Contacts of the helix formed by residues 33 - 45 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.7 32.2 + - - +
27B GLY* 4.9 1.8 - - - +
31B THR 4.0 0.2 + - - -
32B LEU* 1.3 76.2 - - - +
34B GLN* 1.3 65.7 + - - +
35B GLY* 3.1 6.6 + - - -
36B GLU* 2.6 41.0 + - - +
37B PHE* 3.0 20.8 + - - +
63B MET* 3.8 3.6 - - - -
72B LYS 4.0 13.2 - - - +
73B GLN* 4.7 6.5 - - + +
35E GLY* 5.4 2.0 + - - -
39E GLU* 4.7 7.1 + - - +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASN* 1.3 75.4 - - - +
35B GLY* 1.3 63.3 + - - +
37B PHE* 3.5 2.0 + - - +
38B LYS* 3.0 43.8 + - + +
60B GLU* 2.9 54.2 + - - +
63B MET* 3.6 24.0 - - + +
72B LYS 4.4 1.6 + - - +
34E GLN* 3.9 6.6 + - - +
38E LYS* 3.6 23.7 + - - +
56E GLU* 4.0 8.9 - - - +
60E GLU* 4.3 2.3 - - - +
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Residues in contact with GLY 35 (chain B).
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* 5.0 0.2 - - - -
33B ASN* 3.1 7.6 + - - -
34B GLN* 1.3 81.1 - - - +
36B GLU* 1.3 59.8 + - - +
38B LYS* 3.5 8.0 + - - +
39B GLU* 3.2 22.0 + - - +
26E LEU* 3.8 14.5 - - - +
33E ASN* 5.5 2.4 + - - -
35E GLY* 4.4 23.3 - - - -
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.2 27.1 - - - +
23B SER* 3.0 6.4 - - - +
25B LYS* 4.5 4.0 - - + -
26B LEU* 2.7 38.2 + - + +
31B THR 3.0 4.1 - - - +
32B LEU* 3.1 9.9 - - + -
33B ASN* 2.6 47.3 + - - +
35B GLY* 1.3 69.4 - - - +
37B PHE* 1.3 60.5 + - - +
39B GLU* 3.3 6.6 + - - +
40B LEU* 3.0 29.1 + - - +
187B CA 2.3 30.6 - - - -
26E LEU* 4.5 4.9 - - + +
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 4.0 21.0 - - + +
33B ASN 3.0 16.8 + - - +
34B GLN 3.8 3.6 - - - +
36B GLU* 1.3 77.2 - - - +
38B LYS* 1.3 64.0 + - + +
40B LEU* 3.2 4.7 + - + +
41B VAL* 2.9 47.0 + - + +
59B ILE* 3.7 34.8 - - + -
62B ILE* 3.7 23.3 - - + -
63B MET* 3.7 31.2 - - + -
66B LEU* 4.0 10.5 - - + -
74B LEU* 3.7 19.7 - - + -
79B PHE* 4.1 18.2 - + - -
82B LEU* 4.6 6.1 - - + -
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Residues in contact with LYS 38 (chain B).
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* 3.0 37.3 + - + +
35B GLY* 3.8 7.9 - - - +
36B GLU 3.3 0.2 - - - -
37B PHE* 1.3 78.4 - - + +
39B GLU* 1.3 56.4 + - - +
41B VAL* 3.8 1.6 - - - +
42B ARG* 2.8 32.4 + - - +
53B ASN* 4.8 1.0 - - - +
56B GLU* 2.7 39.8 + - + +
59B ILE* 3.8 23.0 - - + +
60B GLU* 2.8 45.5 + - - +
34E GLN* 4.6 8.7 - - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.7 17.9 - - + -
25B LYS* 5.3 1.7 - - - -
35B GLY 3.2 11.0 + - - +
36B GLU 3.6 8.3 - - - +
37B PHE 3.2 0.2 - - - -
38B LYS* 1.3 76.2 - - - +
40B LEU* 1.3 65.6 + - - +
42B ARG* 2.6 38.8 + - - +
43B LYS* 2.9 37.4 + - + +
25E LYS 5.1 0.3 - - - +
26E LEU* 3.6 27.4 - - + +
27E GLY* 3.0 29.3 + - - -
33E ASN* 5.1 3.3 + - - -
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Residues in contact with LEU 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.0 14.6 - - + -
18B THR* 4.4 10.5 - - + +
19B PHE* 4.4 5.8 - - - -
22B TYR* 3.7 40.3 - - + -
32B LEU* 4.2 13.7 - - + -
36B GLU 3.0 14.8 + - - +
37B PHE* 3.5 8.7 - - + +
39B GLU* 1.3 76.2 - - - +
41B VAL* 1.3 57.9 + - + +
44B ASP* 2.7 33.5 + - + +
45B LEU* 4.0 19.1 - - + -
79B PHE* 3.9 36.8 - - + -
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 2.9 54.3 + - + +
38B LYS 3.8 3.8 - - - +
40B LEU* 1.3 74.7 - - + +
42B ARG* 1.3 66.2 + - - +
45B LEU* 3.1 36.3 + - + -
49B LEU* 3.8 23.8 - - + -
53B ASN* 3.1 36.5 + - - +
59B ILE* 4.0 16.2 - - + -
62B ILE* 6.2 0.2 - - + -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS 2.8 19.4 + - - +
39B GLU* 2.6 37.4 + - - +
41B VAL* 1.3 80.1 - - - +
43B LYS* 1.3 96.5 + - - +
46B GLN* 3.5 15.4 - - - +
53B ASN* 3.5 18.0 + - - +
27E GLY* 4.1 14.5 - - - -
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLN* 4.2 11.3 - - - +
22B TYR* 3.4 27.0 + - - +
25B LYS* 6.1 1.2 - - - +
39B GLU* 2.9 36.2 + - + +
42B ARG* 1.3 109.2 - - - +
44B ASP* 1.3 66.5 + - - +
46B GLN* 2.9 24.3 + - - +
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 2.6 35.3 + - - +
7A GLN 5.3 0.5 + - - -
8A LEU* 4.0 22.1 + - + +
9A GLU* 3.3 6.2 - - - +
18B THR* 4.0 8.7 - - + +
21B GLN* 4.8 2.9 + - - +
22B TYR* 2.7 35.2 + - - -
40B LEU* 2.7 18.3 + - + +
43B LYS* 1.3 80.3 - - - +
45B LEU* 1.3 63.8 + - - +
46B GLN* 2.9 8.5 + - - +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.9 18.6 - - + -
9A GLU* 3.1 22.7 - - + -
12A ILE* 4.3 9.9 - - + -
40B LEU* 4.0 20.6 - - + -
41B VAL* 3.1 26.0 + - + +
44B ASP* 1.3 86.1 - - - +
46B GLN* 1.3 58.0 + - - +
48B PHE* 4.3 15.5 - - + -
49B LEU* 2.9 46.4 + - + +
53B ASN* 3.6 2.1 + - - -
79B PHE* 5.3 0.7 - - + -
82B LEU* 3.6 30.5 - - + -
86B LEU* 6.1 0.4 - - + -
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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