Contacts of the helix formed by residues 17 - 32 (chain A) in PDB entry 5DPT
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 PRO 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ASP 4.4 3.6 - - - +
16A HIS* 1.4 91.7 - - + +
18A PHE* 1.3 56.6 + - - +
19A GLU* 3.1 8.3 - - + +
20A TYR* 2.5 42.7 + - + +
21A ARG* 2.8 8.5 + - - +
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 1.3 70.9 - - - +
19A GLU* 1.3 60.3 + - - +
21A ARG* 3.4 20.1 - - + +
22A LYS* 2.8 42.2 + - + +
108A GLU* 3.9 36.1 - - + -
109A ASP* 3.9 22.2 - - + -
74B ARG* 4.5 11.9 - - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO* 2.9 7.2 + - + +
18A PHE* 1.3 82.8 - - + +
20A TYR* 1.3 58.1 + - - +
22A LYS* 4.1 4.3 - - - +
23A LYS* 3.6 19.6 + - - +
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A HIS* 4.2 7.9 - - + +
17A PRO* 2.5 38.3 + - + +
19A GLU* 1.3 72.3 - - - +
21A ARG* 1.3 66.0 + - - +
22A LYS 3.2 1.1 + - - -
23A LYS* 3.4 12.7 + - - +
24A GLU* 3.4 24.7 - - - +
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 2.4 31.8 + - + -
13A LYS* 2.9 42.5 + - - +
14A GLU 3.1 4.6 + - - +
15A ASP 3.3 1.0 - - - +
16A HIS* 2.8 61.1 + - + +
17A PRO* 2.8 13.1 + - - +
18A PHE* 3.4 29.5 - - + +
20A TYR* 1.3 72.9 - - - +
22A LYS* 1.3 66.2 + - - +
24A GLU* 3.7 2.6 + - - +
25A GLY 3.4 4.9 + - - -
109A ASP* 3.7 18.1 - - + +
111A PHE* 3.3 26.3 - - + -
113A TYR* 3.9 17.5 - - - -
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 2.8 32.7 + - + +
19A GLU* 4.1 6.3 - - - +
21A ARG* 1.3 75.9 - - - +
23A LYS* 1.3 54.8 + - - +
25A GLY* 2.7 26.0 + - - -
26A GLU* 2.8 25.9 - - - +
108A GLU 5.1 1.3 - - - +
109A ASP* 3.8 20.9 - - + +
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 3.6 13.9 + - - +
20A TYR* 3.4 11.8 + - - +
21A ARG 3.3 0.4 - - - -
22A LYS* 1.3 78.7 - - - +
24A GLU* 1.3 63.2 + - + +
25A GLY 3.2 0.9 + - - -
26A GLU* 3.2 16.6 - - - +
27A LYS* 3.3 20.5 + - - +
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Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 3.8 20.6 + - - -
16A HIS* 5.3 9.9 + - - -
20A TYR* 3.4 22.0 - - - +
21A ARG* 4.4 3.0 - - - +
22A LYS 3.3 0.4 - - - -
23A LYS* 1.3 75.7 - - + +
25A GLY* 1.3 59.1 + - - +
27A LYS* 3.7 8.5 - - - +
28A ILE* 3.1 35.9 + - + +
55A LYS* 4.3 13.7 + - - -
111A PHE* 4.3 9.7 - - + -
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG 3.4 3.8 + - - -
22A LYS 2.7 17.1 + - - -
24A GLU* 1.3 73.3 - - - +
26A GLU* 1.3 60.3 + - - -
27A LYS 3.3 0.7 + - - -
28A ILE* 3.3 12.0 + - - +
29A ARG* 3.4 18.0 + - - +
37A PRO* 5.1 0.3 - - - +
109A ASP 3.6 17.7 - - - -
110A TYR* 4.1 9.6 - - - +
111A PHE* 4.0 14.8 - - - -
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 2.8 43.7 - - - +
23A LYS* 3.2 15.1 + - - +
25A GLY* 1.3 71.3 - - - +
27A LYS* 1.3 64.6 + - - +
28A ILE 3.3 0.2 - - - -
29A ARG* 3.9 6.6 + - - +
30A LYS* 3.6 21.3 + - - +
110A TYR* 4.1 28.8 - - + +
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS 3.3 16.8 + - - +
24A GLU* 3.7 10.8 - - - +
25A GLY 3.1 0.8 - - - -
26A GLU* 1.3 80.2 - - - +
28A ILE* 1.3 64.2 + - + +
30A LYS* 3.7 4.5 + - - +
31A LYS* 3.3 22.0 + - - +
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLU* 3.1 22.3 + - + +
25A GLY* 3.8 5.2 - - - +
26A GLU 3.3 0.2 - - - -
27A LYS* 1.3 77.2 - - + +
29A ARG* 1.3 54.8 + - - +
30A LYS 3.0 4.7 - - - -
31A LYS* 2.8 6.1 + - + -
32A TYR* 2.5 59.6 + - + +
35A ARG 5.6 0.9 - - - +
37A PRO* 4.4 21.8 - - + -
57A LEU* 3.6 33.9 - - + -
111A PHE* 5.3 3.6 - - + -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 3.4 17.4 + - - +
26A GLU* 3.9 5.4 + - - +
27A LYS 3.5 0.4 - - - -
28A ILE* 1.3 74.5 - - - +
30A LYS* 1.3 59.1 + - - +
32A TYR 3.8 5.4 - - - -
33A PRO* 3.6 43.3 + - - +
34A ASP 5.2 0.2 - - - -
35A ARG 2.8 28.9 + - - +
36A VAL* 4.0 8.8 - - - +
37A PRO* 4.0 15.0 - - + +
60A SER* 5.8 1.4 - - - -
102A TYR* 3.2 44.2 - - - +
110A TYR* 4.3 15.9 - - + -
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Residues in contact with LYS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU 3.6 16.3 + - - +
27A LYS* 4.0 4.7 - - - +
28A ILE 3.0 0.6 - - - -
29A ARG* 1.3 77.1 - - - +
31A LYS* 1.3 64.5 + - - +
32A TYR 3.4 0.2 - - - -
33A PRO* 4.4 6.3 - - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS 3.3 16.1 + - - +
28A ILE* 2.8 7.0 + - + +
30A LYS* 1.3 80.5 - - - +
32A TYR* 1.3 89.0 + - + +
33A PRO* 3.8 5.2 - - - +
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 2.5 46.8 + - + +
29A ARG* 3.8 8.2 - - - +
31A LYS* 1.3 100.6 - - + +
33A PRO* 1.3 63.7 - - - +
34A ASP* 3.3 13.9 - - - +
35A ARG* 3.3 33.8 - - + +
57A LEU* 3.9 25.1 - - + -
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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