Contacts of the helix formed by residues 27 - 38 (chain A) in PDB entry 1E0W
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 ASP 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.1 15.8 + - - +
26A SER* 1.3 76.7 + - - +
28A SER* 1.3 58.9 + - - +
29A THR* 3.0 22.5 + - - -
30A TYR* 3.1 11.2 + - + +
31A THR* 3.0 30.1 + - - +
269A ARG* 2.9 32.3 + - - +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER 3.5 6.8 + - - -
27A ASP* 1.3 70.0 + - - +
29A THR* 1.3 56.7 + - - +
31A THR* 3.4 8.7 + - - -
32A SER* 2.8 37.0 + - - -
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ASP* 3.0 9.7 + - - -
28A SER* 1.3 74.3 - - - +
30A TYR* 1.3 65.8 + - - +
32A SER* 3.5 3.3 + - - -
33A ILE* 3.1 51.5 + - + +
269A ARG* 4.2 13.9 - - - +
286A ASP 4.5 7.0 - - - +
287A GLY* 4.4 13.0 - - - +
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 3.7 5.2 + - - -
20A ILE* 3.4 27.9 - - + -
21A ALA* 3.1 26.6 + - - +
24A ARG* 3.5 45.6 - - + -
25A LEU* 4.3 9.9 - - + -
27A ASP* 3.1 18.2 + - + +
29A THR* 1.3 78.9 - - - +
31A THR* 1.4 64.3 + - + +
33A ILE* 4.2 2.7 - - - +
34A ALA* 3.0 33.1 + - + +
70A TRP* 6.4 0.2 - + - -
267A GLY* 6.2 0.2 - - - -
268A VAL* 3.7 22.6 - - + +
269A ARG* 3.7 23.9 - - - +
272A ASP* 3.5 28.5 - - + -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.3 51.4 - - + +
27A ASP 3.0 10.5 + - - +
28A SER* 3.4 14.0 + - - -
30A TYR* 1.4 79.8 - - + +
32A SER* 1.3 60.2 + - - +
35A GLY* 2.9 25.8 + - - -
70A TRP* 3.7 24.2 - - + +
74A ASN* 5.4 0.5 - - - +
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER 2.8 21.4 + - - -
29A THR* 3.5 5.9 + - - -
31A THR* 1.3 79.1 + - - +
33A ILE* 1.3 68.4 + - - +
35A GLY* 3.5 1.0 + - - -
36A ARG* 3.1 25.2 + - - +
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Residues in contact with ILE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 3.1 30.1 + - + +
30A TYR* 4.2 1.3 - - - +
32A SER* 1.3 76.0 - - - +
34A ALA* 1.3 66.0 + - - +
36A ARG* 3.3 21.6 + - - +
37A GLU* 3.0 28.6 + - + +
38A PHE* 5.4 0.2 - - + -
268A VAL* 4.1 17.0 - - + -
269A ARG* 5.5 4.7 - - + -
283A PHE* 3.9 32.8 - - + -
287A GLY* 3.5 38.1 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 4.8 0.4 - - + -
20A ILE* 4.0 19.5 - - + -
30A TYR* 3.0 20.6 + - + +
31A THR* 4.7 0.2 - - - -
33A ILE* 1.3 77.0 - - - +
35A GLY* 1.3 60.9 + - - +
38A PHE* 3.4 35.8 + - + +
70A TRP* 3.9 18.4 - - + -
76A LYS* 3.6 8.8 - - - -
268A VAL* 4.2 13.4 - - + +
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A THR 2.9 19.8 + - - -
32A SER* 3.9 1.8 - - - -
33A ILE 3.3 0.2 - - - -
34A ALA* 1.3 76.6 - - - +
36A ARG* 1.3 59.4 + - - +
70A TRP* 3.9 7.3 - - - -
74A ASN* 4.5 10.2 - - - +
76A LYS* 2.8 31.1 + - - -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A THR* 3.8 29.3 + - + +
32A SER 3.1 19.1 + - - +
33A ILE* 3.3 24.7 + - - +
35A GLY* 1.3 78.6 - - - +
37A GLU* 1.3 91.3 + - - +
38A PHE 3.7 0.6 + - - +
283A PHE* 4.2 10.5 - - - -
287A GLY 5.4 1.6 + - - -
289A LYS* 3.9 20.2 - - - +
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A SER 4.8 0.2 - - - +
4A THR* 3.5 10.7 - - - +
5A LEU* 3.2 27.4 + - + +
6A GLY* 2.8 27.8 + - - -
33A ILE 3.0 18.6 + - - +
35A GLY 3.5 0.2 - - - -
36A ARG* 1.3 115.8 + - - +
38A PHE* 1.3 77.2 + - + +
283A PHE* 3.9 15.3 - - + -
289A LYS* 4.1 3.5 + - - -
293A TYR* 2.7 38.6 + - - -
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Residues in contact with PHE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 4.1 9.4 - - + -
6A GLY* 4.7 1.1 - - - -
16A PHE* 3.4 23.1 - + - +
17A GLY 3.5 25.6 - - - -
18A THR* 3.6 31.6 - - + -
33A ILE 4.7 0.4 - - - -
34A ALA* 3.4 27.3 + - - +
35A GLY 4.2 0.3 - - - +
36A ARG 5.1 0.3 - - - -
37A GLU* 1.3 91.4 - - + +
39A ASN* 1.3 60.9 + - - +
40A MET 3.6 12.6 - - - +
41A VAL* 5.9 0.7 - - + -
76A LYS* 2.8 31.3 + - - -
265A VAL* 3.9 16.6 - - + -
267A GLY 4.8 3.1 - - - -
268A VAL* 4.4 12.8 - - + -
282A LEU* 5.7 0.9 - - + -
283A PHE* 4.3 20.2 - + - -
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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