Contacts of the helix formed by residues 33 - 44 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26F LEU* 3.1 29.7 - - - +
32F LEU* 1.3 72.5 - - - +
34F GLN* 1.3 58.9 + - - +
35F GLY* 2.7 13.0 + - - -
36F GLU* 2.6 63.7 + - - -
37F PHE* 3.0 24.3 + - - +
63F MET* 3.2 13.0 - - - +
72F LYS 5.0 0.7 - - - +
73F GLN* 3.2 21.9 + - - +
187F CA 4.4 1.0 - - - -
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Residues in contact with GLN 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ASN* 1.3 80.3 - - - +
35F GLY* 1.3 60.0 + - - +
37F PHE* 3.5 4.1 + - - +
38F LYS* 2.9 29.5 + - + +
60F GLU* 3.0 49.1 + - + +
63F MET* 3.5 25.6 - - + +
64F GLU* 6.0 1.8 - - - +
72F LYS 5.4 0.2 + - - -
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Residues in contact with GLY 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 5.1 5.8 - - - -
33F ASN* 2.7 11.4 + - - -
34F GLN* 1.3 71.7 - - - +
36F GLU* 1.3 54.0 + - - -
37F PHE 3.0 1.6 - - - -
38F LYS* 3.2 5.9 + - - +
39F GLU* 2.7 40.0 + - - +
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Residues in contact with GLU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TYR* 2.9 39.8 - - - +
23F SER* 3.0 4.9 - - - +
25F LYS* 4.6 3.1 - - + -
26F LEU* 2.8 34.3 + - + +
32F LEU* 3.2 12.9 - - + +
33F ASN* 2.6 55.7 + - - +
35F GLY* 1.3 70.9 - - - +
37F PHE* 1.3 59.4 + - - +
39F GLU* 3.4 14.5 - - - +
40F LEU* 3.2 17.3 + - - +
187F CA 2.6 29.5 - - - -
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Residues in contact with PHE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F LEU* 3.8 18.8 - - + +
33F ASN 3.0 22.2 + - - +
34F GLN* 3.6 4.9 - - + +
35F GLY 3.0 0.2 - - - -
36F GLU* 1.3 76.7 - - - +
38F LYS* 1.3 65.6 + - - +
39F GLU 3.1 1.3 - - - -
40F LEU* 3.0 10.6 + - + +
41F VAL* 2.9 33.3 + - + +
49F LEU* 5.9 0.2 - - + -
59F ILE* 3.6 24.7 - - + -
62F ILE* 4.2 8.7 - - + -
63F MET* 3.5 37.5 - - + -
66F LEU* 3.6 26.0 - - + -
74F LEU* 3.5 21.3 - - + -
79F PHE* 4.5 9.2 - + - -
82F LEU* 4.5 15.9 - - + -
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Residues in contact with LYS 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F GLN* 2.9 19.8 + - + +
35F GLY* 3.8 5.6 - - - +
37F PHE* 1.3 76.4 - - - +
39F GLU* 1.3 57.5 + - - +
41F VAL* 3.9 9.4 - - - -
42F ARG* 2.7 70.6 + - + +
53F ASN* 4.2 16.8 + - - +
56F GLU* 4.2 30.8 + - + +
59F ILE* 4.5 13.2 - - + -
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Residues in contact with GLU 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TYR* 3.5 12.4 - - + -
25F LYS* 2.7 43.3 + - - +
26F LEU* 6.1 0.5 - - - +
35F GLY 2.7 16.6 + - - +
36F GLU* 3.4 16.5 + - - +
38F LYS* 1.3 84.0 - - - +
40F LEU* 1.3 56.0 + - - +
42F ARG* 4.2 17.6 + - - +
43F LYS* 2.9 33.6 + - + +
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Residues in contact with LEU 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 3.7 22.0 - - + -
18F THR* 4.1 19.7 - - + +
19F PHE* 5.2 2.2 - - - -
22F TYR* 3.6 20.0 - - + -
32F LEU* 4.7 13.0 - - + -
36F GLU 3.2 11.4 + - - +
37F PHE* 3.0 13.2 + - + +
39F GLU* 1.3 74.0 - - - +
41F VAL* 1.3 72.2 + - + +
43F LYS* 4.5 0.4 - - - -
44F ASP* 3.3 19.2 + - - +
45F LEU* 3.5 27.6 + - + -
79F PHE* 3.7 35.4 - - + -
82F LEU* 5.2 0.7 - - + -
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Residues in contact with VAL 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F PHE* 2.9 34.1 + - + +
38F LYS* 3.1 8.5 + - - +
40F LEU* 1.3 80.2 - - + +
42F ARG* 1.3 60.1 + - - +
45F LEU* 2.5 41.8 - - + +
49F LEU* 3.3 32.5 - - + -
53F ASN* 3.6 18.4 - - - +
59F ILE* 3.4 39.7 - - + -
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Residues in contact with ARG 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F LYS* 2.7 46.2 + - - +
39F GLU* 4.2 14.5 + - - +
41F VAL* 1.3 70.5 - - - +
43F LYS* 1.3 92.8 + - - +
46F GLN* 2.9 26.1 - - - +
53F ASN* 2.9 17.2 - - - +
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Residues in contact with LYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLN* 5.4 4.9 + - - +
22F TYR* 3.0 26.3 + - + +
39F GLU* 2.9 22.0 + - + +
40F LEU 4.3 0.7 - - - +
42F ARG* 1.3 94.2 - - - +
44F ASP* 1.3 84.0 + - - +
46F GLN* 2.6 30.9 + - - +
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Residues in contact with ASP 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E MET* 3.3 10.7 - - - +
6E SER* 3.2 37.7 + - - +
7E GLN* 4.9 7.1 - - - +
8E LEU* 3.8 30.0 - - + +
18F THR* 4.2 9.9 - - - +
22F TYR* 3.6 12.0 + - - -
40F LEU* 3.3 8.9 + - - +
43F LYS* 1.3 106.8 + - - +
45F LEU* 1.3 58.1 + - + +
46F GLN* 2.7 22.5 + - - +
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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