Contacts of the helix formed by residues 16 - 28 (chain Z) in PDB entry 5JPQ
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 16 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14Z SER 3.4 0.8 + - - -
15Z GLN* 1.3 73.2 - - + +
17Z PHE* 1.3 64.9 + - - +
18Z ARG 3.4 2.9 - - - -
19Z LEU* 3.2 18.7 + - + -
20Z ARG* 2.9 24.2 + - + +
324Z ILE* 6.4 3.6 - - + -
325Z LEU* 6.6 0.2 - - - -
328Z ASP* 5.6 9.0 - - + -
84a ASP* 5.0 1.2 - - - +
85a LEU* 4.6 25.5 - - + +
86a GLU* 4.7 10.8 - - - +
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Residues in contact with PHE 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Z SER* 3.2 22.0 + - - +
15Z GLN 3.1 4.0 + - - -
16Z ASN* 1.3 74.6 - - - +
18Z ARG* 1.4 62.4 + - - +
20Z ARG* 3.4 5.0 + - - +
21Z ILE* 3.1 24.4 + - - +
49Z GLU* 5.5 10.8 - - + -
86a GLU* 5.2 6.3 - - + +
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Residues in contact with ARG 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z ASN 3.4 0.6 - - - -
17Z PHE* 1.4 77.6 - - - +
19Z LEU* 1.4 57.1 + - - +
21Z ILE* 3.4 5.6 + - - +
22Z VAL* 2.8 32.2 + - - +
98Z TYR 5.7 3.8 - - - +
102Z PRO* 4.3 22.9 - - + +
86a GLU* 6.0 4.2 - - - +
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Residues in contact with LEU 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z ASN* 3.2 22.0 + - + +
18Z ARG* 1.4 77.1 - - - +
20Z ARG* 1.4 53.4 + - - +
22Z VAL* 3.2 6.3 + - - +
23Z LEU* 2.8 37.4 + - - +
328Z ASP* 5.9 5.2 - - + -
85a LEU* 5.1 10.5 - - + -
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Residues in contact with ARG 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Z PHE* 5.4 12.6 - - + -
15Z GLN 5.4 1.8 - - - +
16Z ASN* 2.9 22.8 + - + +
17Z PHE* 3.9 5.4 - - - +
19Z LEU* 1.4 71.0 - - - +
21Z ILE* 1.4 57.1 + - - +
23Z LEU* 3.9 5.5 - - - +
24Z ALA* 3.0 28.6 + - - +
31Z ILE* 5.4 3.8 - - - +
328Z ASP* 6.0 7.6 - - + -
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Residues in contact with ILE 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z PHE 3.1 16.5 + - - +
18Z ARG* 3.9 5.2 - - - +
20Z ARG* 1.4 71.7 - - - +
22Z VAL* 1.4 59.4 + - - +
24Z ALA* 3.4 7.4 + - - +
25Z THR* 2.9 29.2 + - - -
56Z ILE* 6.0 6.7 - - + -
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Residues in contact with VAL 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Z ARG 2.8 19.6 + - - +
19Z LEU* 3.6 7.9 - - - +
21Z ILE* 1.4 75.9 - - - +
23Z LEU* 1.4 55.0 + - - +
25Z THR* 3.1 8.6 + - - -
26Z LEU* 2.9 30.3 + - - +
102Z PRO* 5.0 12.3 - - + +
105Z TYR* 4.6 20.9 - - + -
106Z LEU* 6.6 0.4 - - + -
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Residues in contact with LEU 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z LEU 2.8 20.5 + - - +
20Z ARG* 3.9 6.1 - - - +
22Z VAL* 1.4 68.6 - - - +
24Z ALA* 1.3 59.7 + - - +
26Z LEU* 3.9 6.1 - - - +
27Z SER* 3.0 32.3 + - - -
328Z ASP* 5.4 5.2 - - + +
329Z ILE* 5.9 3.4 - - - -
332Z ILE* 4.2 21.8 - - + +
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Residues in contact with ALA 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Z ARG 3.0 18.3 + - - +
21Z ILE* 3.6 8.3 - - - +
22Z VAL 3.3 0.2 - - - -
23Z LEU* 1.3 75.8 - - - +
25Z THR* 1.4 53.2 + - - +
27Z SER* 4.8 1.3 - - - -
28Z GLY* 2.8 31.9 + - - -
29Z LYS* 3.3 28.6 + - - +
31Z ILE* 4.4 16.8 - - + +
76Z TYR* 5.3 8.7 - - + +
78Z PRO* 3.8 7.3 - - + +
332Z ILE* 5.3 3.1 - - - +
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Residues in contact with THR 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Z ILE 2.9 13.9 + - - -
22Z VAL* 3.1 11.2 + - - -
24Z ALA* 1.4 78.1 - - - +
26Z LEU* 1.3 60.0 + - - +
28Z GLY* 3.6 7.6 + - - -
78Z PRO* 3.9 16.8 - - - +
79Z GLY 4.7 7.9 - - - +
81Z ILE* 6.0 1.0 + - - +
106Z LEU* 6.1 5.4 - - - -
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Residues in contact with LEU 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Z VAL 2.9 14.8 + - - +
23Z LEU* 4.0 7.0 - - - +
25Z THR* 1.3 76.8 - - - +
27Z SER* 1.3 59.2 + - - +
28Z GLY 3.8 0.2 + - - -
105Z TYR 5.6 5.8 - - - +
303Z ILE* 5.6 10.3 - - + -
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Residues in contact with SER 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Z LEU 3.0 18.3 + - - -
24Z ALA* 4.1 1.1 - - - -
26Z LEU* 1.3 75.7 - - - +
28Z GLY* 1.3 60.1 + - - +
29Z LYS* 3.2 20.0 + - - +
332Z ILE* 4.8 16.6 - - - -
333Z PHE* 5.6 4.7 - - - -
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Residues in contact with GLY 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z ALA 2.8 10.6 + - - -
25Z THR 3.6 6.0 + - - -
26Z LEU 3.4 3.0 - - - -
27Z SER* 1.3 77.2 - - - +
29Z LYS* 1.3 59.1 + - - +
30Z PRO 3.9 1.7 - - - -
78Z PRO* 4.6 17.6 - - - +
79Z GLY 6.0 0.7 - - - -
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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