Contacts of the helix formed by residues 40 - 51 (chain B) in PDB entry 1PR9
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 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LYS* 4.6 3.1 + - - +
38B SER* 3.5 1.7 + - - -
39B ARG* 1.3 88.4 + - - +
41B GLN* 1.3 65.1 + - - +
42B ALA* 3.9 14.8 - - + +
43B ASP* 3.0 36.7 + - - +
44B LEU* 3.5 8.0 + - - +
58B CYS* 4.2 1.3 - - - -
1245B NAP 2.6 25.0 + - - -
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Residues in contact with GLN 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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40B THR* 1.3 72.6 - - - +
42B ALA* 1.3 59.6 + - - +
44B LEU* 3.1 17.9 + - - +
45B ASP* 2.6 61.1 + - - +
56B PRO* 5.1 7.1 - - - +
58B CYS* 3.6 35.8 - - - +
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Residues in contact with ALA 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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40B THR* 3.2 10.3 + - + +
41B GLN* 1.3 78.9 - - - +
43B ASP* 1.3 63.4 + - - +
45B ASP* 3.7 11.3 - - - +
46B SER* 3.2 23.0 + - - -
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Residues in contact with ASP 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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16B GLY* 3.5 32.6 - - - +
17B LYS* 2.6 38.9 + - - +
21B ARG* 3.3 10.2 + - - +
38B SER* 5.0 0.8 + - - +
40B THR* 3.0 26.9 + - - +
42B ALA* 1.3 78.0 - - - +
44B LEU* 1.3 64.2 + - + +
46B SER* 3.0 18.5 + - - -
47B LEU* 3.1 9.2 + - - +
1245B NAP 3.8 2.3 + - - -
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Residues in contact with LEU 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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16B GLY 5.1 3.8 - - - +
36B ALA* 3.6 32.8 - - + +
38B SER* 3.9 25.8 - - - +
40B THR 4.0 8.7 - - - +
41B GLN* 3.1 17.6 + - - +
43B ASP* 1.3 74.9 - - - +
45B ASP* 1.3 68.2 + - - +
47B LEU* 3.2 7.8 + - + +
48B VAL* 2.9 28.2 + - - +
54B ILE* 5.9 0.9 - - + -
56B PRO* 3.9 14.1 - - + -
57B VAL 3.6 16.2 - - - +
58B CYS* 3.5 36.1 - - + +
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Residues in contact with ASP 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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41B GLN* 2.6 53.1 + - - +
42B ALA* 3.7 9.3 - - - +
43B ASP 3.2 0.2 - - - -
44B LEU* 1.3 78.3 - - - +
46B SER* 1.3 62.8 + - - +
48B VAL* 3.1 25.8 - - + +
49B ARG* 3.2 14.8 + - - +
56B PRO* 5.9 0.9 - - - +
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Residues in contact with SER 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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21B ARG* 3.3 18.6 + - - -
42B ALA 3.2 13.1 + - - -
43B ASP* 3.0 16.5 + - - -
45B ASP* 1.3 77.3 - - - +
47B LEU* 1.3 58.0 + - - +
49B ARG* 3.0 20.6 + - - +
50B GLU* 2.9 35.7 + - - +
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Residues in contact with LEU 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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15B ALA* 3.2 33.0 - - + +
16B GLY* 4.7 0.9 - - - -
21B ARG* 3.7 32.8 - - + +
24B VAL* 4.3 22.4 - - + -
25B GLN* 4.5 4.5 - - + -
36B ALA* 4.6 3.1 - - + -
43B ASP 3.1 16.2 + - - +
44B LEU* 3.7 8.3 - - + +
46B SER* 1.3 79.6 + - - +
48B VAL* 1.3 57.2 + - - +
50B GLU* 4.4 5.2 - - - +
51B CYS* 2.7 54.6 + - - +
54B ILE* 3.8 16.4 - - + -
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Residues in contact with VAL 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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44B LEU 2.9 18.3 + - - +
45B ASP* 3.1 24.2 - - - +
47B LEU* 1.3 74.8 - - - +
49B ARG* 1.3 68.0 + - + +
51B CYS 4.0 6.7 - - - -
52B PRO* 3.7 20.3 - - + +
53B GLY 6.0 0.7 - - - +
54B ILE* 3.6 24.5 - - + +
56B PRO* 3.6 32.3 - - + -
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Residues in contact with ARG 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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45B ASP* 3.2 16.8 + - - +
46B SER* 3.0 19.8 + - - +
48B VAL* 1.3 83.3 - - + +
50B GLU* 1.3 69.8 + - - +
52B PRO* 4.1 6.8 - - - +
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Residues in contact with GLU 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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21B ARG* 3.1 26.3 + - - +
25B GLN* 3.5 20.3 + - - +
28B HIS* 4.9 1.2 - - - -
46B SER* 2.9 18.6 + - - +
47B LEU* 4.0 4.2 - - - +
49B ARG* 1.3 88.7 + - - +
51B CYS* 1.3 66.9 + - - +
52B PRO* 3.2 9.6 - - - +
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Residues in contact with CYS 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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24B VAL* 4.9 0.9 - - + -
25B GLN* 4.0 27.4 - - - -
28B HIS* 3.7 22.2 - - + +
47B LEU* 2.7 36.7 + - + +
48B VAL* 3.8 4.5 - - - +
50B GLU* 1.3 81.8 - - - +
52B PRO* 1.3 68.0 - - - +
53B GLY 3.4 0.2 + - - -
54B ILE* 3.3 36.0 + - + +
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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