Contacts of the helix formed by residues 14 - 36 (chain F) in PDB entry 3PUY
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 ALA 14 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F SER* 3.3 4.6 - - - -
13F ASP* 1.3 74.8 - - - +
15F LEU* 1.3 63.4 + - - +
16F LYS 3.2 2.9 + - - -
17F TRP* 3.5 13.0 + - + +
18F SER* 3.5 22.3 + - - -
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLN* 3.8 31.9 - - + -
12F SER* 3.3 33.7 + - - +
13F ASP 3.2 0.8 - - - -
14F ALA* 1.3 77.9 - - - +
16F LYS* 1.3 60.3 + - - +
18F SER* 3.7 9.3 + - - -
19F VAL* 3.3 32.0 + - + +
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Residues in contact with LYS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F SER 4.3 2.9 + - - +
13F ASP* 3.9 11.4 + - - +
14F ALA 3.2 0.6 - - - -
15F LEU* 1.3 77.4 - - - +
17F TRP* 1.3 66.5 + - + +
19F VAL* 3.3 8.2 + - + +
20F LEU* 2.9 34.8 + - + +
57F PHE* 3.4 33.6 + - - -
58F ALA 4.1 6.4 + - - -
60F ARG* 3.1 41.6 - - - +
66F ARG* 3.9 6.2 - - - +
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Residues in contact with TRP 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ASP 4.3 15.0 - - - -
14F ALA* 3.5 10.6 + - - +
15F LEU 3.5 0.2 - - - -
16F LYS* 1.3 82.6 - - + +
18F SER* 1.3 59.4 + - - +
20F LEU* 3.7 33.7 - - + +
21F GLY* 2.9 23.9 + - - -
58F ALA* 5.5 14.6 - - + -
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Residues in contact with SER 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ALA 3.5 12.4 + - - -
15F LEU* 3.9 13.8 - - - -
16F LYS 3.3 0.4 - - - -
17F TRP* 1.3 75.4 - - - +
19F VAL* 1.3 62.2 + - - +
21F GLY* 5.0 0.7 - - - -
22F LEU* 3.1 42.1 + - - +
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Residues in contact with VAL 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU* 3.3 20.6 + - + +
16F LYS* 3.3 12.0 + - + +
18F SER* 1.3 77.7 - - - +
20F LEU* 1.3 57.9 + - - +
22F LEU* 3.6 4.7 + - - +
23F LEU* 3.1 43.9 + - + +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LYS* 2.9 22.8 + - + +
17F TRP* 3.7 40.4 - - + +
18F SER 3.3 0.2 - - - -
19F VAL* 1.3 78.1 - - - +
21F GLY* 1.3 57.7 + - - +
23F LEU* 3.7 8.0 + - + +
24F GLY* 2.9 23.7 + - - -
54F LEU* 4.2 38.7 - - + +
57F PHE* 4.7 12.6 - - + +
58F ALA* 4.5 21.3 - - + -
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Residues in contact with GLY 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TRP 2.9 17.5 + - - -
18F SER* 4.0 1.1 - - - -
19F VAL 3.3 0.4 - - - -
20F LEU* 1.3 76.3 - - - +
22F LEU* 1.3 62.7 - - - +
24F GLY* 3.2 4.4 + - - -
25F LEU* 2.9 27.0 + - - +
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Residues in contact with LEU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F SER* 3.1 30.7 + - - +
19F VAL* 4.1 5.4 - - - +
21F GLY* 1.3 77.0 - - - +
23F LEU* 1.3 59.1 + - + +
25F LEU* 3.5 27.8 - - + +
26F LEU* 3.4 31.0 + - + +
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Residues in contact with LEU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F VAL* 3.1 37.2 + - + +
20F LEU* 4.0 7.4 - - + +
22F LEU* 1.3 73.7 - - - +
24F GLY* 1.3 59.0 + - - +
25F LEU 3.0 4.7 - - - -
26F LEU* 3.5 18.7 + - + +
27F VAL* 3.0 38.3 + - + +
54F LEU* 4.1 23.1 - - + -
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Residues in contact with GLY 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU 2.9 17.5 + - - -
21F GLY* 3.2 8.5 + - - -
23F LEU* 1.3 74.0 - - - +
25F LEU* 1.3 55.4 + - - +
27F VAL* 2.9 17.1 - - - +
54F LEU* 4.1 16.5 - - - +
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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 GLY 2.9 13.8 + - - +
22F LEU* 3.5 31.6 - - + +
23F LEU 3.0 0.2 - - - -
24F GLY* 1.3 76.5 - - - +
26F LEU* 1.3 71.0 + - + +
27F VAL 3.0 8.6 - - - +
28F GLY* 4.0 0.3 - - - -
29F TYR* 3.0 28.2 + - + +
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Residues in contact with LEU 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 LEU* 3.4 17.4 + - + +
23F LEU* 3.5 24.0 + - + +
25F LEU* 1.3 81.6 - - + +
27F VAL* 1.3 57.6 + - + +
29F TYR* 3.2 11.1 + - + +
30F LEU* 2.7 56.2 + - + +
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 3.0 20.7 + - + +
24F GLY* 2.9 28.4 - - - +
25F LEU 3.0 3.3 - - - +
26F LEU* 1.3 74.9 - - + +
28F GLY* 1.3 61.6 + - - +
30F LEU* 5.0 3.6 - - + -
31F VAL* 4.0 17.0 - - + -
46F THR 5.0 0.7 - - - +
47F LEU* 5.2 7.9 - - + +
50F SER* 3.5 39.9 - - - +
51F SER 5.6 0.4 - - - +
54F LEU* 4.9 9.9 - - + -
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Residues in contact with GLY 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU 4.1 0.2 - - - -
26F LEU 3.5 0.6 + - - -
27F VAL* 1.3 73.5 - - - +
29F TYR* 1.3 58.3 + - - +
30F LEU 3.5 0.2 - - - -
31F VAL* 3.5 23.4 - - - +
32F VAL* 3.0 37.0 + - - +
47F LEU* 6.0 1.6 - - - -
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Residues in contact with TYR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F LEU* 3.0 30.5 + - + +
26F LEU* 3.6 10.5 - - + +
28F GLY* 1.3 75.4 - - - +
30F LEU* 1.3 67.3 + - + +
32F VAL* 4.2 2.6 - - - +
33F LEU* 3.1 44.0 + - + +
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Residues in contact with LEU 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 LEU* 2.7 40.4 + - + +
27F VAL* 5.0 3.6 - - + -
29F TYR* 1.3 80.5 - - + +
31F VAL* 1.3 58.5 + - + +
33F LEU* 3.9 10.3 - - + +
34F MET* 3.2 43.8 + - + +
46F THR* 5.8 0.2 - - - -
150G TYR* 4.0 39.5 - - + +
151G ILE* 4.9 15.5 - - + -
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Residues in contact with VAL 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 VAL* 4.0 16.6 - - + -
28F GLY* 3.5 25.5 + - - +
29F TYR 3.3 0.4 - - - -
30F LEU* 1.3 76.6 - - + +
32F VAL* 1.3 63.4 + - + +
34F MET* 3.2 7.4 + - - +
35F TYR* 3.0 28.2 + - + +
43F ALA* 4.6 18.5 - - + +
46F THR* 4.0 22.4 - - + -
47F LEU* 3.9 27.6 - - + -
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Residues in contact with VAL 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F GLY* 3.0 23.1 + - - +
29F TYR* 4.3 2.7 - - - +
31F VAL* 1.3 78.1 - - + +
33F LEU* 1.3 63.0 + - - +
35F TYR* 3.1 19.3 + - + +
36F ALA* 3.2 13.3 + - + +
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Residues in contact with LEU 33 (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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29F TYR* 3.1 38.1 + - + +
30F LEU* 4.0 11.4 - - + +
31F VAL 3.3 0.2 - - - -
32F VAL* 1.3 76.6 - - - +
34F MET* 1.3 58.0 + - - +
36F ALA* 4.0 8.6 + - + +
37F GLN* 3.2 32.9 - - - +
150G TYR* 3.6 31.7 - - + -
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Residues in contact with MET 34 (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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30F LEU* 3.2 33.7 + - + +
31F VAL 3.2 5.7 + - - +
32F VAL 3.1 0.4 - - - -
33F LEU* 1.3 74.0 - - - +
35F TYR* 1.3 64.2 + - - +
36F ALA 3.2 9.5 - - - +
39F GLU* 3.0 34.1 + - + +
42F PHE* 3.6 47.6 - - + +
43F ALA* 4.4 5.2 - - + -
46F THR* 4.1 18.8 - - - +
147G LEU* 6.2 0.9 - - + -
150G TYR* 3.5 50.7 - - + +
151G ILE* 6.0 2.0 - - + -
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Residues in contact with TYR 35 (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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31F VAL* 3.0 14.4 + - + +
32F VAL* 3.1 14.8 + - + +
34F MET* 1.3 77.3 - - - +
36F ALA* 1.3 60.4 + - - +
38F GLY 4.3 0.2 + - - -
39F GLU 4.8 2.0 - - - -
40F TYR* 3.5 55.4 + + - -
43F ALA* 4.7 13.9 - - + +
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Residues in contact with ALA 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F VAL* 3.2 14.0 + - + +
33F LEU* 4.1 8.1 - - + +
34F MET 3.2 9.3 - - - +
35F TYR* 1.3 78.0 - - - +
37F GLN* 1.3 73.9 - - - +
38F GLY 2.5 21.4 + - - -
40F TYR* 5.6 0.2 - - - -
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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
------------------------------------------------------------
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