Contacts of the helix formed by residues 67 - 81 (chain E) in PDB entry 2Q9Q
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 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64E GLU 3.3 6.2 - - - +
65E TRP 2.9 7.1 + - - +
66E MET* 1.3 75.7 - - - +
68E VAL* 1.3 65.1 + - + +
69E GLU* 3.4 30.4 - - + +
70E LYS* 2.9 48.1 + - - +
71E LEU* 2.9 26.4 + - - +
108E PRO* 6.5 0.9 - - + -
109E LYS* 6.5 0.4 - - + -
113E ILE* 4.3 4.5 - - - -
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Residues in contact with VAL 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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67E ASP* 1.3 71.4 - - + +
69E GLU* 1.3 100.4 + - + +
72E GLU* 2.8 39.0 + - - +
109E LYS* 3.9 32.5 - - + +
112E GLU* 3.7 32.3 - - + +
113E ILE* 4.4 8.3 - - + +
116E LEU* 3.5 28.9 - - + -
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Residues in contact with GLU 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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67E ASP* 3.2 14.8 + - + +
68E VAL* 1.3 105.5 - - + +
70E LYS* 1.3 65.0 + - + +
72E GLU* 3.7 7.5 + - - +
73E LYS* 3.4 27.7 + - - +
109E LYS* 5.1 4.9 + - - -
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Residues in contact with LYS 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLU* 3.4 39.4 + - - +
65E TRP* 4.3 7.4 - - - +
67E ASP* 2.9 42.7 + - - +
69E GLU* 1.3 73.8 - - + +
71E LEU* 1.3 62.0 + - - +
73E LYS* 3.1 11.8 + - + +
74E MET* 2.9 45.7 + - + +
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Residues in contact with LEU 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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65E TRP* 3.7 22.0 - - + +
66E MET* 4.7 2.2 - - + -
67E ASP 2.9 29.6 + - - +
68E VAL 3.8 3.1 - - - +
70E LYS* 1.3 75.5 - - - +
72E GLU* 1.3 64.6 + - - +
74E MET* 2.9 28.3 + - + +
75E ARG* 2.8 24.7 + - - +
87E MET* 6.4 1.1 - - + -
88E PRO* 4.9 2.7 - - + -
113E ILE* 4.0 29.4 - - + -
116E LEU* 4.1 23.6 - - + -
117E VAL* 4.1 18.4 - - + -
120E MET* 4.4 6.7 - - + +
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Residues in contact with GLU 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 VAL* 2.8 31.0 + - - +
69E GLU* 4.0 7.4 - - - +
71E LEU* 1.3 72.4 - - - +
73E LYS* 1.3 56.5 + - + +
75E ARG* 3.5 20.9 + - - +
76E ASP* 2.6 40.3 + - - +
116E LEU* 3.5 30.3 - - + +
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Residues in contact with LYS 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 GLU* 3.4 17.2 + - - +
70E LYS* 3.1 12.4 + - - +
72E GLU* 1.3 74.9 - - + +
74E MET* 1.3 65.5 + - + +
76E ASP* 3.6 7.6 + - - +
77E HIS* 3.1 23.9 + - - +
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Residues in contact with MET 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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65E TRP* 3.8 12.1 - - + +
70E LYS* 2.9 43.1 + - + +
71E LEU* 2.9 28.0 + - + +
73E LYS* 1.3 76.3 - - + +
75E ARG* 1.3 64.7 + - - +
77E HIS* 3.3 9.1 + - - +
78E GLU* 3.1 19.1 + - - +
85E THR* 4.8 2.9 + - - -
86E PRO 5.7 3.4 - - - +
87E MET* 6.2 0.2 - - - -
88E PRO* 3.1 38.6 - - + -
120E MET* 3.3 18.9 - - + +
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Residues in contact with ARG 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 LEU 2.8 14.8 + - - +
72E GLU* 3.6 32.3 + - - +
74E MET* 1.3 73.8 - - - +
76E ASP* 1.3 92.0 + - - +
78E GLU* 3.1 13.3 + - - +
79E ARG* 3.3 40.2 + - - +
116E LEU* 3.8 18.7 - - + +
119E ASP* 2.6 59.4 + - + +
120E MET* 3.2 23.7 - - + +
123E THR* 4.8 4.4 - - - +
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Residues in contact with ASP 76 (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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72E GLU* 2.6 23.7 + - - +
73E LYS* 4.0 7.4 - - - +
75E ARG* 1.3 103.3 + - - +
77E HIS* 1.3 63.3 + - - +
79E ARG* 3.3 22.8 + - - +
80E LYS* 3.4 29.2 + - - +
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Residues in contact with HIS 77 (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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73E LYS 3.1 19.6 + - - +
74E MET* 3.5 7.9 + - - +
75E ARG 3.2 0.2 - - - -
76E ASP* 1.3 76.8 - - - +
78E GLU* 1.3 62.6 + - - +
79E ARG 3.5 0.2 + - - -
80E LYS* 3.5 14.6 + - + +
81E GLU* 3.2 43.6 + - + +
85E THR* 3.8 28.9 + - + +
86E PRO* 5.2 5.6 - - + -
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Residues in contact with GLU 78 (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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74E MET 3.1 13.2 + - - +
75E ARG 3.1 10.3 + - - +
77E HIS* 1.3 76.2 - - - +
79E ARG* 1.3 61.8 + - - +
81E GLU* 3.2 6.1 + - - +
83E THR 3.6 0.2 - - - +
84E PHE* 3.5 2.1 - - - -
85E THR* 2.8 34.6 + - - +
120E MET* 4.1 11.7 - - - +
123E THR* 3.8 23.3 - - + -
124E ARG* 2.7 44.4 + - + -
127E LYS* 2.6 57.3 + - - +
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Residues in contact with ARG 79 (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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75E ARG* 3.3 36.9 + - - +
76E ASP* 3.3 14.8 + - - +
77E HIS 3.3 0.6 - - - -
78E GLU* 1.3 78.6 - - - +
80E LYS* 1.3 61.6 + - + +
81E GLU 3.3 4.9 + - - +
119E ASP* 3.2 31.3 + - - -
123E THR* 4.1 24.2 + - + +
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Residues in contact with LYS 80 (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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76E ASP* 3.4 24.6 + - - +
77E HIS* 3.5 11.0 + - + +
78E GLU 3.3 0.6 - - - -
79E ARG* 1.3 78.1 - - + +
81E GLU* 1.3 75.3 + - - +
82E GLU* 4.1 3.8 + - - +
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Residues in contact with GLU 81 (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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77E HIS* 3.2 33.2 + - + +
78E GLU 3.2 4.2 + - - +
79E ARG* 3.1 6.1 - - - +
80E LYS* 1.3 100.8 - - - +
82E GLU* 1.3 62.0 + - - +
83E THR* 3.6 19.5 + - - +
85E THR* 3.5 20.0 - - + -
127E LYS* 2.8 22.4 + - - +
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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