Contacts of the helix formed by residues 19 - 34 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J ASP 3.1 8.3 + - - +
18J HIS* 1.3 73.9 + - - +
20J GLU* 1.3 62.5 + - - +
21J TYR 3.1 0.2 - - - -
22J GLN* 3.0 39.8 + - - +
23J TYR 4.3 0.2 + - - -
55J ARG 3.9 8.2 - - - +
56J PHE* 3.4 28.4 - - + +
57J SER* 2.9 44.8 + - - +
62J THR* 5.7 0.3 - - - +
64J PRO* 5.0 0.2 - - - +
277J PHE* 3.7 19.1 - - + -
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Residues in contact with GLU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J HIS* 2.9 20.0 + - + +
19J GLU* 1.3 77.7 - - - +
21J TYR* 1.3 62.3 + - - +
22J GLN 3.1 0.2 - - - -
23J TYR* 3.1 17.5 + - + +
24J LEU* 3.1 17.1 + - + +
56J PHE* 4.9 2.2 - - - -
66J LEU* 3.7 21.1 - - + +
67J THR* 2.9 36.0 + - - -
68J THR* 2.6 41.6 + - - -
274J PRO* 3.7 12.7 - - + +
277J PHE* 3.7 17.8 - - + -
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Residues in contact with TYR 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J PRO* 4.0 32.1 - - + +
18J HIS* 3.1 41.8 + - + +
20J GLU* 1.3 74.3 - - - +
22J GLN* 1.3 57.7 + - - +
24J LEU* 3.7 19.5 - - + -
25J ASP* 2.7 53.8 + - - +
28J ARG* 6.2 0.4 - - - -
272J ARG 5.2 2.0 - - - -
273J GLU* 3.8 16.7 + - + +
274J PRO* 3.4 28.1 - - + +
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Residues in contact with GLN 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J HIS 4.5 0.6 + - - +
19J GLU* 3.0 28.8 + - - +
20J GLU 3.1 0.4 - - - -
21J TYR* 1.3 79.1 - - - +
23J TYR* 1.3 62.1 + - - +
25J ASP* 4.0 4.2 - - - +
26J LEU* 3.1 18.7 + - - +
53J SER 4.3 4.4 + - - -
54J PHE* 3.4 35.8 - - + +
55J ARG* 3.0 48.8 + - - +
56J PHE* 3.6 10.7 - - + -
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Residues in contact with TYR 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J GLU* 3.1 10.8 + - + +
22J GLN* 1.3 78.8 - - - +
24J LEU* 1.3 78.7 + - + +
26J LEU* 3.4 2.8 + - - +
27J ILE* 3.2 48.9 + - + +
54J PHE* 3.7 17.5 - + + -
56J PHE* 5.4 2.5 - - + -
66J LEU* 3.7 39.3 - - + -
68J THR* 5.0 1.3 - - - -
69J LYS* 5.0 0.2 + - - -
220J LEU* 2.6 36.1 + - + +
221J GLY* 3.7 6.8 + - - -
224J VAL* 3.9 25.8 - - + -
225J PRO* 3.5 10.3 - - + +
228J ILE* 4.7 4.3 - - + -
266J LEU* 4.4 3.6 - - - +
269J GLN* 3.8 19.9 + - - -
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Residues in contact with LEU 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J GLU* 3.1 11.3 + - + +
21J TYR* 3.9 23.6 - - + +
23J TYR* 1.3 91.0 - - + +
25J ASP* 1.3 64.9 + - - +
27J ILE* 3.3 2.7 + - + -
28J ARG* 3.1 27.4 + - - +
68J THR* 3.8 38.8 - - + +
269J GLN* 4.3 14.1 - - + +
270J LEU* 3.4 35.2 - - + +
272J ARG 4.0 9.6 - - - +
274J PRO* 3.9 17.5 - - + -
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Residues in contact with ASP 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 2.7 44.0 + - - +
22J GLN* 4.0 4.6 - - - +
24J LEU* 1.3 72.2 - - - +
26J LEU* 1.3 57.8 + - - +
28J ARG* 3.3 22.8 + - - +
29J ARG* 2.9 29.0 + - - +
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Residues in contact with LEU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J GLN 3.1 18.8 + - - +
23J TYR 3.8 2.7 - - - +
24J LEU 3.3 0.2 - - - -
25J ASP* 1.3 76.6 - - - +
27J ILE* 1.3 57.8 + - - +
29J ARG* 3.2 11.5 + - - +
30J ILE* 2.8 50.1 + - + +
48J LEU* 4.6 8.1 - - + -
51J PRO* 3.9 30.7 - - + -
52J PRO* 5.9 0.4 - - + -
54J PHE* 3.4 29.6 - - + -
220J LEU* 3.7 20.2 - - + -
253J MET* 3.9 17.3 - - + -
256J ALA* 4.7 0.4 - - + -
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Residues in contact with ILE 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J TYR* 3.2 53.2 + - + +
24J LEU* 3.6 9.9 - - + +
25J ASP 3.3 0.2 - - - -
26J LEU* 1.3 76.4 - - - +
28J ARG* 1.3 64.6 + - - +
30J ILE* 3.3 7.7 + - - +
31J ILE* 3.0 43.3 + - + +
220J LEU* 3.7 21.8 - - + -
258J VAL* 4.5 2.7 - - + -
266J LEU* 3.8 36.3 - - + -
269J GLN* 5.5 0.7 - - - +
270J LEU* 4.2 13.2 - - + -
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Residues in contact with ARG 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J TYR* 6.2 0.6 - - - -
24J LEU* 3.1 20.9 + - - +
25J ASP* 3.4 30.5 + - - +
27J ILE* 1.3 77.5 - - - +
29J ARG* 1.3 57.9 + - - +
31J ILE* 3.5 4.3 + - - +
32J ASN* 3.0 49.7 + - - +
270J LEU* 3.5 52.5 + - + +
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Residues in contact with ARG 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ASP 2.9 17.0 + - - +
26J LEU* 3.5 13.2 - - - +
28J ARG* 1.3 74.9 - - - +
30J ILE* 1.3 59.9 + - - +
32J ASN* 3.2 5.7 + - - -
33J VAL* 2.8 52.5 + - + +
48J LEU* 3.6 24.3 - - + +
51J PRO* 4.2 12.1 - - - +
52J PRO* 3.7 28.3 - - - +
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Residues in contact with ILE 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J LEU* 2.8 37.4 + - + +
27J ILE 3.7 4.0 - - - +
29J ARG* 1.3 71.8 - - - +
31J ILE* 1.3 59.6 + - - +
34J GLY* 2.7 29.6 + - - +
46J VAL* 3.0 47.5 - - + +
47J ALA* 4.1 4.5 - - - -
48J LEU* 3.9 23.1 - - + -
220J LEU* 3.6 32.8 - - + -
256J ALA* 3.9 14.6 - - + +
258J VAL* 3.7 13.7 - - + -
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Residues in contact with ILE 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J ILE* 3.0 34.3 + - + +
28J ARG* 3.8 5.2 - - - +
30J ILE* 1.3 77.3 - - - +
32J ASN* 1.3 70.8 + - - +
34J GLY 4.5 1.0 + - - +
46J VAL* 4.6 10.0 - - - +
258J VAL* 4.6 13.9 - - + -
263J VAL* 4.2 45.1 - - + +
266J LEU* 4.7 2.7 - - + -
267J LYS* 4.6 13.2 - - + -
270J LEU* 4.4 15.0 - - + -
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Residues in contact with ASN 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J ARG* 3.0 37.5 + - - +
29J ARG* 3.2 5.8 + - - +
31J ILE* 1.3 89.2 - - - +
33J VAL* 1.3 69.3 + - + +
34J GLY 5.0 1.1 - - - +
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Residues in contact with VAL 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ARG* 2.8 44.5 + - + +
32J ASN* 1.3 82.9 - - + +
34J GLY* 1.3 67.7 + - - +
35J GLU* 3.8 0.7 + - - +
48J LEU* 4.0 14.4 - - + +
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Residues in contact with GLY 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J ARG 3.6 2.4 + - - -
30J ILE* 2.7 29.4 + - - -
31J ILE 4.5 0.9 - - - +
32J ASN 3.6 1.8 - - - +
33J VAL* 1.3 77.8 - - - +
35J GLU* 1.3 60.1 + - - -
36J VAL* 3.9 3.8 + - - +
46J VAL* 3.4 12.6 - - - +
47J ALA 3.6 10.3 - - - -
48J LEU* 3.8 9.4 - - - -
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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