Contacts of the helix formed by residues 19 - 34 (chain F) in PDB entry 2AAZ
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 GLU 19 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ASP 3.1 6.4 + - - +
18F HIS* 1.3 75.2 + - - +
20F GLU* 1.3 62.2 + - - +
21F TYR 3.1 0.2 - - - -
22F GLN* 3.1 39.0 + - - +
23F TYR 4.3 0.2 + - - -
55F ARG 3.9 8.0 - - - +
56F PHE* 3.4 29.0 - - + +
57F SER* 2.9 44.4 + - - +
62F THR* 5.6 0.3 - - - +
64F PRO* 5.0 0.2 - - - +
277F PHE* 3.6 19.3 - - + -
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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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18F HIS* 2.9 21.5 + - + +
19F GLU* 1.3 77.5 - - - +
21F TYR* 1.3 62.1 + - - +
22F GLN 3.0 0.2 - - - -
23F TYR* 3.0 18.6 + - + +
24F LEU* 3.1 16.4 + - + +
56F PHE* 4.9 2.5 - - - -
66F LEU* 3.7 23.3 - - + +
67F THR* 2.8 34.6 + - - -
68F THR* 2.6 45.4 + - - +
274F PRO* 3.8 12.6 - - + +
277F PHE* 3.7 13.8 - - + -
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Residues in contact with TYR 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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13F ARG* 3.3 66.5 - - + +
14F SER 4.8 0.7 + - - -
15F ASN* 3.1 28.1 + - + -
16F PRO 3.8 11.9 - - - +
18F HIS* 3.0 29.6 + - + +
20F GLU* 1.3 78.5 - - - +
22F GLN* 1.3 54.2 + - - +
23F TYR 3.2 0.2 - - - -
24F LEU* 3.7 19.1 - - + -
25F ASP* 2.7 42.2 + - - +
272F ARG 5.2 1.8 - - - -
273F GLU* 3.8 14.9 - - - +
274F PRO* 3.4 28.4 - - + +
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Residues in contact with GLN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F HIS 5.5 0.2 - - - +
19F GLU* 3.1 28.5 + - - +
20F GLU 3.0 0.2 - - - -
21F TYR* 1.3 79.2 - - - +
23F TYR* 1.3 62.5 + - - +
25F ASP* 4.1 4.0 - - - +
26F LEU* 3.1 19.4 + - - +
53F SER 4.2 4.8 + - - -
54F PHE* 3.4 36.0 - - + +
55F ARG* 2.9 49.8 + - - +
56F PHE* 3.6 11.2 - - + -
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Residues in contact with TYR 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 GLU 4.3 0.6 + - - +
20F GLU* 3.0 12.6 + - + +
22F GLN* 1.3 77.4 - - - +
24F LEU* 1.3 78.4 + - + +
26F LEU* 3.4 3.1 + - - +
27F ILE* 3.2 50.3 + - + +
54F PHE* 3.7 17.2 - + + -
56F PHE* 5.4 2.2 - - + -
66F LEU* 3.7 39.5 - - + -
68F THR* 5.0 0.4 - - - -
69F LYS* 4.9 0.3 + - - -
220F LEU* 2.6 34.9 + - + +
221F GLY* 3.7 6.6 + - - -
224F VAL* 4.0 27.4 - - + -
225F PRO* 3.6 9.4 - - + +
228F ILE* 4.6 3.8 - - + -
266F LEU* 4.4 4.2 - - - +
269F GLN* 3.8 18.3 + - - -
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Residues in contact with LEU 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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13F ARG* 5.9 0.2 - - - +
20F GLU* 3.1 13.9 + - + +
21F TYR* 4.0 21.8 - - + +
23F TYR* 1.3 89.6 - - + +
25F ASP* 1.3 63.8 + - - +
27F ILE* 3.3 2.7 + - + -
28F ARG* 3.1 27.3 + - - +
68F THR* 3.8 39.5 - - + +
269F GLN* 4.3 13.7 - - + +
270F LEU* 3.4 35.6 - - + +
272F ARG 4.0 8.3 - - - +
274F PRO* 3.9 17.3 - - + -
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Residues in contact with ASP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ARG* 2.7 43.7 + - - -
21F TYR* 2.7 31.3 + - - +
22F GLN* 4.1 4.1 - - - +
24F LEU* 1.3 71.9 - - - +
26F LEU* 1.3 57.0 + - - +
28F ARG* 3.3 14.0 + - - +
29F ARG* 2.9 28.8 + - - +
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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 GLN 3.1 19.5 + - - +
23F TYR 3.8 3.6 - - - +
25F ASP* 1.3 77.1 - - - +
27F ILE* 1.3 58.7 + - - +
29F ARG* 3.2 11.4 + - - +
30F ILE* 2.8 55.1 + - + +
48F LEU* 4.6 8.7 - - + -
51F PRO* 3.9 31.4 - - + -
52F PRO* 5.5 0.4 - - + +
54F PHE* 3.4 28.5 - - + -
220F LEU* 3.7 14.8 - - + -
253F MET* 3.9 18.4 - - + -
256F ALA* 5.3 0.2 - - + -
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Residues in contact with ILE 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 TYR* 3.2 52.1 + - + +
24F LEU* 3.7 10.3 - - + +
26F LEU* 1.3 77.2 - - - +
28F ARG* 1.3 65.5 + - - +
30F ILE* 3.3 8.4 + - - +
31F ILE* 3.0 42.9 + - + +
220F LEU* 3.7 23.1 - - + -
258F VAL* 4.5 3.4 - - + -
266F LEU* 3.9 33.2 - - + -
269F GLN* 5.5 0.4 - - - +
270F LEU* 4.2 15.0 - - + -
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Residues in contact with ARG 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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13F ARG* 3.8 11.1 - - - +
24F LEU* 3.1 19.9 + - - +
25F ASP* 3.4 30.6 + - - +
27F ILE* 1.3 78.4 - - - +
29F ARG* 1.3 56.4 + - - +
31F ILE* 3.4 4.4 + - - +
32F ASN* 2.9 50.2 + - - +
270F LEU* 3.6 50.8 + - + +
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Residues in contact with ARG 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 ASP 2.9 15.1 + - - +
26F LEU* 3.5 15.5 - - - +
28F ARG* 1.3 77.8 - - - +
30F ILE* 1.3 58.7 + - - +
32F ASN* 4.4 4.7 - - - -
33F VAL* 2.8 49.8 + - + +
48F LEU* 3.6 26.7 - - + +
51F PRO* 4.1 12.1 - - - +
52F PRO* 3.7 27.3 - - - +
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Residues in contact with ILE 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* 2.8 38.4 + - + +
27F ILE 3.3 3.8 + - - +
29F ARG* 1.3 72.9 - - - +
31F ILE* 1.3 59.5 + - - +
34F GLY 2.7 24.8 + - - +
46F VAL* 3.0 53.5 - - + +
47F ALA* 4.1 5.2 - - - -
48F LEU* 3.9 21.8 - - + -
220F LEU* 3.6 33.0 - - + -
256F ALA* 3.8 13.9 - - + +
258F VAL* 3.7 13.5 - - + -
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Residues in contact with ILE 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 ILE* 3.0 39.2 + - + +
28F ARG* 3.7 3.6 - - - +
30F ILE* 1.3 77.2 - - - +
32F ASN* 1.3 71.0 + - - +
34F GLY 4.5 1.2 + - - +
46F VAL* 4.5 10.7 - - + +
258F VAL* 4.7 15.3 - - + -
263F VAL* 4.2 43.5 - - + +
266F LEU* 4.8 2.5 - - + -
267F LYS* 4.6 13.5 - - + -
270F LEU* 4.3 15.5 - - + -
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Residues in contact with ASN 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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28F ARG* 2.9 37.0 + - - +
29F ARG* 3.7 5.7 - - - +
31F ILE* 1.3 89.8 + - - +
33F VAL* 1.3 69.6 + - + +
34F GLY 5.1 0.7 - - - +
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Residues in contact with VAL 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 ARG* 2.8 46.0 + - + +
32F ASN* 1.3 82.5 - - + +
34F GLY* 1.3 65.3 + - - +
35F GLU* 3.8 0.9 + - - +
48F LEU* 4.0 13.7 - - + +
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Residues in contact with GLY 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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29F ARG 3.5 2.6 + - - -
30F ILE* 2.7 29.6 + - - -
31F ILE 5.3 0.7 - - - +
32F ASN 3.7 1.9 - - - +
33F VAL* 1.3 77.7 - - - +
35F GLU* 1.3 60.0 + - - -
36F VAL* 3.9 3.5 + - - +
46F VAL* 3.4 14.1 - - - +
47F ALA 3.6 10.3 - - - -
48F LEU* 3.8 9.9 - - - -
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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