Contacts of the helix formed by residues 55 - 70 (chain E) in PDB entry 1ZUM
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 55 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E SER* 6.0 4.9 - - - +
35E LYS* 5.3 5.9 + - - -
53E GLU* 4.6 9.3 - - - +
54E GLY* 1.3 72.6 - - - +
56E LYS* 1.3 84.7 + - - +
57E GLU* 3.3 12.3 - - - +
58E ASP* 2.8 13.6 + - - +
59E VAL* 3.0 27.5 + - - +
227E THR* 3.4 33.7 - - - +
228E ALA* 4.5 6.7 - - - +
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Residues in contact with LYS 56 (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 ASP* 1.3 87.1 + - - +
57E GLU* 1.3 67.5 + - + +
59E VAL* 3.2 3.3 + - - +
60E ASP* 2.9 30.1 + - + +
227E THR 5.6 0.2 - - - +
231E ALA* 3.9 25.6 - - + +
235E HIS* 5.9 3.7 - - + -
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Residues in contact with GLU 57 (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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32E VAL* 3.9 32.3 - - + +
55E ASP* 3.3 9.6 - - - +
56E LYS* 1.3 88.9 + - + +
58E ASP* 1.3 61.7 + - - +
60E ASP* 3.5 7.9 + - - +
61E LYS* 3.2 27.2 + - - +
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Residues in contact with ASP 58 (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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22E ILE* 4.4 12.1 - - + +
24E ILE* 3.7 5.7 - - + +
30E ASP 4.1 2.8 - - - +
31E ALA* 3.4 9.2 - - - +
32E VAL* 2.9 41.1 + - - +
33E SER* 5.1 1.0 + - - -
53E GLU 4.2 2.1 - - - +
54E GLY* 3.5 13.4 - - - -
55E ASP* 2.8 34.1 + - - +
57E GLU* 1.3 74.4 - - - +
59E VAL* 1.3 65.9 + - - +
61E LYS* 3.2 12.1 + - - +
62E ALA* 3.1 20.8 + - - +
221E VAL* 4.3 9.1 - - + +
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Residues in contact with VAL 59 (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 ASP 3.0 16.6 + - - +
56E LYS 3.6 7.2 - - - +
58E ASP* 1.3 75.2 - - - +
60E ASP* 1.3 59.6 + - - +
62E ALA* 3.0 8.9 + - - +
63E VAL* 2.8 39.5 + - + +
190E VAL* 4.7 1.1 - - + -
221E VAL* 4.1 15.9 - - + -
228E ALA* 3.6 28.7 - - + +
231E ALA* 3.8 12.8 - - + +
232E ILE* 3.6 39.5 - - + +
235E HIS* 4.6 4.7 - - + -
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Residues in contact with ASP 60 (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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56E LYS* 2.9 19.1 + - + +
57E GLU* 3.7 9.9 - - - +
58E ASP 3.2 0.2 - - - -
59E VAL* 1.3 77.1 - - - +
61E LYS* 1.3 61.7 + - - +
63E VAL* 3.5 1.2 + - - +
64E LYS* 3.1 53.0 + - - +
235E HIS* 2.7 37.2 + - + +
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Residues in contact with LYS 61 (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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24E ILE* 4.0 20.7 - - + +
29E HIS* 3.7 33.7 + - - +
30E ASP 4.8 4.9 + - - -
32E VAL* 4.1 22.8 - - + +
57E GLU 3.2 17.7 + - - +
58E ASP* 3.2 10.5 + - - +
60E ASP* 1.3 76.2 - - + +
62E ALA* 1.3 62.6 + - - +
64E LYS* 3.5 10.2 + - + +
65E ALA* 3.1 24.4 + - - +
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Residues in contact with ALA 62 (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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24E ILE* 3.9 15.0 - - + +
58E ASP 3.1 11.8 + - - +
59E VAL 3.0 8.4 + - - +
61E LYS* 1.3 77.2 - - - +
63E VAL* 1.3 57.6 + - - +
65E ALA* 3.2 4.0 + - - +
66E ALA* 2.9 28.6 + - - +
190E VAL* 3.8 17.6 - - + +
219E ASN* 3.8 16.6 + - + -
221E VAL* 3.9 22.0 - - + -
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Residues in contact with VAL 63 (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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59E VAL* 2.8 26.7 + - + +
60E ASP 4.0 0.9 - - - +
62E ALA* 1.3 74.1 - - - +
64E LYS* 1.3 58.6 + - + +
66E ALA* 3.2 2.5 + - - +
67E ARG* 2.8 29.3 + - - +
161E VAL* 4.5 4.6 - - + +
190E VAL* 3.9 18.6 - - + -
235E HIS* 3.5 42.0 - - + +
237E ASP* 3.9 26.5 - - + +
238E VAL* 3.8 23.1 - - + -
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Residues in contact with LYS 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 ASP* 3.1 45.3 + - - +
61E LYS* 3.7 9.4 - - + +
63E VAL* 1.3 78.3 - - + +
65E ALA* 1.3 56.2 + - - +
67E ARG* 3.5 6.6 + - - +
68E ALA* 3.0 28.8 + - - +
235E HIS* 6.0 1.1 - - + +
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Residues in contact with ALA 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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24E ILE* 3.7 12.8 - - + -
25E ASN* 3.6 37.2 - - - +
61E LYS 3.1 18.0 + - - +
62E ALA 3.6 4.0 - - - +
64E LYS* 1.3 77.5 - - - +
66E ALA* 1.3 56.4 + - - +
68E ALA* 3.3 7.4 + - - +
69E ALA* 3.0 28.9 + - - +
216E GLY* 3.9 4.8 - - - -
219E ASN* 4.0 6.5 - - - +
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Residues in contact with ALA 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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62E ALA 2.9 17.3 + - - +
63E VAL 3.5 4.3 - - - +
65E ALA* 1.3 77.2 - - - +
67E ARG* 1.3 62.2 + - - +
69E ALA* 3.1 3.1 + - - +
70E PHE 3.0 18.5 + - - -
161E VAL* 4.0 16.4 - - + -
188E VAL* 3.4 27.8 - - + +
189E VAL 4.7 1.6 - - - +
190E VAL* 4.0 6.3 - - + -
216E GLY 3.3 19.2 + - - +
219E ASN* 3.8 5.8 - - - +
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Residues in contact with ARG 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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63E VAL 2.8 17.5 + - - +
64E LYS* 3.7 7.4 - - - +
66E ALA* 1.3 74.8 - - - +
68E ALA* 1.3 59.6 + - - +
70E PHE* 3.2 36.9 + - - -
71E GLN* 2.7 45.7 + - - +
161E VAL* 3.6 16.5 - - + +
237E ASP* 2.8 57.2 + - - +
239E ASP* 2.9 30.1 + - - -
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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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64E LYS 3.0 17.5 + - - +
65E ALA* 3.6 7.9 - - - +
67E ARG* 1.3 79.3 - - - +
69E ALA* 1.3 60.7 + - - +
70E PHE 3.3 0.9 + - - -
71E GLN* 3.3 26.1 + - - +
74E SER* 4.3 4.2 - - - -
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Residues in contact with ALA 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 ALA 3.0 14.6 + - - +
66E ALA 3.1 5.4 + - - +
68E ALA* 1.3 76.2 - - - +
70E PHE* 1.3 54.5 + - - +
71E GLN 3.4 0.7 - - - -
74E SER* 2.8 26.6 + - - -
75E PRO* 6.3 0.4 - - - -
76E TRP* 3.7 13.7 - - + +
188E VAL* 4.1 6.5 - - + -
214E PRO* 5.7 1.6 - - + -
215E PRO 3.5 24.9 - - - +
216E GLY 3.7 13.2 - - - -
217E VAL* 3.9 8.1 - - + +
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Residues in contact with PHE 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 ALA 3.0 15.1 + - - +
67E ARG* 3.2 30.5 + - - +
68E ALA 3.1 0.4 - - - -
69E ALA* 1.3 77.2 - - - +
71E GLN* 1.3 60.9 + - - +
72E LEU 3.5 0.2 + - - -
76E TRP* 5.0 0.9 - + - -
77E ARG* 2.9 63.6 + - - -
158E PRO* 3.7 26.0 - - + -
159E VAL 4.7 2.2 - - - -
160E GLY* 3.6 26.0 - - - -
186E GLY 3.6 20.4 - - - -
187E ASN* 4.6 0.4 - - - -
188E VAL* 3.8 21.3 - - + -
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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