Contacts of the helix formed by residues 21 - 33 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C PRO* 3.3 7.5 - - - +
20C GLY* 1.3 77.1 - - - +
22C PRO* 1.3 73.3 - - - +
23C LEU* 2.8 33.7 + - - +
24C ARG* 3.0 38.4 + - + +
25C ALA 3.2 8.1 + - - -
61C GLY* 4.6 1.3 - - - -
215C ALA 5.7 0.2 - - - -
216C GLU* 4.1 17.8 - - - +
250C PO4 4.2 3.7 + - - +
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Residues in contact with PRO 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLY 3.6 6.5 - - - +
21C ASP* 1.3 92.5 - - - +
23C LEU* 1.3 60.2 + - + +
25C ALA* 3.2 10.8 + - + +
26C LYS* 3.1 24.1 + - - +
44C GLY 3.3 24.0 - - - +
45C MET* 3.6 26.0 - - + -
46C LEU* 3.7 21.1 - - + +
61C GLY* 4.5 6.3 - - - -
63C GLY* 5.8 0.2 - - - -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ASP* 2.8 18.6 + - - +
22C PRO* 1.3 74.8 - - + +
24C ARG* 1.3 60.1 + - - +
26C LYS* 3.4 18.5 + - + +
27C TYR* 3.0 25.3 + - - +
46C LEU* 4.8 13.0 - - + -
216C GLU* 3.2 37.4 - - - +
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Residues in contact with ARG 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 3.4 18.1 - - + +
20C GLY 4.5 0.7 - - - -
21C ASP* 3.0 33.2 + - + +
23C LEU* 1.3 75.7 - - - +
25C ALA* 1.3 61.0 + - - +
27C TYR* 3.2 7.7 + - + +
28C ILE* 2.8 44.9 + - + +
88C VAL 2.7 21.8 + - - -
89C GLY* 3.1 10.3 - - - -
90C SER* 4.8 0.8 + - - -
215C ALA* 3.0 36.8 + - - +
216C GLU* 4.0 14.8 - - - +
221C PHE* 4.7 11.0 - - - -
224C MET* 4.1 12.1 - - - +
225C ILE* 5.6 1.3 - - + -
250C PO4 2.4 43.8 + - - -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PRO* 3.8 7.1 - - + +
21C ASP 3.2 2.8 + - - -
22C PRO 3.2 11.6 + - - +
24C ARG* 1.3 78.5 - - - +
26C LYS* 1.3 59.1 + - - +
28C ILE* 3.3 0.9 + - - +
29C ALA* 3.0 29.5 + - - +
46C LEU 3.9 9.9 - - - +
48C PHE* 3.8 3.5 - - + -
59C VAL* 3.6 31.3 - - + +
60C MET* 4.0 1.8 - - - +
61C GLY 3.9 24.2 - - - +
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Residues in contact with LYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO 3.1 11.9 + - - +
23C LEU* 3.5 24.7 - - + +
25C ALA* 1.3 77.4 - - - +
27C TYR* 1.3 62.4 + - - +
29C ALA* 3.3 2.6 + - - +
30C GLU* 3.0 53.5 + - + +
38C GLU* 5.4 4.0 + - - -
46C LEU* 5.1 8.4 - - + +
48C PHE* 3.4 30.8 - - + -
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Residues in contact with TYR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C LEU 3.0 14.5 + - - +
24C ARG* 3.2 11.9 + - + +
26C LYS* 1.3 78.2 - - - +
28C ILE* 1.3 64.8 + - + +
30C GLU* 3.4 10.4 + - - -
31C THR* 2.9 64.6 + - - +
32C PHE* 4.2 8.7 - + - -
216C GLU* 3.6 20.4 - - + +
217C ARG* 3.4 33.3 - - + +
218C GLN 4.9 0.4 + - - -
221C PHE* 5.7 2.0 - - + -
222C ASN* 2.7 37.0 + - - -
225C ILE* 5.6 3.1 - - + -
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.9 8.5 - - + -
19C PRO* 4.3 2.7 - - + -
24C ARG* 2.8 38.0 + - + +
25C ALA* 3.7 4.7 - - - +
26C LYS 3.3 0.2 - - - -
27C TYR* 1.3 83.7 - - + +
29C ALA* 1.3 62.3 + - - +
32C PHE* 2.8 36.5 + - + +
33C LEU* 3.5 6.3 + - + +
59C VAL* 3.8 29.2 - - + -
88C VAL* 4.2 13.5 - - + -
225C ILE* 3.5 49.6 - - + -
229C LEU* 5.2 2.0 - - + -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA 3.0 17.0 + - - +
26C LYS 3.6 4.3 - - - +
28C ILE* 1.3 76.9 - - - +
30C GLU* 1.3 59.9 + - + +
33C LEU* 3.1 40.3 + - + +
36C ALA* 3.7 16.1 - - + +
48C PHE* 3.6 37.2 - - + -
59C VAL* 4.0 3.3 - - + +
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Residues in contact with GLU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 3.0 51.1 + - + +
27C TYR* 3.8 10.9 - - + +
29C ALA* 1.3 80.3 - - + +
31C THR* 1.3 61.6 + - - +
33C LEU 5.0 2.1 - - - +
36C ALA* 5.7 0.2 - - - -
48C PHE* 6.4 0.9 - - + -
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Residues in contact with THR 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 2.9 48.1 + - + +
30C GLU* 1.3 80.4 - - - +
32C PHE* 1.3 86.7 + - + +
222C ASN* 4.7 0.7 - - - +
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 4.2 7.2 - + - -
28C ILE* 2.8 27.6 + - + +
31C THR* 1.3 104.0 - - + +
33C LEU* 1.3 61.4 + - + +
34C GLU* 3.0 19.1 - - - +
51C THR 4.0 0.2 - - - +
52C TYR* 3.7 21.9 - + - -
222C ASN* 3.4 31.4 - - + -
225C ILE* 3.8 31.4 - - + -
226C LYS* 4.1 24.7 - - + -
229C LEU* 3.8 26.7 - - + -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.5 5.1 + - + +
29C ALA* 3.1 30.8 + - + +
30C GLU 5.0 2.4 - - - +
32C PHE* 1.3 85.2 + - + +
34C GLU* 1.3 62.4 + - - +
35C ASP 3.7 2.3 + - - -
36C ALA* 4.0 12.9 + - + +
48C PHE 4.6 0.9 - - - +
49C THR 4.4 2.2 - - - -
50C GLY* 3.6 13.7 - - - +
51C THR 3.4 7.0 - - - +
52C TYR* 4.1 7.4 - - + -
57C ILE* 3.3 51.1 - - + +
58C SER* 4.6 2.5 - - - -
59C VAL* 4.2 22.7 - - + -
229C LEU* 4.5 10.8 - - + -
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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