Contacts of the helix formed by residues 15 - 32 (chain F) in PDB entry 6P59
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 15 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F VAL* 1.3 77.3 - - - +
16F ARG* 1.3 87.6 + - - +
17F ARG* 3.2 23.8 + - + +
18F LYS* 2.9 30.4 + - + +
19F ILE 3.6 3.1 + - - -
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Residues in contact with ARG 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F VAL 3.6 2.4 + - - -
15F ASP* 1.3 80.9 + - - +
17F ARG* 1.3 76.0 + - - +
19F ILE* 3.1 17.0 + - + +
20F GLU* 2.1 50.2 + - + +
86F TYR* 3.6 58.2 - - + -
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Residues in contact with ARG 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASP* 3.1 20.0 + - + +
16F ARG* 1.3 92.5 - - - +
18F LYS* 1.3 62.2 + - + +
20F GLU* 2.9 36.0 + - - +
21F GLN* 3.3 59.4 + - - +
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Residues in contact with LYS 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F VAL* 4.6 1.1 - - + -
15F ASP* 2.9 24.1 + - + +
17F ARG* 1.3 80.0 - - + +
19F ILE* 1.3 60.7 + - - +
21F GLN* 3.2 14.7 + - - +
22F TRP* 2.9 27.5 + - - +
214F TYR* 3.4 58.9 + - + +
215F LEU* 3.9 20.2 - - + +
217F GLY 3.8 15.1 + - - -
218F THR* 5.5 1.4 - - - +
219F LEU* 5.1 4.4 - - - +
220F ALA 4.1 17.6 + - - +
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Residues in contact with ILE 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F VAL* 3.7 22.9 - - + -
15F ASP 4.2 3.1 - - - +
16F ARG* 3.1 8.8 + - + +
18F LYS* 1.3 73.3 - - - +
20F GLU* 1.3 61.0 + - + +
22F TRP* 3.2 1.7 + - + +
23F HIS* 2.9 62.1 + - + +
55F HIS* 4.9 12.8 - - + +
72F THR* 4.4 16.4 - - + -
73F TYR 4.5 0.4 - - - +
86F TYR* 3.7 36.6 - - + -
87F GLY 4.2 13.0 - - - +
88F ALA* 5.7 0.2 - - + -
215F LEU* 4.0 13.7 - - + -
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Residues in contact with GLU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ARG* 2.1 58.2 + - + +
17F ARG* 2.9 37.7 + - - +
19F ILE* 1.3 76.3 - - + +
21F GLN* 1.3 62.0 + - - +
23F HIS* 3.6 4.7 + - - +
24F SER* 3.1 26.7 + - - -
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Residues in contact with GLN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ARG* 3.3 46.1 + - - +
18F LYS* 3.2 14.7 + - - +
20F GLU* 1.3 76.5 - - - +
22F TRP* 1.3 60.1 + - - +
24F SER* 3.1 19.8 + - - -
25F LEU* 3.4 19.4 + - + +
214F TYR* 2.4 43.5 + - + -
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Residues in contact with TRP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F LYS 2.9 15.4 + - - +
19F ILE* 3.2 3.1 + - + +
21F GLN* 1.3 75.6 - - - +
23F HIS* 1.3 88.1 + + - +
25F LEU* 3.0 9.4 + - + +
26F VAL* 3.0 35.5 + - + +
40F TRP* 4.8 5.8 - + - -
58F VAL* 3.5 41.7 - - + -
60F ILE* 5.0 2.5 - - + -
70F VAL* 3.5 29.4 - - + -
72F THR* 4.8 4.5 - - + -
210F PRO* 3.6 23.5 - - + +
211F SER 3.8 24.3 - - - +
212F LEU* 3.6 27.2 - - + +
214F TYR* 5.7 5.1 - + + -
215F LEU* 3.7 26.0 - - + -
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Residues in contact with HIS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ILE* 2.9 47.7 + - + +
20F GLU* 4.1 4.3 - - - +
22F TRP* 1.3 93.2 - + - +
24F SER* 1.3 63.5 + - - +
26F VAL* 3.2 6.3 + - + +
27F LYS* 3.0 32.4 + - + +
42F TYR* 3.2 36.8 - + - -
55F HIS* 4.7 6.8 + + - -
56F SER* 2.7 30.1 + - - -
58F VAL* 4.6 4.3 - - + +
72F THR* 3.9 11.9 - - + -
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Residues in contact with SER 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F GLU 3.1 16.2 + - - -
21F GLN* 3.1 15.4 + - - -
23F HIS* 1.3 75.9 - - - +
25F LEU* 1.3 63.7 + - - +
27F LYS* 4.1 4.6 - - - +
28F TYR* 3.2 28.1 + - - +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLN* 3.4 16.4 + - + +
22F TRP* 3.0 11.7 + - + +
24F SER* 1.3 83.5 + - - +
26F VAL* 1.3 64.5 + - - +
28F TYR* 3.5 3.1 + - + +
29F HIS* 3.2 31.2 + - - +
207F VAL* 4.1 16.8 - - + -
208F HIS* 3.4 33.9 - - + +
209F PHE 3.7 22.4 - - - +
210F PRO* 4.2 15.7 - - + -
211F SER 5.3 0.2 - - - +
214F TYR* 6.0 2.5 - - + -
302F GOL 4.1 10.8 - - - +
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Residues in contact with VAL 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F TRP* 3.0 37.0 + - + +
23F HIS* 3.8 7.2 - - + +
25F LEU* 1.3 74.4 - - - +
27F LYS* 1.3 67.4 + - + +
28F TYR 3.3 0.2 + - - -
29F HIS* 3.3 4.1 + - - +
30F MET* 3.1 38.7 + - - +
37F ALA* 4.6 2.0 - - - +
40F TRP* 3.7 29.2 - - + -
41F GLU 5.9 0.2 - - - +
42F TYR* 5.3 6.5 - - + -
58F VAL* 4.4 17.9 - - + -
210F PRO* 3.7 24.5 - - + -
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Residues in contact with LYS 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F HIS* 3.0 22.6 + - + +
24F SER* 4.3 4.5 - - - +
26F VAL* 1.3 76.0 - - + +
28F TYR* 1.3 63.1 + - - +
30F MET* 3.4 20.9 - - - +
31F TYR* 3.4 47.2 + - + +
32F LYS* 5.6 0.2 - - - +
42F TYR* 4.0 41.8 - - + +
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F SER 3.2 20.3 + - - +
25F LEU* 3.8 5.4 - - + +
26F VAL 3.2 0.2 - - - -
27F LYS* 1.3 78.4 - - - +
29F HIS* 1.3 83.3 + + - +
32F LYS* 3.2 24.6 + - + +
33F GLY* 2.9 55.8 + - - -
34F LYS 4.9 0.8 + - - -
207F VAL* 3.6 41.3 - - + +
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Residues in contact with HIS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 3.2 25.0 + - - +
26F VAL 3.3 0.8 + - - +
28F TYR* 1.3 105.1 - + - +
30F MET* 1.3 56.9 + - - +
33F GLY* 4.8 3.8 - - - +
34F LYS 5.4 0.6 + - - -
35F LYS* 3.2 6.0 - - - -
36F GLU* 3.0 28.5 + - + +
37F ALA* 2.8 41.8 + - + +
119F PHE* 5.3 0.7 - - + -
205F SER* 5.7 0.9 - - - -
207F VAL* 4.1 7.4 - - + +
208F HIS 2.8 24.7 + - - -
209F PHE* 3.8 24.0 - + - -
210F PRO* 3.6 22.2 - - + -
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Residues in contact with MET 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F VAL* 3.1 37.0 + - - +
27F LYS* 3.4 24.9 - - - +
29F HIS* 1.3 79.7 - - - +
31F TYR* 1.3 98.0 + - + +
35F LYS* 4.2 7.4 - - - +
37F ALA 3.2 21.1 - - - +
38F ARG* 3.8 23.6 - - - +
40F TRP* 3.4 31.0 - - - +
41F GLU* 4.3 0.4 - - - -
42F TYR* 4.1 19.3 - - + +
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Residues in contact with TYR 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F LYS* 3.4 47.4 + - - +
28F TYR 3.5 0.6 + - - -
30F MET* 1.3 120.1 - - + +
32F LYS* 1.3 77.8 + - + +
33F GLY 3.7 1.1 - - - -
35F LYS* 3.9 21.8 - - - -
38F ARG 5.8 2.0 - - - -
42F TYR* 5.9 0.9 - - - +
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Residues in contact with LYS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG 4.2 16.2 + - - -
91A GLU* 4.8 18.8 - - + +
92A ALA 5.8 0.2 - - - +
27F LYS 4.4 0.4 + - - +
28F TYR* 3.2 25.2 + - + +
31F TYR* 1.3 89.5 + - + +
33F GLY* 1.3 68.7 + - - +
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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