Contacts of the helix formed by residues 17 - 33 (chain E) in PDB entry 3EBL
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 PRO 17 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E VAL* 1.3 90.1 - - + +
18E LEU* 1.3 61.6 + - - +
19E HIS 4.4 0.7 - - - +
20E THR* 3.1 9.8 + - + +
21E TRP* 2.9 24.8 + - - +
333E ASN* 3.5 33.0 - - + +
334E THR* 3.6 31.2 - - + -
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Residues in contact with LEU 18 (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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16E VAL 3.5 2.9 + - - -
17E PRO* 1.3 72.0 - - - +
19E HIS* 1.3 58.1 + - - +
21E TRP* 3.0 12.7 + - + +
22E VAL* 2.8 37.1 + - + +
21F TRP* 3.8 30.5 - - + -
25F SER* 6.3 0.9 - - - -
29F LEU* 4.0 30.7 - - + -
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Residues in contact with HIS 19 (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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17E PRO* 3.3 2.2 - - - +
18E LEU* 1.3 78.4 - - - +
20E THR* 1.3 57.1 + - - +
22E VAL* 3.6 3.5 + - + -
23E LEU* 3.0 31.2 + - + +
331E LEU* 3.8 14.8 - - + +
333E ASN* 4.1 13.7 - - - +
26F ASN* 3.7 22.1 + - - -
29F LEU* 3.9 49.2 + - + +
30F SER* 4.1 10.5 + - - -
33F ILE* 6.0 5.4 - - + -
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Residues in contact with THR 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E VAL* 3.9 11.9 - - + -
17E PRO* 3.1 17.3 + - + +
19E HIS* 1.3 75.8 - - - +
21E TRP* 1.3 64.7 + - - +
23E LEU* 4.7 0.2 - - - -
24E ILE* 3.0 38.4 + - + +
245E PHE* 4.8 0.9 - - + -
325E THR* 3.9 21.8 - - - +
326E VAL 4.9 1.6 - - - +
328E PHE* 5.2 6.9 - - + -
331E LEU* 3.3 24.5 - - + +
333E ASN* 3.1 25.3 + - - +
334E THR* 5.5 0.7 - - - +
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Residues in contact with TRP 21 (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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16E VAL* 3.8 17.9 - - + +
17E PRO 2.9 14.2 + - - +
18E LEU* 3.4 15.5 - - + +
20E THR* 1.3 76.9 - - - +
22E VAL* 1.3 61.1 + - + +
25E SER* 2.6 48.6 + - - -
245E PHE* 3.7 28.5 - + - -
18F LEU* 3.9 25.4 - - + -
21F TRP* 3.3 35.2 - + - -
22F VAL* 3.9 12.8 - - + -
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Residues in contact with VAL 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LEU* 2.8 29.0 + - + +
19E HIS* 3.9 6.3 - - + +
21E TRP* 1.3 74.7 - - + +
23E LEU* 1.3 66.3 + - - +
26E ASN* 3.0 20.1 + - - +
21F TRP* 4.0 19.7 - - + -
22F VAL* 3.4 19.8 - - - +
25F SER* 3.9 19.7 - - - +
26F ASN* 3.5 40.8 - - + +
29F LEU* 4.2 12.6 - - + -
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Residues in contact with LEU 23 (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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19E HIS* 3.0 24.1 + - + +
20E THR 3.2 2.7 + - - +
22E VAL* 1.3 78.2 - - - +
24E ILE* 1.3 71.8 + - + +
26E ASN* 3.2 14.0 + - - +
27E PHE* 3.2 30.4 + - + -
51E ARG* 4.1 16.2 - - - +
133E ILE* 4.6 14.1 - - + -
330E LEU* 4.8 6.3 - - + -
331E LEU* 4.0 32.8 - - + -
501E MPD 3.7 26.5 - - + -
701E PO4 4.8 7.9 - - - +
26F ASN* 4.0 15.9 - - - +
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Residues in contact with ILE 24 (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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20E THR* 3.0 31.6 + - + +
23E LEU* 1.3 90.8 - - + +
25E SER* 1.3 60.4 + - - +
27E PHE* 3.2 6.4 + - + +
28E LYS* 2.8 27.0 + - - +
245E PHE* 3.4 39.9 - - + -
326E VAL* 4.2 10.3 - - + +
327E GLY* 4.4 12.1 - - - +
330E LEU* 4.6 7.2 - - + -
331E LEU* 5.2 0.7 - - + -
401E GA4 3.8 42.2 - - + +
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Residues in contact with SER 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TRP* 2.6 41.5 + - - -
22E VAL 3.8 2.9 - - - -
24E ILE* 1.3 78.3 - - - +
26E ASN* 1.3 57.4 + - - +
28E LYS* 4.1 10.2 - - - +
29E LEU* 2.9 38.6 + - - +
245E PHE* 3.5 15.8 - - - -
18F LEU* 6.1 0.9 - - - -
22F VAL* 3.9 22.0 - - - -
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Residues in contact with ASN 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 VAL 3.0 14.2 + - - +
23E LEU 3.2 11.2 + - - +
25E SER* 1.3 73.8 - - - +
27E PHE* 1.3 64.1 + - - +
29E LEU* 4.2 2.7 - - - +
30E SER* 3.0 37.6 + - - -
501E MPD 3.7 30.0 - - + +
19F HIS* 3.8 12.4 + - - -
22F VAL* 3.5 13.4 + - + +
23F LEU* 3.8 29.2 - - - +
26F ASN* 3.3 21.9 - - - +
51F ARG* 5.6 0.3 + - - -
501F MPD 3.9 1.6 - - - +
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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
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23E LEU* 3.2 46.4 + - + -
24E ILE* 3.2 10.4 + - + +
26E ASN* 1.3 79.3 - - - +
28E LYS* 1.3 56.9 + - - +
30E SER 3.3 0.7 + - - -
31E TYR* 2.9 68.9 + + + -
50E ASP* 4.7 8.3 - - - -
51E ARG* 5.8 0.9 - - + -
127E SER* 5.1 2.2 - - - -
133E ILE* 3.7 33.2 - - + -
330E LEU* 5.6 0.2 - - + -
401E GA4 3.5 37.0 - - + -
501E MPD 3.8 35.2 - - + +
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Residues in contact with LYS 28 (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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24E ILE 2.8 20.4 + - - +
25E SER* 3.2 8.9 + - - +
27E PHE* 1.3 74.6 - - - +
29E LEU* 1.3 67.1 + - + +
31E TYR* 3.4 3.6 + - - +
32E ASN* 3.1 47.6 + - - +
35E ARG* 5.1 0.5 + - - -
242E GLY 4.9 9.1 + - - -
245E PHE* 3.4 45.4 + - + +
247E THR* 5.0 10.5 - - - +
401E GA4 4.1 19.0 - - + +
18F LEU* 6.4 0.9 - - - -
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Residues in contact with LEU 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 SER* 2.9 25.4 + - - +
26E ASN 4.2 0.2 - - - +
28E LYS* 1.3 81.7 - - + +
30E SER* 1.3 66.2 + - - +
32E ASN* 3.5 29.7 - - - +
33E ILE* 4.0 9.2 + - - +
18F LEU* 3.9 39.3 - - + -
19F HIS* 3.9 45.6 + - + +
22F VAL* 4.3 12.3 - - + -
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Residues in contact with SER 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 ASN* 3.0 29.5 + - - -
27E PHE 3.6 3.4 - - - -
29E LEU* 1.3 77.1 - - - +
31E TYR* 1.3 66.4 + - - +
33E ILE* 3.2 24.8 + - - +
34E LEU* 3.4 12.9 - - - +
49E LEU* 5.1 13.4 - - - +
501E MPD 3.7 24.0 - - - +
19F HIS* 4.0 13.2 + - - -
51F ARG* 5.5 1.9 + - - -
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Residues in contact with TYR 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* 2.9 52.6 + + - +
28E LYS 4.0 2.9 - - - +
30E SER* 1.3 73.7 - - - +
32E ASN* 1.3 66.5 + - - +
33E ILE 3.0 3.1 + - - -
34E LEU* 3.1 26.3 + - + +
35E ARG* 3.4 34.0 + - - +
50E ASP* 4.7 5.5 + - - -
122E GLY* 5.6 1.6 - - - -
126E HIS* 3.4 57.5 - + + +
127E SER* 3.8 9.4 + - - -
401E GA4 4.1 35.4 + - + +
501E MPD 3.9 19.5 - - + -
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Residues in contact with ASN 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 LYS* 3.1 34.6 + - - +
29E LEU* 3.5 30.6 - - - +
31E TYR* 1.3 77.7 - - - +
33E ILE* 1.3 65.1 + - + +
34E LEU 3.7 0.3 + - - -
35E ARG* 3.1 36.2 + - - +
601E NO3 4.7 3.6 + - - -
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Residues in contact with ILE 33 (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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29E LEU 4.2 10.3 - - - +
30E SER* 3.2 16.1 + - - +
31E TYR 3.0 1.0 - - - -
32E ASN* 1.3 83.9 - - + +
34E LEU* 1.3 65.4 + - + +
35E ARG 3.5 3.6 - - - +
42E GLU* 3.8 12.8 - - - +
45E LEU* 3.9 26.8 - - + +
49E LEU* 5.0 7.4 - - + -
19F HIS* 6.2 1.8 - - + -
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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