Contacts of the helix formed by residues 67 - 82 (chain E) in PDB entry 1NZB
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 67 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62E LYS* 5.0 4.1 + - + -
65E PRO 3.6 5.2 + - - +
66E ALA* 1.3 74.1 - - - +
68E PRO* 1.3 77.7 - - + +
69E GLU* 3.0 12.4 + - + +
70E ASP* 3.0 31.6 + - - +
71E VAL* 3.4 9.8 + - - +
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Residues in contact with PRO 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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66E ALA 3.6 3.9 - - - +
67E GLU* 1.3 95.1 - - + +
69E GLU* 1.3 63.9 + - + +
71E VAL* 3.6 4.9 + - + -
72E ARG* 3.1 20.8 + - - +
107E PRO* 5.0 6.5 - - + +
110E SER* 2.9 39.5 - - - +
112E ALA* 4.4 8.7 - - + +
113E VAL* 3.4 16.2 - - + +
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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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25B LYS* 5.6 5.9 + - - -
29B ASP* 5.1 0.2 - - - +
32B ARG* 3.4 35.3 + - - -
61E ARG* 5.8 1.3 - - - +
67E GLU* 3.0 7.5 + - + -
68E PRO* 1.3 83.0 - - + +
70E ASP* 1.3 62.8 + - - +
72E ARG* 3.2 26.2 + - - +
73E ASP* 2.6 34.7 - - - +
112E ALA* 4.3 7.1 - - - +
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Residues in contact with ASP 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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52E TRP* 4.0 17.9 - - + -
55E TRP* 3.8 3.4 - - + -
61E ARG* 3.0 55.4 + - + +
62E LYS* 4.2 9.2 + - - +
67E GLU* 3.0 21.8 + - - +
69E GLU* 1.3 79.1 - - - +
71E VAL* 1.3 56.5 + - - +
73E ASP* 2.8 9.9 + - - +
74E TYR* 2.7 33.4 + - - +
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Residues in contact with VAL 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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52E TRP* 3.8 13.2 - - + -
66E ALA* 4.0 20.9 - - + -
67E GLU 3.4 13.7 + - - +
68E PRO 3.8 5.6 - - - +
70E ASP* 1.3 75.8 - - - +
72E ARG* 1.3 65.4 + - - +
74E TYR* 2.9 6.9 + - + -
75E LEU* 2.8 49.7 + - + +
92E LEU* 5.2 3.4 - - + -
95E LEU* 5.1 13.0 - - + -
107E PRO* 4.0 26.5 - - + -
113E VAL* 4.1 11.9 - - + -
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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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32B ARG* 2.8 60.8 - - - +
33B ASP* 3.1 30.4 + - - -
68E PRO 3.1 12.5 + - - +
69E GLU* 3.2 21.3 + - - +
71E VAL* 1.3 79.1 - - - +
73E ASP* 1.3 68.8 + - - +
75E LEU* 3.6 5.2 + - - +
76E LEU* 3.1 38.7 + - + +
112E ALA* 4.0 10.3 - - + -
113E VAL* 4.2 3.1 - - + +
116E VAL* 3.0 44.2 - - + +
119E ARG* 5.8 1.0 - - - -
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Residues in contact with ASP 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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55E TRP* 3.7 19.9 - - + -
61E ARG* 3.7 20.3 + - - -
69E GLU* 2.6 33.7 - - - +
70E ASP 2.8 9.6 + - - +
72E ARG* 1.3 77.9 + - - +
74E TYR* 1.3 68.3 + - - +
76E LEU* 2.8 23.1 + - - +
77E TYR* 3.0 10.9 + - - +
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Residues in contact with TYR 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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48E VAL* 4.5 2.9 - - + +
51E SER* 3.1 34.7 + - - -
52E TRP* 3.2 50.2 + + + -
55E TRP* 3.8 30.1 - + + -
70E ASP 2.7 9.5 + - - +
71E VAL* 2.9 8.9 + - + +
73E ASP* 1.3 70.9 - - - +
75E LEU* 1.3 56.6 + - + +
77E TYR* 2.8 32.3 + + - +
78E LEU* 2.7 48.1 - - + +
91E HIS* 2.8 29.9 + - + -
95E LEU* 4.4 21.5 - - + -
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Residues in contact with LEU 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 VAL* 2.8 39.3 + - + +
72E ARG* 3.9 5.8 - - - +
74E TYR* 1.3 78.3 - - + +
76E LEU* 1.3 63.7 + - - +
77E TYR 2.9 1.2 + - - -
78E LEU* 3.0 23.4 + - + +
79E GLN* 3.1 11.4 + - - +
88E ILE* 3.5 27.1 - - + +
91E HIS* 5.0 1.3 - - + -
92E LEU* 3.4 50.0 - - + +
113E VAL* 3.7 11.7 - - + +
116E VAL* 5.2 3.4 - - + -
117E MET* 4.3 6.1 - - + -
120E ILE* 4.2 17.6 - - + +
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Residues in contact with LEU 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 ARG* 3.1 45.8 + - + +
73E ASP* 2.8 20.5 + - - +
75E LEU* 1.3 72.4 - - - +
77E TYR* 1.3 58.5 + - - +
79E GLN* 3.4 25.1 - - - +
80E ALA* 3.4 16.8 + - - +
116E VAL* 3.9 12.8 - - + -
119E ARG* 3.3 29.6 - - - +
120E ILE* 4.5 3.3 - - + +
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Residues in contact with TYR 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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51E SER* 5.4 0.9 - - - -
55E TRP* 3.1 48.7 - + + +
73E ASP 3.0 6.3 + - - +
74E TYR* 2.8 24.1 + + - +
76E LEU* 1.3 74.9 - - - +
78E LEU* 1.3 67.8 + - + -
79E GLN 2.8 2.0 - - - -
80E ALA* 2.7 23.2 + - + +
81E ARG* 2.9 60.4 + - + -
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Residues in contact with LEU 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 TYR* 2.7 69.3 - - + +
75E LEU* 3.0 14.1 + - + +
77E TYR* 1.3 77.6 - - + +
79E GLN* 1.3 61.0 + - - +
81E ARG* 3.4 15.5 + - - +
82E GLY 3.3 4.0 + - - -
83E LEU* 3.2 51.4 + - + +
88E ILE* 4.1 17.7 - - + -
91E HIS* 3.2 33.4 - - + +
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Residues in contact with GLN 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 LEU 3.1 10.6 + - - +
76E LEU* 3.4 33.2 - - - +
77E TYR 2.8 0.2 - - - -
78E LEU* 1.3 76.3 - - - +
80E ALA* 1.3 59.8 + - - +
82E GLY* 2.8 25.5 + - - -
83E LEU 4.8 2.9 - - - +
88E ILE* 4.0 16.3 - - + +
120E ILE* 3.6 16.0 - - + +
123E GLU* 3.5 30.9 + - - +
124E ASN* 2.7 34.2 + - - +
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Residues in contact with ALA 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 LEU 3.4 9.3 + - - +
77E TYR* 2.7 22.9 + - + +
79E GLN* 1.3 77.1 - - - +
81E ARG* 1.3 59.9 + - - +
82E GLY* 3.2 1.7 + - - -
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Residues in contact with ARG 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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51E SER* 3.8 21.2 + - - -
77E TYR* 2.9 52.5 + - + +
78E LEU* 3.5 16.3 - - - +
80E ALA* 1.3 76.9 - - - +
82E GLY* 1.3 58.9 + - - +
83E LEU* 3.5 23.1 - - + +
91E HIS* 4.7 0.4 - - - -
111H T 4.8 1.8 - - - -
112H A 2.5 42.9 + - - -
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Residues in contact with GLY 82 (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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78E LEU 3.3 0.2 + - - -
79E GLN 2.8 15.9 + - - -
80E ALA 3.0 1.9 - - - -
81E ARG* 1.3 80.0 - - - +
83E LEU* 1.3 68.8 + - - +
84E ALA* 3.6 1.7 + - - -
124E ASN* 5.9 0.9 - - - -
129E GLU* 5.4 0.3 - - - +
113H T 4.5 5.5 + - - -
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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