Contacts of the helix formed by residues 16 - 32 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E ILE* 5.2 2.6 - - - +
15E LYS* 1.3 72.2 - - - +
17E TYR* 1.3 58.6 + - - -
19E GLY* 3.5 1.0 + - - -
20E LEU* 3.1 24.5 + - - +
293E VAL* 3.6 17.8 - - - +
296E ASP* 3.2 27.6 - - - -
297E LYS* 3.8 19.0 + - - +
299E LEU* 5.9 0.6 - - - +
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Residues in contact with TYR 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ILE* 3.7 27.6 - - + -
12E ASN 4.4 1.1 - - - -
13E GLY* 3.3 24.7 - - - -
15E LYS 3.1 16.3 + - - -
16E GLY* 1.3 69.8 - - - +
18E ASN* 1.3 99.3 + - - +
20E LEU* 3.2 5.9 + - - +
21E ALA* 2.9 28.0 + - - +
37E VAL* 3.8 14.7 - - + +
39E HIS* 3.4 47.0 + + - +
296E ASP* 3.5 0.8 + - - -
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Residues in contact with ASN 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E TYR* 1.3 106.2 + - - +
19E GLY* 1.3 60.4 + - - +
21E ALA* 3.1 9.2 + - - +
22E GLU* 2.9 27.8 + - - +
296E ASP* 3.1 18.7 + - - +
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Residues in contact with GLY 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLY 3.5 3.3 + - - -
18E ASN* 1.3 75.4 - - - +
20E LEU* 1.3 60.0 + - - +
22E GLU* 3.3 10.4 - - - +
23E VAL* 3.2 23.2 + - - +
292E ALA* 3.7 22.9 - - - +
293E VAL* 4.1 8.3 - - - -
296E ASP* 3.0 18.7 + - - -
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 3.9 26.0 - - + -
11E ILE* 3.8 26.5 - - + -
16E GLY 3.1 13.8 + - - +
17E TYR* 3.2 9.6 + - - +
19E GLY* 1.3 76.1 - - - +
21E ALA* 1.3 58.7 + - - +
23E VAL* 3.1 8.7 + - + +
24E GLY* 2.8 23.4 + - - -
37E VAL* 4.3 17.3 - - + +
61E PHE* 4.1 7.4 - - + -
279E PHE* 4.2 20.9 - - + -
284E LEU* 4.0 32.3 - - + -
293E VAL* 4.0 11.3 - - + +
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Residues in contact with ALA 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E TYR 2.9 13.5 + - - +
18E ASN* 3.1 12.5 + - - +
20E LEU* 1.3 73.4 - - - +
22E GLU* 1.3 53.5 + - - +
24E GLY* 2.9 4.0 + - - +
25E LYS* 2.7 35.4 + - - +
35E VAL 5.6 3.4 - - - +
37E VAL* 4.0 21.0 - - + +
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Residues in contact with GLU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E ASN 2.9 12.2 + - - +
19E GLY* 3.3 14.8 - - - +
21E ALA* 1.3 75.3 - - - +
23E VAL* 1.3 60.5 + - - +
25E LYS* 3.3 9.1 + - - +
26E LYS* 3.2 21.5 + - - +
292E ALA* 4.8 9.6 - - + -
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E GLY 3.5 12.6 - - - +
20E LEU* 3.1 11.9 + - + +
22E GLU* 1.3 72.5 - - - +
24E GLY* 1.3 67.0 + - - +
26E LYS* 3.3 9.1 + - + +
27E PHE* 3.0 20.4 + - - +
279E PHE* 3.7 21.1 - - + -
283E TYR* 3.8 29.7 - - + +
284E LEU* 4.1 6.3 - - + +
289E GLY* 3.5 30.3 - - - +
292E ALA* 3.9 8.1 - - + -
293E VAL* 4.2 8.7 - - + -
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Residues in contact with GLY 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU 2.8 13.1 + - - -
21E ALA* 2.9 7.8 + - - -
23E VAL* 1.3 75.8 - - - +
25E LYS* 1.3 56.1 + - - +
27E PHE* 3.1 5.5 + - - +
28E GLU* 2.9 25.6 + - - +
35E VAL* 3.3 37.5 - - - +
279E PHE* 4.2 7.3 - - - -
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Residues in contact with LYS 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA 2.7 14.5 + - - +
22E GLU* 3.3 12.1 + - - +
24E GLY* 1.3 72.5 - - - +
26E LYS* 1.3 56.5 + - - +
28E GLU* 3.3 9.1 + - - +
29E LYS* 2.9 30.7 + - - +
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Residues in contact with LYS 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E GLU 3.2 11.8 + - - +
23E VAL* 3.3 11.4 + - + +
25E LYS* 1.3 75.0 - - - +
27E PHE* 1.3 59.7 + - - +
29E LYS* 4.1 5.3 - - - +
30E ASP* 3.4 30.9 + - - +
283E TYR* 4.1 11.1 - - + -
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Residues in contact with PHE 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E LEU* 4.2 13.9 - - + -
23E VAL 3.0 12.5 + - - +
24E GLY 3.1 8.5 + - - +
26E LYS* 1.3 73.6 - - - +
28E GLU* 1.3 59.5 + - - +
30E ASP* 3.2 1.4 + - - +
31E THR* 2.8 67.5 + - + +
33E ILE* 4.1 20.9 - - + -
35E VAL* 3.7 20.0 - - + -
275E LEU* 3.9 21.1 - - + -
278E GLU* 4.5 6.5 - - + -
279E PHE* 3.7 29.4 - + + -
283E TYR* 3.3 43.4 - + + -
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Residues in contact with GLU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLY 2.9 14.5 + - - +
25E LYS* 3.6 11.9 - - - +
27E PHE* 1.3 71.0 - - - +
29E LYS* 1.3 59.0 + - - +
32E GLY* 2.8 30.4 + - - -
33E ILE 3.3 27.2 + - - +
34E LYS* 4.8 4.7 - - - -
35E VAL* 4.7 3.1 - - + +
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Residues in contact with LYS 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LYS 2.9 15.9 + - - +
26E LYS* 4.1 7.0 - - - +
27E PHE 3.2 0.2 - - - -
28E GLU* 1.3 79.2 - - - +
30E ASP* 1.3 67.7 + - - +
32E GLY* 4.4 1.4 + - - -
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Residues in contact with ASP 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LYS* 3.4 15.1 + - - +
27E PHE 3.2 2.2 + - - +
29E LYS* 1.3 85.4 - - - +
31E THR* 1.3 61.5 + - - +
32E GLY 3.8 0.2 + - - -
283E TYR* 3.1 34.1 + - - +
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Residues in contact with THR 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E PHE* 2.8 58.6 + - + +
30E ASP* 1.3 75.7 - - - +
32E GLY* 1.3 61.6 + - - +
33E ILE* 3.3 37.4 - - + +
283E TYR* 5.1 3.4 - - - -
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Residues in contact with GLY 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLU* 2.8 25.4 + - - -
29E LYS 4.4 1.3 + - - -
30E ASP 3.5 1.8 + - - -
31E THR* 1.3 73.8 - - - +
33E ILE* 1.3 60.5 + - - +
34E LYS 4.4 0.3 + - - -
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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