Contacts of the helix formed by residues 33 - 45 (chain E) in PDB entry 1IRJ
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 ASN 33 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B GLY* 5.5 2.8 + - - -
39B GLU* 5.1 3.6 + - - +
26E LEU* 3.7 31.3 - - - +
27E GLY* 4.9 2.6 - - - +
32E LEU* 1.3 75.6 - - - +
34E GLN* 1.3 66.4 + - - +
35E GLY* 3.2 6.2 + - - -
36E GLU* 2.7 40.5 + - - +
37E PHE* 2.9 19.6 + - - +
63E MET* 4.0 2.9 - - - -
72E LYS 4.0 4.9 - - - +
73E GLN* 3.5 29.2 + - - +
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Residues in contact with GLN 34 (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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34B GLN* 3.9 12.3 + - - +
38B LYS* 4.6 6.9 - - - +
56B GLU* 5.6 2.8 + - - +
60B GLU* 4.5 10.5 + - - -
33E ASN* 1.3 76.4 - - - +
35E GLY* 1.3 59.0 + - - +
37E PHE* 3.3 2.3 + - - +
38E LYS* 2.9 65.3 + - + +
60E GLU* 3.2 29.8 + - - +
63E MET* 3.8 29.9 - - + +
64E GLU* 5.7 1.7 - - - +
72E LYS 4.5 1.6 + - - -
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Residues in contact with GLY 35 (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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26B LEU* 3.7 13.1 - - - +
33B ASN* 5.4 2.7 + - - -
35B GLY* 4.4 24.2 - - - -
26E LEU* 5.0 0.2 - - - -
33E ASN* 3.2 6.7 + - - -
34E GLN* 1.3 80.9 - - - +
36E GLU* 1.3 61.8 + - - +
38E LYS* 3.4 8.6 + - - +
39E GLU* 3.1 23.4 + - - +
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.6 5.6 - - + -
22E TYR* 2.8 32.5 - - + +
23E SER* 2.8 8.6 - - - +
25E LYS* 4.4 3.8 - - + -
26E LEU* 2.6 40.1 + - + +
31E THR 3.0 2.8 - - - +
32E LEU* 4.2 4.0 - - - -
33E ASN* 2.7 41.9 + - - +
35E GLY* 1.3 76.1 - - - +
37E PHE* 1.3 64.0 + - - +
39E GLU* 3.2 7.7 + - - +
40E LEU* 3.1 21.8 + - - +
187E CA 2.3 30.6 - - - -
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Residues in contact with PHE 37 (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 LEU* 4.2 21.0 - - + +
33E ASN 2.9 16.6 + - - +
34E GLN 3.6 3.6 - - - +
36E GLU* 1.3 77.8 - - - +
38E LYS* 1.3 65.5 + - + +
40E LEU* 3.2 5.3 + - + +
41E VAL* 3.0 42.4 + - + +
59E ILE* 3.8 33.0 - - + -
62E ILE* 3.9 21.3 - - + -
63E MET* 3.8 33.0 - - + -
66E LEU* 4.0 11.9 - - + -
74E LEU* 3.5 21.8 - - + -
79E PHE* 4.3 9.6 - + - -
82E LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 38 (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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34B GLN* 3.6 8.5 + - - +
34E GLN* 2.9 42.4 + - + +
35E GLY* 3.7 8.5 - - - +
36E GLU 3.3 0.2 - - - -
37E PHE* 1.3 77.4 - - + +
39E GLU* 1.3 58.3 + - - +
41E VAL* 3.4 2.1 + - - +
42E ARG* 2.9 32.0 + - - +
53E ASN* 4.9 0.3 - - - +
56E GLU* 3.2 33.7 + - + +
59E ILE* 3.8 24.4 - - + +
60E GLU* 2.6 48.2 + - - +
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Residues in contact with GLU 39 (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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26B LEU* 3.5 39.5 - - + +
27B GLY* 2.6 29.6 + - - -
33B ASN* 4.7 6.4 + - - +
22E TYR* 4.2 10.3 - - + -
25E LYS* 5.1 3.3 + - - -
35E GLY 3.1 9.9 + - - +
36E GLU 3.6 7.9 - - - +
37E PHE 3.2 0.2 - - - -
38E LYS* 1.3 73.7 - - - +
40E LEU* 1.3 60.1 + - - +
42E ARG* 2.8 40.4 + - - -
43E LYS* 2.9 47.2 + - - +
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Residues in contact with LEU 40 (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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18E THR* 4.6 4.0 - - + +
19E PHE* 4.5 11.7 - - - -
22E TYR* 3.7 39.8 - - + -
32E LEU* 4.2 16.4 - - + -
36E GLU 3.1 11.9 + - - +
37E PHE* 3.2 8.7 + - + +
39E GLU* 1.3 75.7 - - - +
41E VAL* 1.3 59.3 + - + +
44E ASP* 2.7 33.0 + - - +
45E LEU* 3.8 15.7 + - + -
79E PHE* 3.8 31.6 - - + -
8F LEU* 3.9 25.6 - - + -
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Residues in contact with VAL 41 (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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37E PHE* 3.0 49.5 + - + +
38E LYS* 3.7 5.2 - - - +
40E LEU* 1.3 76.2 - - + +
42E ARG* 1.3 62.9 + - - +
45E LEU* 3.0 40.5 + - + +
49E LEU* 3.8 21.8 - - + -
53E ASN* 3.4 30.1 + - - +
59E ILE* 3.9 17.7 - - + -
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Residues in contact with ARG 42 (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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27B GLY* 3.5 16.6 - - - -
38E LYS 2.9 18.1 + - - +
39E GLU* 2.8 40.6 + - - +
41E VAL* 1.3 77.5 - - - +
43E LYS* 1.3 77.1 + - - +
46E GLN* 3.0 33.5 + - - +
53E ASN* 3.3 18.5 + - + +
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Residues in contact with LYS 43 (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 GLN* 5.1 6.9 - - - +
22E TYR* 3.7 24.6 + - + +
25E LYS* 6.0 2.7 - - - +
39E GLU* 2.9 34.2 + - - +
42E ARG* 1.3 104.2 - - - +
44E ASP* 1.3 66.3 + - - +
45E LEU 3.7 0.4 - - - -
46E GLN* 3.9 17.1 - - - +
6F SER* 4.7 4.7 - - - -
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Residues in contact with ASP 44 (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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18E THR* 4.0 8.7 - - - +
21E GLN* 4.9 1.9 + - - +
22E TYR* 2.6 38.6 + - - -
40E LEU* 2.7 16.6 + - + +
43E LYS* 1.3 80.9 - - - +
45E LEU* 1.3 71.1 + - - +
46E GLN 3.7 2.0 - - - -
6F SER* 2.8 32.8 + - - +
7F GLN* 5.5 0.9 + - - +
8F LEU* 3.9 26.5 + - + +
9F GLU* 3.3 2.1 - - - +
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Residues in contact with LEU 45 (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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40E LEU* 3.9 15.9 - - + -
41E VAL* 3.0 35.9 + - + +
44E ASP* 1.3 86.4 - - - +
46E GLN* 1.3 59.3 - - - +
47E ASN 3.1 3.1 - - - -
48E PHE* 4.2 16.8 - - + -
49E LEU* 3.0 57.2 + - + +
53E ASN* 3.5 1.9 + - - -
79E PHE* 5.3 0.7 - - + -
82E LEU* 3.9 18.4 - - + -
86E LEU* 5.0 2.2 - - + -
8F LEU* 4.0 12.6 - - + -
9F GLU* 3.2 18.8 - - + -
12F ILE* 4.4 9.0 - - + -
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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