Contacts of the helix formed by residues 14 - 25 (chain F) in PDB entry 5ITZ
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 LEU 14 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13F ASP* 1.3 76.7 + - - +
15F GLY* 1.3 58.7 + - - +
17F LYS* 3.3 15.3 + - + +
18F LEU* 2.7 32.1 + - - +
33F LEU* 3.9 21.8 - - + +
36F ASN* 3.3 42.0 - - + +
37F GLY 4.2 2.7 - - - +
38F ALA* 3.7 25.0 - - + +
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Residues in contact with GLY 15 (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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13F ASP* 3.2 11.1 + - - -
14F LEU* 1.3 79.2 - - - +
16F LYS* 1.3 57.1 + - - +
18F LEU* 3.3 6.0 + - - +
19F LEU* 2.9 32.5 + - - +
39F ASP* 4.5 13.3 - - - +
42F ALA* 3.6 26.5 - - - +
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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
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13F ASP* 3.2 26.9 + - + +
15F GLY* 1.3 72.8 - - - +
17F LYS* 1.3 61.5 + - + +
19F LEU* 3.2 20.4 + - + +
20F GLU* 2.9 29.6 + - - +
43F THR 4.9 6.5 - - - +
44F ASP* 5.2 7.6 - - + +
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Residues in contact with LYS 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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13F ASP 3.1 28.1 + - - +
14F LEU* 3.6 18.6 - - + +
16F LYS* 1.3 76.6 - - + +
18F LEU* 1.3 57.0 + - - +
20F GLU* 3.3 6.5 + - - +
21F ALA* 2.8 30.1 + - - +
29F GLU* 5.2 3.5 - - - +
33F LEU* 3.6 28.1 - - + +
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Residues in contact with LEU 18 (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 LEU 2.7 21.4 + - - +
15F GLY 3.5 4.3 - - - +
17F LYS* 1.3 73.4 - - - +
19F LEU* 1.3 57.5 + - - +
22F ALA* 2.8 30.2 + - + +
30F VAL* 3.9 44.6 - - + +
33F LEU* 3.6 10.0 - - + +
34F MET* 4.6 8.1 - - + -
38F ALA* 4.1 13.9 - - + -
39F ASP 3.3 27.1 - - - +
40F VAL* 3.8 12.6 - - - +
50F PRO* 3.7 19.7 - - + -
66F LEU* 4.6 8.5 - - + -
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Residues in contact with LEU 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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15F GLY 2.9 22.4 + - - +
16F LYS* 3.4 21.8 - - + +
18F LEU* 1.3 76.8 - - - +
20F GLU* 1.3 62.5 + - - +
22F ALA* 3.2 2.1 + - - +
23F ARG* 3.0 20.8 + - - +
42F ALA* 4.1 5.2 - - + +
43F THR 3.6 27.4 - - - +
44F ASP* 3.7 12.3 - - + +
48F LEU 3.3 23.6 - - - +
49F THR* 3.6 2.2 - - - -
50F PRO* 3.5 32.8 - - + -
53F LEU* 3.6 28.0 - - + +
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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 LYS 2.9 19.6 + - - +
17F LYS* 3.7 6.7 - - - +
19F LEU* 1.3 73.1 - - - +
21F ALA* 1.3 62.6 + - - +
23F ARG* 3.3 15.5 + - - +
24F ALA* 3.0 26.8 + - - +
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Residues in contact with ALA 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 LYS 2.8 21.6 + - - +
18F LEU 3.6 3.8 - - - +
20F GLU* 1.3 72.4 - - - +
22F ALA* 1.3 61.3 + - - +
24F ALA* 3.5 0.6 + - - -
25F GLY* 3.1 3.5 + - - -
26F GLN* 3.0 36.3 + - + -
29F GLU* 3.8 23.1 - - + +
30F VAL* 3.9 11.5 - - + +
33F LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 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 LEU* 2.8 20.9 + - + +
19F LEU 3.7 3.8 - - - +
21F ALA* 1.3 73.7 - - - +
23F ARG* 1.3 60.9 + - - +
25F GLY* 3.4 1.9 + - - -
30F VAL* 4.0 9.6 - - + +
50F PRO* 3.5 37.7 - - + +
53F LEU* 4.7 0.2 - - + -
54F ALA* 3.8 9.7 - - + +
59F HIS* 3.1 21.3 - - - +
62F ILE* 4.2 17.2 - - + +
66F LEU* 4.5 0.2 - - + -
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Residues in contact with ARG 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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406B HIS* 5.3 8.5 - - - +
19F LEU* 3.0 16.3 + - - +
20F GLU* 3.8 13.7 - - - +
22F ALA* 1.3 77.3 - - - +
24F ALA* 1.3 60.8 + - + +
44F ASP* 5.3 7.8 + - - +
48F LEU* 6.2 0.4 - - - +
53F LEU* 3.9 41.6 - - + +
57F TYR* 3.7 42.5 + - + +
59F HIS* 3.0 16.5 + - - -
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Residues in contact with ALA 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 3.0 17.2 + - - +
22F ALA 3.2 0.2 - - - -
23F ARG* 1.3 76.8 - - + +
25F GLY* 1.3 62.1 + - - +
26F GLN* 3.4 24.3 + - + -
59F HIS* 3.5 7.5 + - - -
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Residues in contact with GLY 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 ALA 3.1 3.4 + - - -
24F ALA* 1.3 79.0 - - - +
26F GLN* 1.3 63.3 + - - +
27F ASP* 3.1 20.3 + - - +
59F HIS* 3.2 35.9 + - - -
62F ILE* 3.5 10.5 - - - -
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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