Contacts of the helix formed by residues 26 - 39 (chain C) in PDB entry 1E3O
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 THR 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C ARG* 3.9 2.7 - - - +
24C GLY 5.3 2.0 - - - +
25C PHE* 1.3 78.6 - - - +
27C GLN* 1.3 64.8 + - - +
28C GLY* 3.4 5.1 + - - -
29C ASP* 2.9 36.2 + - - +
30C VAL* 3.2 21.0 + - - +
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Residues in contact with GLN 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A A 5.4 0.3 - - - -
17C LYS* 6.0 1.0 - - - +
20C ARG* 3.6 25.2 - - - +
26C THR* 1.3 73.6 - - - +
28C GLY* 1.3 63.4 + - - +
30C VAL* 3.3 2.6 + - - +
31C GLY 3.0 17.7 + - - -
44C GLN* 3.0 35.6 + - + +
47C ILE* 3.6 32.2 - - + +
48C SER* 3.4 27.0 + - - +
51C GLU* 3.1 19.8 + - - +
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Residues in contact with GLY 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR* 3.1 6.3 + - - -
27C GLN* 1.3 80.2 - - - +
29C ASP* 1.3 60.6 + - - +
31C GLY* 3.1 2.9 + - - -
32C LEU* 2.9 34.7 + - - +
42C PHE 5.1 0.3 - - - +
44C GLN* 4.1 23.5 - - - +
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Residues in contact with ASP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY 4.3 2.9 - - - +
25C PHE* 3.6 28.3 - - + -
26C THR* 2.9 48.0 + - - +
28C GLY* 1.3 75.4 - - - +
30C VAL* 1.3 59.5 - - - +
32C LEU* 3.2 13.3 + - - +
33C ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.7 25.8 - - + -
20C ARG* 3.5 36.6 - - + -
25C PHE* 4.1 3.6 - - + -
26C THR 3.2 6.0 + - - +
27C GLN 3.7 7.0 - - - +
29C ASP* 1.3 77.4 - - - +
31C GLY* 1.3 63.3 + - - +
33C ALA* 3.1 7.2 + - - +
34C MET* 2.9 36.1 + - + +
47C ILE* 4.2 13.0 - - + -
67C LEU* 4.5 0.4 - - + -
70C TRP* 3.7 34.1 - - + +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLN 3.0 14.2 + - - -
28C GLY 3.1 3.5 + - - -
30C VAL* 1.3 77.2 - - - +
32C LEU* 1.3 61.4 - - - +
34C MET* 3.5 7.4 + - - +
41C ASP* 3.5 6.1 - - - +
42C PHE* 3.1 50.1 + - - -
43C SER 5.0 0.7 - - - -
47C ILE* 4.0 10.3 - - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLY* 2.9 22.7 + - - +
29C ASP* 3.6 14.6 - - - +
31C GLY* 1.3 78.3 - - - +
33C ALA* 1.3 61.2 + - - +
35C GLY* 3.0 13.2 + - - -
36C LYS* 3.0 23.3 + - + +
41C ASP* 4.8 7.7 - - + +
42C PHE 5.8 1.1 - - - +
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Residues in contact with ALA 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PHE* 6.1 4.9 - - + -
29C ASP 2.9 17.9 + - - +
30C VAL* 3.1 5.6 + - - +
32C LEU* 1.3 73.5 - - - +
34C MET* 1.3 57.7 + - - +
36C LYS* 4.3 9.6 - - - +
37C LEU* 2.7 49.4 + - + +
70C TRP* 3.8 25.6 - - + +
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Residues in contact with MET 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 2.9 22.9 + - + +
31C GLY* 3.5 10.3 - - - +
32C LEU 3.2 0.2 - - - -
33C ALA* 1.3 77.4 - - - +
35C GLY* 1.3 58.2 + - - +
38C TYR* 3.1 35.8 + - + +
39C GLY 3.2 6.2 + - - -
40C ASN* 3.2 38.2 + - - +
41C ASP* 4.4 0.2 - - - -
42C PHE* 4.4 10.5 - - + -
47C ILE* 5.3 0.2 - - + -
66C LEU* 3.3 31.0 - - + +
67C LEU* 3.8 22.4 - - + -
70C TRP* 3.4 31.4 - - + -
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Residues in contact with GLY 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 3.0 6.5 + - - -
34C MET* 1.3 81.4 - - - +
36C LYS* 1.3 63.2 + - - +
39C GLY* 3.0 20.6 + - - -
40C ASN 3.6 2.2 - - - -
41C ASP* 3.2 35.5 - - - +
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Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.0 22.6 + - + +
33C ALA* 3.2 8.5 + - - +
35C GLY* 1.3 78.9 - - - +
37C LEU* 1.3 69.2 + - + +
39C GLY 4.9 0.3 + - - -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ALA* 2.7 34.9 + - + +
36C LYS* 1.3 84.8 - - + +
38C TYR* 1.3 99.5 + - + +
39C GLY 3.7 0.4 - - - -
70C TRP* 4.7 6.1 - - + +
73C ASP* 4.9 9.0 - - + +
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Residues in contact with TYR 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C MET* 3.1 33.4 + - + +
37C LEU* 1.3 112.6 - - + +
39C GLY* 1.3 60.9 + - - +
40C ASN* 3.2 23.6 - - - +
69C LYS* 3.5 35.0 + - + +
70C TRP* 3.7 27.0 - + + -
73C ASP* 3.0 41.0 - - + +
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C GLY* 3.0 17.6 + - - -
36C LYS 4.7 0.4 + - - -
37C LEU 3.7 1.0 - - - -
38C TYR* 1.3 78.3 - - - +
40C ASN* 1.3 59.3 + - - +
41C ASP 4.1 0.4 - - - -
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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