Contacts of the helix formed by residues 45 - 57 (chain B) in PDB entry 2R28
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 THR 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ASN 3.6 3.8 + - - +
44B PRO* 1.3 76.7 - - - +
46B GLU* 1.3 65.2 + - - +
47B ALA* 3.6 8.8 + - - +
48B GLU* 3.1 26.7 + - - +
49B LEU* 3.1 23.1 + - - +
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Residues in contact with GLU 46 (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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30B THR* 4.2 16.8 + - - +
31B LYS* 5.3 1.6 + - - -
38B ARG* 5.5 4.5 + - - -
44B PRO 5.3 1.2 - - - +
45B THR* 1.3 71.3 - - - +
47B ALA* 1.3 65.1 + - - +
49B LEU* 3.4 25.3 + - - +
50B GLN* 3.1 25.6 + - - +
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Residues in contact with ALA 47 (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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45B THR* 3.3 8.6 + - - +
46B GLU* 1.3 74.6 - - - +
48B GLU* 1.3 65.8 - - - +
50B GLN* 3.4 4.9 + - - +
51B ASP* 3.0 25.3 + - - +
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Residues in contact with GLU 48 (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 MET* 5.6 2.3 - - - +
42B GLN* 5.1 8.5 + - - -
43B ASN 5.0 0.2 - - - -
44B PRO* 3.3 28.6 - - + +
45B THR* 3.1 25.6 + - - +
47B ALA* 1.3 76.4 - - - +
49B LEU* 1.3 58.4 + - - +
51B ASP* 3.4 6.4 + - - +
52B MET* 3.0 41.6 + - + +
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Residues in contact with LEU 49 (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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30B THR* 3.6 24.9 - - - +
33B LEU* 3.6 22.3 - - + +
34B GLY* 3.5 40.4 - - - +
37B MET* 4.1 8.7 - - - -
38B ARG* 6.1 0.2 - - - +
44B PRO* 4.0 21.8 - - + +
45B THR 3.1 16.5 + - - +
46B GLU* 3.9 30.5 - - - +
47B ALA 3.2 0.2 - - - -
48B GLU* 1.3 77.9 - - - +
50B GLN* 1.3 61.1 + - - +
52B MET* 3.2 9.8 + - - +
53B ILE* 3.1 25.1 + - - +
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Residues in contact with GLN 50 (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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30B THR* 3.8 22.4 - - + +
46B GLU 3.1 16.3 + - - +
47B ALA* 4.1 5.6 - - - +
49B LEU* 1.3 71.9 - - - +
51B ASP* 1.3 55.9 + - - +
53B ILE* 3.3 10.2 + - - +
54B ASN* 2.7 76.3 + - - +
62B GLY* 5.0 13.1 - - - +
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Residues in contact with ASP 51 (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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47B ALA 3.0 17.8 + - - +
48B GLU* 3.8 6.0 - - - +
50B GLN* 1.3 77.5 - - - +
52B MET* 1.3 66.2 + - - +
54B ASN* 4.0 9.3 - - - +
55B GLU* 3.0 46.3 + - - +
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Residues in contact with MET 52 (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 LEU* 4.1 11.7 - - + -
37B MET* 3.8 29.6 - - + +
48B GLU* 3.0 30.0 + - + +
49B LEU* 3.2 14.1 + - - +
51B ASP* 1.3 81.9 + - - +
53B ILE* 1.3 61.5 + - - +
55B GLU* 3.7 14.0 - - - +
56B VAL* 3.8 5.5 - - - +
72B MET* 3.1 39.3 - - + +
76B LYS* 3.1 35.8 + - - +
410C PHE* 3.7 23.3 - - + -
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Residues in contact with ILE 53 (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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28B ILE 4.1 8.7 - - - +
29B THR 4.0 4.9 - - - -
30B THR* 3.5 43.3 - - + +
33B LEU* 3.7 9.6 - - + -
49B LEU 3.1 8.7 + - - +
50B GLN* 3.8 11.0 - - - +
52B MET* 1.3 74.5 - - - +
54B ASN* 1.3 69.3 + - - +
56B VAL* 3.0 5.2 + - - +
57B ASP* 2.9 33.9 + - + +
62B GLY* 3.7 34.5 - - - +
63B THR* 4.1 7.4 - - - +
64B ILE* 3.7 25.1 - - + -
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Residues in contact with ASN 54 (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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50B GLN* 2.7 58.0 + - - +
51B ASP* 3.3 9.6 + - - +
53B ILE* 1.3 76.1 - - - +
55B GLU* 1.3 62.3 + - - +
56B VAL 3.1 1.2 + - - -
57B ASP* 3.4 19.9 + - - +
62B GLY* 5.3 1.7 - - - -
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Residues in contact with GLU 55 (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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51B ASP* 3.0 39.7 + - - +
52B MET* 3.7 9.6 - - - +
54B ASN* 1.3 75.7 - - - +
56B VAL* 1.3 58.2 + - + +
57B ASP 3.7 0.4 + - - -
75B ARG* 2.8 41.9 + - - +
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Residues in contact with VAL 56 (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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52B MET 3.8 11.0 - - - +
53B ILE 3.0 12.1 + - - +
55B GLU* 1.3 77.4 - - + +
57B ASP* 1.3 60.3 + - - +
58B ALA* 3.0 11.3 + - - +
64B ILE* 4.2 19.5 - - + -
68B GLU* 3.2 38.0 - - - +
71B THR* 3.7 22.3 - - + +
72B MET* 3.7 25.6 - - + +
75B ARG* 3.2 25.6 - - - +
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Residues in contact with ASP 57 (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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53B ILE* 2.9 21.1 + - + +
54B ASN* 3.4 16.4 + - - +
55B GLU 3.7 0.2 - - - -
56B VAL* 1.3 73.6 - - - +
58B ALA* 1.3 58.9 + - - +
59B ASP* 2.6 10.7 - - - +
60B GLY* 3.1 20.5 + - - -
61B ASN* 2.8 9.4 + - - +
62B GLY* 2.5 34.4 + - - -
63B THR 3.7 5.2 - - - +
64B ILE* 6.1 0.4 - - + -
68B GLU* 3.6 2.9 - - - -
1002B CA 2.0 34.5 - - - -
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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