Contacts of the helix formed by residues 21 - 33 (chain B) in PDB entry 1PR1
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 ASP 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B PRO* 3.3 4.4 - - - +
20B GLY* 1.3 77.0 - - - +
22B PRO* 1.3 66.8 - - - +
23B LEU* 2.9 35.1 + - - +
24B ARG* 2.7 54.2 + - + +
25B ALA 3.3 4.2 + - - -
61B GLY* 4.4 2.0 - - - -
249B PO4 4.0 5.5 + - - +
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Residues in contact with PRO 22 (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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20B GLY 3.7 8.0 - - - +
21B ASP* 1.3 89.4 - - - +
23B LEU* 1.3 67.7 + - + +
25B ALA* 3.2 17.3 + - - +
26B LYS 3.5 4.5 + - - -
44B GLY 3.3 27.1 - - - +
45B MET* 4.1 16.6 - - + -
46B LEU* 3.9 23.2 - - + +
61B GLY* 4.3 13.0 - - - +
63B GLY* 5.7 0.4 - - - -
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Residues in contact with LEU 23 (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 ASP* 2.9 21.2 + - - +
22B PRO* 1.3 82.1 - - + +
24B ARG* 1.3 61.5 + - - +
26B LYS* 3.7 13.3 + - + +
27B TYR* 3.3 19.6 + - - +
46B LEU* 4.6 14.8 - - + -
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Residues in contact with ARG 24 (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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19B PRO* 3.8 18.2 - - + -
21B ASP* 2.7 40.3 + - + +
23B LEU* 1.3 74.4 - - - +
25B ALA* 1.3 57.8 + - - +
27B TYR* 3.2 40.5 + - - +
28B ILE* 2.9 33.5 + - + +
218B GLN* 6.2 3.0 - - - +
221B PHE* 3.7 38.0 - - + -
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Residues in contact with ALA 25 (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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19B PRO* 3.7 9.6 - - + +
21B ASP 3.3 2.2 + - - -
22B PRO 3.2 10.5 + - - +
24B ARG* 1.3 77.7 - - - +
26B LYS* 1.3 60.7 + - - +
28B ILE* 3.7 2.3 - - - +
29B ALA* 2.9 29.1 + - - +
46B LEU 3.7 11.0 - - - +
48B PHE* 3.8 4.9 - - + -
59B VAL* 4.0 14.8 - - - +
60B MET* 3.8 10.8 - - - +
61B GLY 3.7 26.0 - - - +
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Residues in contact with LYS 26 (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 PRO 3.5 6.7 + - - +
23B LEU* 3.9 14.1 - - + +
24B ARG 3.3 0.2 - - - -
25B ALA* 1.3 76.4 - - - +
27B TYR* 1.3 61.5 + - - +
29B ALA* 3.6 1.1 - - - +
30B GLU* 2.9 58.0 + - - +
38B GLU* 5.3 3.2 + - - -
46B LEU* 4.2 17.3 - - + -
48B PHE* 3.4 34.4 - - + -
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Residues in contact with TYR 27 (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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23B LEU 3.3 11.9 + - - +
24B ARG* 3.2 43.9 + - - +
26B LYS* 1.3 80.5 - - - +
28B ILE* 1.3 60.7 + - + +
30B GLU* 3.8 2.7 - - - +
31B THR* 2.7 59.1 + - + +
32B PHE* 4.8 5.8 - + - -
218B GLN* 5.1 7.1 + - - +
221B PHE* 3.8 19.5 - + - -
222B ASN* 2.7 37.7 + - - -
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Residues in contact with ILE 28 (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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17B LEU* 4.8 6.1 - - + -
19B PRO* 4.1 11.4 - - + -
24B ARG 2.9 19.5 + - - +
25B ALA 3.7 4.7 - - - +
26B LYS 3.3 0.2 - - - -
27B TYR* 1.3 86.4 - - + +
29B ALA* 1.3 67.5 + - - +
32B PHE* 2.9 32.8 + - + +
33B LEU* 3.8 3.4 + - + +
59B VAL* 3.8 35.2 - - + -
88B VAL* 4.1 13.5 - - + -
221B PHE* 4.9 4.3 - - + -
225B ILE* 3.6 48.7 - - + -
229B LEU* 5.4 2.0 - - + -
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Residues in contact with ALA 29 (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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25B ALA 2.9 17.3 + - - +
26B LYS 3.6 4.9 - - - +
28B ILE* 1.3 77.0 - - - +
30B GLU* 1.3 59.8 + - + +
33B LEU* 3.1 47.7 + - + +
36B ALA* 4.3 13.5 - - + +
48B PHE* 3.7 36.1 - - + -
59B VAL* 4.8 1.5 - - + +
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Residues in contact with GLU 30 (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 LYS* 2.9 55.8 + - - +
27B TYR* 4.2 3.8 - - - +
29B ALA* 1.3 78.2 - - + +
31B THR* 1.3 60.6 + - - +
33B LEU 4.8 3.8 - - - +
36B ALA* 5.9 2.0 - - + -
48B PHE* 5.7 0.9 - - - -
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Residues in contact with THR 31 (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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27B TYR* 2.7 46.6 + - - +
28B ILE 3.2 0.2 + - - -
30B GLU* 1.3 80.8 - - - +
32B PHE* 1.3 91.2 + - + +
33B LEU 5.2 0.4 - - - -
222B ASN* 5.0 4.7 - - - +
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Residues in contact with PHE 32 (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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27B TYR* 4.8 4.9 - + - -
28B ILE* 2.9 19.5 + - + +
31B THR* 1.3 100.8 - - + +
33B LEU* 1.3 65.3 + - + +
34B GLU* 4.2 3.4 + - - +
51B THR 4.2 2.4 - - - +
52B TYR* 3.5 26.4 - + + -
222B ASN* 3.8 37.9 - - + -
225B ILE* 3.7 26.5 - - + -
226B LYS* 3.4 28.3 - - + -
229B LEU* 3.4 28.3 - - + -
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Residues in contact with LEU 33 (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* 4.3 4.0 - - + +
29B ALA* 3.1 33.9 + - + +
30B GLU* 4.8 4.9 - - - +
31B THR 5.2 0.2 - - - -
32B PHE* 1.3 86.6 - - + +
34B GLU* 1.3 64.2 - - - +
35B ASP 4.4 0.3 + - - -
36B ALA* 4.5 6.4 - - + +
48B PHE 5.0 1.8 - - - +
49B THR 4.7 2.2 - - - -
50B GLY* 4.0 11.9 - - - +
51B THR 3.4 11.2 - - - +
52B TYR* 3.9 22.7 - - + -
57B ILE* 3.7 34.1 - - + +
59B VAL* 3.6 28.7 - - + -
229B LEU* 4.4 9.4 - - + -
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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