 1.3 60.2 + - - +
77E GLY* 3.4 10.2 + - - -
78E TRP 3.8 19.6 - - - +
80E ALA* 3.6 40.2 + - - +
83E ALA* 3.9 4.6 - - + +
84E ASP* 5.9 1.4 - - - +
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Residues in contact with GLU 75 (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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71E LYS* 2.9 17.1 + - + +
72E ARG* 2.9 42.1 + - + +
74E ARG* 1.3 75.3 - - - +
76E ARG* 1.3 71.9 + - - +
77E GLY* 3.2 2.5 + - - -
125E ASP* 5.5 1.0 - - - +
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Residues in contact with ARG 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG* 2.9 14.5 + - - +
73E LEU* 3.1 31.3 + - - +
75E GLU* 1.3 92.3 + - - +
77E GLY* 1.3 56.4 + - - +
78E TRP* 3.6 12.5 - - + +
125E ASP* 2.5 42.8 + - - -
128E ALA* 3.4 18.4 - - - +
129E ALA* 3.8 17.4 - - - +
132E ASP* 4.1 22.3 + - - +
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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
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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