Contacts of the helix formed by residues 22 - 33 (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 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E ASP* 1.3 79.6 - - + +
23E VAL* 1.3 70.3 + - + +
24E ARG 3.0 2.7 - - - -
25E LYS* 3.3 17.0 + - + +
26E ASN* 3.0 35.4 + - - +
103E GLY 5.5 3.5 - - - +
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Residues in contact with VAL 23 (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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21E ASP 4.3 15.0 - - - +
22E GLU* 1.3 80.4 - - + +
24E ARG* 1.3 68.8 + - + +
26E ASN* 3.6 1.6 - - - +
27E LEU* 2.8 37.3 + - + +
64E PHE* 4.3 25.6 - - + -
65E PRO* 5.4 3.1 - - + -
102E SER* 3.6 26.7 - - - +
103E GLY 5.6 0.2 - - - -
104E LEU* 3.8 29.2 - - + -
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Residues in contact with ARG 24 (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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21E ASP* 3.5 33.0 + - - +
23E VAL* 1.3 90.5 - - + +
25E LYS* 1.3 62.3 + - - +
27E LEU* 3.9 6.4 - - - +
28E MET* 3.2 31.8 + - - +
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Residues in contact with LYS 25 (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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21E ASP 4.5 0.8 + - - +
22E GLU* 3.3 18.9 + - + +
24E ARG* 1.3 79.8 - - - +
26E ASN* 1.3 71.2 + - - +
28E MET* 3.0 29.4 + - + +
29E ASP* 2.9 39.2 + - - +
69F GLU* 4.7 11.4 + - - +
112F ALA* 6.0 2.0 - - - +
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Residues in contact with ASN 26 (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 GLU* 3.0 32.6 + - - +
23E VAL* 3.6 5.8 - - - +
24E ARG 3.3 0.2 - - - -
25E LYS* 1.3 85.1 + - - +
27E LEU* 1.3 52.1 + - - +
29E ASP* 3.2 14.5 + - - +
30E MET* 2.6 35.7 + - - +
101E ARG 4.2 3.8 - - - +
102E SER* 3.0 39.2 + - - +
103E GLY* 3.9 8.8 - - - -
111F ASN* 4.6 14.8 + - - +
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Residues in contact with LEU 27 (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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23E VAL* 2.8 25.7 + - + +
24E ARG* 3.9 5.4 - - - +
26E ASN* 1.3 73.1 - - - +
28E MET* 1.3 53.2 + - - +
30E MET* 3.0 26.0 - - + +
31E PHE* 2.7 54.8 + - + +
64E PHE* 4.9 16.6 - - + -
98E LEU* 4.9 11.7 - - + +
101E ARG 4.2 3.4 - - - +
102E SER* 4.0 23.1 - - - -
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Residues in contact with MET 28 (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 ARG* 3.2 23.8 + - - +
25E LYS* 3.0 22.1 + - + +
27E LEU* 1.3 73.5 - - - +
29E ASP* 1.3 60.6 + - - +
31E PHE* 2.9 7.0 + - - +
32E ARG* 2.5 39.4 + - - +
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Residues in contact with ASP 29 (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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25E LYS* 2.9 47.8 + - - +
26E ASN* 3.5 9.9 - - - +
28E MET* 1.3 80.6 - - - +
30E MET* 1.3 62.4 + - - +
32E ARG* 3.5 43.9 + - - +
33E ASP* 3.4 21.3 + - - +
69F GLU* 3.9 7.0 - - - +
111F ASN* 5.2 3.7 - - + +
112F ALA* 4.7 14.2 + - - +
115F LEU* 3.9 6.9 - - - +
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Residues in contact with MET 30 (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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26E ASN 2.6 19.3 + - - +
27E LEU* 3.0 28.0 - - + +
29E ASP* 1.3 74.1 - - - +
31E PHE* 1.3 73.4 + - + +
33E ASP 3.0 24.4 - - - +
34E ARG* 4.2 1.7 - - - -
37E PHE* 4.5 10.3 - - + -
42E TRP* 3.8 23.7 - - + -
45E LEU* 5.0 8.5 - - + -
97E MET* 4.4 7.6 - - + +
98E LEU* 4.9 13.0 - - + -
101E ARG* 3.4 45.3 - - + +
111F ASN* 4.5 1.8 - - - +
115F LEU* 3.8 12.2 - - - +
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Residues in contact with PHE 31 (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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27E LEU* 2.7 37.0 + - + +
28E MET* 3.8 4.3 - - - +
30E MET* 1.3 84.7 - - + +
32E ARG* 1.3 63.2 + - - +
33E ASP 2.9 7.2 + - - -
34E ARG* 3.3 27.8 + - + +
42E TRP* 3.4 35.2 - + - -
46E LEU* 6.3 2.0 - - + -
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Residues in contact with ARG 32 (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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28E MET 2.5 22.4 + - - +
29E ASP* 3.5 32.0 + - - +
30E MET 3.3 0.2 - - - -
31E PHE* 1.3 72.6 - - - +
33E ASP* 1.3 74.6 + - - +
34E ARG 3.9 0.2 - - - -
69F GLU* 3.2 31.1 + - - -
72F ARG* 2.9 52.0 - - - +
112F ALA* 3.7 12.1 - - - +
119F ARG* 3.9 7.8 + - - +
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Residues in contact with ASP 33 (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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29E ASP 3.4 11.2 + - - +
30E MET 3.0 12.1 - - - +
31E PHE 2.9 0.4 - - - -
32E ARG* 1.3 106.0 + - - +
34E ARG* 1.3 62.0 + - - +
35E GLN* 3.4 3.4 - - - +
36E ALA* 3.5 16.1 - - + +
37E PHE* 4.9 1.7 - - - -
72F ARG* 2.9 20.0 + - - -
112F ALA 4.5 0.5 - - - +
115F LEU* 4.3 16.6 - - + +
116F VAL* 4.3 11.3 + - - +
119F ARG* 2.8 44.3 + - - +
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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