Contacts of the helix formed by residues 16 - 32 (chain J) in PDB entry 5TJ4
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 GLY 16 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J ILE* 5.2 2.2 - - - +
15J LYS* 1.3 72.4 - - - +
17J TYR* 1.3 59.4 + - - -
19J GLY 3.5 0.7 + - - -
20J LEU* 3.1 24.4 + - - +
293J VAL* 3.6 18.0 - - - +
296J ASP* 3.2 26.5 - - - -
297J LYS* 3.8 19.7 + - - +
299J LEU* 5.9 0.4 - - - +
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Residues in contact with TYR 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ILE* 3.7 27.3 - - + +
12J ASN 4.3 1.3 - - - -
13J GLY* 3.3 30.5 - - - -
15J LYS 3.1 9.5 + - - -
16J GLY* 1.3 69.0 - - - +
18J ASN* 1.3 103.7 + - - +
20J LEU* 3.2 5.5 + - - +
21J ALA* 2.9 27.5 + - - +
37J VAL* 3.8 14.8 - - + +
39J HIS* 3.5 49.5 + + - +
296J ASP* 3.5 0.8 + - - -
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Residues in contact with ASN 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J TYR* 1.3 104.6 + - - +
19J GLY* 1.3 60.7 + - - +
21J ALA* 3.1 9.2 + - - +
22J GLU* 2.9 27.4 + - - +
296J ASP* 3.1 18.0 + - - +
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Residues in contact with GLY 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J GLY 3.5 3.3 + - - -
17J TYR 3.3 0.2 - - - -
18J ASN* 1.3 75.3 - - - +
20J LEU* 1.3 61.6 + - - +
22J GLU* 3.2 10.5 - - - +
23J VAL* 3.2 23.7 + - - +
292J ALA* 3.7 22.9 - - - +
293J VAL* 4.1 8.1 - - - -
296J ASP* 3.0 19.5 + - - +
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Residues in contact with LEU 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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9J ILE* 3.9 26.5 - - + -
11J ILE* 3.8 25.6 - - + -
16J GLY 3.1 14.9 + - - +
17J TYR 3.2 9.4 + - - +
19J GLY* 1.3 74.6 - - - +
21J ALA* 1.3 58.4 + - - +
23J VAL* 3.1 8.8 + - + +
24J GLY* 2.8 23.7 + - - -
37J VAL* 4.3 17.0 - - + +
61J PHE* 4.1 7.9 - - + -
279J PHE* 4.1 21.3 - - + -
284J LEU* 4.0 32.5 - - + -
293J VAL* 4.0 10.7 - - + +
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J TYR 2.9 13.8 + - - +
18J ASN* 3.1 13.0 + - - +
20J LEU* 1.3 73.9 - - - +
22J GLU* 1.3 53.0 + - - +
24J GLY* 3.0 4.1 + - - +
25J LYS* 2.7 34.4 + - - +
35J VAL 5.6 3.2 - - - +
37J VAL* 4.0 21.0 - - + +
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Residues in contact with GLU 22 (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 ASN 2.9 12.4 + - - +
19J GLY* 3.2 15.5 - - - +
21J ALA* 1.3 75.2 - - - +
23J VAL* 1.3 60.4 + - - +
25J LYS* 3.2 9.2 + - - +
26J LYS* 3.1 21.3 + - - +
292J ALA* 4.8 9.2 - - + -
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Residues in contact with VAL 23 (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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19J GLY 3.2 13.4 + - - +
20J LEU* 3.1 11.3 + - + +
22J GLU* 1.3 72.5 - - - +
24J GLY* 1.3 66.6 + - - +
26J LYS* 3.3 9.9 + - + +
27J PHE* 3.0 20.1 + - - +
279J PHE* 3.8 21.3 - - + -
283J TYR* 3.8 29.9 - - + +
284J LEU* 4.0 6.7 - - + +
289J GLY* 3.5 29.8 - - - +
292J ALA* 3.9 7.9 - - + -
293J VAL* 4.2 8.7 - - + -
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Residues in contact with GLY 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU 2.8 14.0 + - - -
21J ALA* 3.0 7.5 + - - -
23J VAL* 1.3 77.0 - - - +
25J LYS* 1.3 55.2 + - - +
27J PHE* 3.1 5.2 + - - +
28J GLU* 2.9 26.1 + - - +
35J VAL* 3.3 38.1 - - - +
37J VAL* 5.7 0.2 - - - -
279J PHE* 4.2 6.2 - - - -
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Residues in contact with LYS 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 ALA 2.7 15.4 + - - +
22J GLU* 3.2 11.9 + - - +
24J GLY* 1.3 71.4 - - - +
26J LYS* 1.3 56.9 + - - +
28J GLU* 3.2 8.7 + - - +
29J LYS* 2.9 31.9 + - - +
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Residues in contact with LYS 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 GLU 3.1 13.1 + - - +
23J VAL* 3.3 11.4 + - + +
25J LYS* 1.3 75.4 - - - +
27J PHE* 1.3 60.9 + - - +
29J LYS* 3.5 12.3 - - + +
30J ASP* 3.4 30.8 + - - +
283J TYR* 3.7 9.3 - - + -
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Residues in contact with PHE 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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7J LEU* 4.2 17.7 - - + -
23J VAL 3.0 13.1 + - - +
24J GLY 3.1 9.2 + - - +
26J LYS* 1.3 73.3 - - - +
28J GLU* 1.3 60.4 + - - +
30J ASP 3.2 1.2 + - - -
31J THR* 2.8 50.2 + - - -
33J ILE* 4.1 23.1 - - + -
35J VAL* 3.7 19.7 - - + -
275J LEU* 3.8 24.7 - - + -
278J GLU* 4.5 8.5 - - + -
279J PHE* 3.7 33.0 - + + -
283J TYR* 3.5 36.7 - + + -
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Residues in contact with GLU 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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24J GLY 2.9 15.6 + - - +
25J LYS* 3.2 12.5 + - - +
27J PHE* 1.3 70.6 - - - +
29J LYS* 1.3 58.3 + - - +
32J GLY* 2.8 30.8 + - - -
33J ILE 3.4 25.8 + - - +
34J LYS* 4.9 4.7 - - - -
35J VAL* 4.8 2.7 - - + +
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Residues in contact with LYS 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 LYS 2.9 13.3 + - - +
26J LYS* 3.5 17.3 - - + +
27J PHE 3.2 0.4 - - - -
28J GLU* 1.3 79.8 - - - +
30J ASP* 1.3 79.3 + - - +
32J GLY* 4.4 0.9 + - - -
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Residues in contact with ASP 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 LYS* 3.4 12.1 - - - +
27J PHE 3.2 2.2 + - - +
29J LYS* 1.3 97.3 - - - +
31J THR* 1.3 61.3 + - - +
32J GLY 3.8 0.2 + - - -
283J TYR* 3.1 31.4 + - - +
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Residues in contact with THR 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 PHE* 2.8 42.4 + - - -
30J ASP* 1.3 76.8 - - - +
32J GLY* 1.3 61.8 + - - +
33J ILE* 3.7 7.7 + - - +
283J TYR* 5.2 2.2 - - - -
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Residues in contact with GLY 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 GLU* 2.8 24.7 + - - -
29J LYS 4.4 1.1 + - - -
30J ASP 3.5 2.0 + - - -
31J THR* 1.3 74.6 - - - +
33J ILE* 1.3 56.9 + - - +
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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