Contacts of the helix formed by residues 20 - 32 (chain C) in PDB entry 2E52
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 PHE 20 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C GLN 3.7 1.8 + - - -
19C GLU* 1.3 73.3 - - - +
21C LYS* 1.3 57.4 + - - +
23C ALA* 3.4 5.5 + - - +
24C THR* 2.8 46.3 + - - -
58C THR* 4.2 9.2 - - + -
61C LYS* 3.7 28.9 - - + -
62C LEU* 3.5 38.4 - - + -
65C LYS* 4.5 9.0 - - + -
88C ARG* 4.0 16.4 - - - -
11H G 3.4 63.5 - - - +
12H C 3.6 11.7 - - - +
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Residues in contact with LYS 21 (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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19C GLU* 3.2 3.6 + - + +
20C PHE* 1.3 79.8 - - - +
22C GLN* 1.3 61.1 + - - +
24C THR* 3.4 9.5 + - + -
25C ASN* 3.2 37.8 + - - +
86C GLU* 4.3 29.5 + - - +
12H C 4.3 13.7 + - - +
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Residues in contact with GLN 22 (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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18C GLN* 3.5 35.0 + - - +
19C GLU* 3.0 29.4 + - + +
21C LYS* 1.3 75.5 - - - +
23C ALA* 1.3 64.8 + - - +
25C ASN* 3.0 23.6 + - + +
26C SER* 3.1 15.4 + - - -
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Residues in contact with ALA 23 (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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15C LEU* 3.5 32.4 - - + +
18C GLN* 3.7 17.5 - - + +
19C GLU 2.7 20.1 + - - +
20C PHE* 3.5 8.7 - - - +
22C GLN* 1.3 72.3 - - - +
24C THR* 1.3 59.6 + - - +
26C SER 3.3 1.7 + - - -
27C LEU* 3.2 19.4 + - - +
62C LEU* 3.6 25.4 - - + -
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Residues in contact with THR 24 (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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20C PHE* 2.8 41.6 + - - -
21C LYS* 3.5 11.2 - - + +
22C GLN 3.2 0.2 - - - -
23C ALA* 1.3 70.0 - - - +
25C ASN* 1.3 61.8 + - - +
27C LEU* 3.1 11.9 + - - +
28C ILE* 2.9 42.5 + - + +
62C LEU* 4.6 1.1 - - - +
65C LYS* 3.7 35.0 - - + +
69C ILE* 4.4 2.9 - - + -
84C PRO* 6.0 0.9 - - + -
12H C 5.2 0.7 + - - -
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Residues in contact with ASN 25 (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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21C LYS* 3.2 35.4 + - - +
22C GLN* 3.0 14.8 + - + +
24C THR* 1.3 77.4 - - - +
26C SER* 1.3 56.3 + - - +
28C ILE* 3.3 17.8 + - - +
29C SER* 2.9 29.9 + - - -
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Residues in contact with SER 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 4.1 10.6 - - - +
15C LEU* 3.8 19.5 - - - +
18C GLN* 3.2 25.3 + - - -
22C GLN 3.1 4.8 + - - -
23C ALA 3.6 8.3 - - - -
24C THR 3.3 0.2 - - - -
25C ASN* 1.3 75.5 - - - +
27C LEU* 1.3 57.7 + - - +
29C SER* 3.5 7.3 + - - -
30C PHE* 3.0 30.3 + - - +
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Residues in contact with LEU 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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8C LEU* 3.9 23.3 - - + -
11C LEU* 3.8 23.3 - - + -
12C ILE* 4.2 8.5 - - + -
15C LEU* 4.1 10.1 - - + -
23C ALA 3.2 14.3 + - - +
24C THR* 3.1 10.4 + - - +
26C SER* 1.3 73.2 - - - +
28C ILE* 1.3 59.4 - - - +
30C PHE* 3.3 1.6 + - - +
31C ILE* 2.9 36.9 + - + +
62C LEU* 3.4 47.8 - - + +
65C LYS* 4.4 4.3 - - + -
66C ALA* 4.0 10.1 - - + +
69C ILE* 3.6 15.0 - - + -
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Residues in contact with ILE 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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24C THR* 2.9 30.2 + - + +
25C ASN* 3.6 19.1 - - - +
27C LEU* 1.3 75.4 - - - +
29C SER* 1.3 57.7 + - - +
32C TYR* 2.9 59.5 + - + +
69C ILE* 3.7 28.0 - - + -
84C PRO* 4.4 19.1 - - + -
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Residues in contact with SER 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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25C ASN 2.9 16.7 + - - -
26C SER* 3.6 9.0 - - - -
28C ILE* 1.3 78.9 - - - +
30C PHE* 1.3 61.7 + - - +
32C TYR* 4.4 1.0 - - - +
33C LYS* 3.2 54.8 + - - +
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Residues in contact with PHE 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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4C ALA 3.9 7.0 - - - -
7C LYS* 3.7 44.6 - - + -
8C LEU* 3.7 29.6 - - + -
11C LEU* 3.6 25.1 - - + -
26C SER 3.0 18.6 + - - +
27C LEU 3.7 1.8 - - - +
29C SER* 1.3 76.8 + - - +
31C ILE* 1.3 74.6 + - + +
33C LYS* 3.7 4.4 + - - +
34C LEU* 3.4 40.7 + - + +
42C LEU* 4.3 13.0 - - + -
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Residues in contact with ILE 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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8C LEU* 4.6 5.8 - - + -
27C LEU* 2.9 27.7 + - + +
30C PHE* 1.3 84.3 - - + +
32C TYR* 1.3 66.0 + - - +
34C LEU* 3.2 27.5 + - + +
39C VAL* 4.4 7.8 - - + +
42C LEU* 4.0 11.9 - - + -
66C ALA* 3.8 33.4 - - + +
69C ILE* 3.7 30.5 - - + -
70C VAL* 3.9 23.8 - - + -
73C LYS* 4.2 13.9 - - + -
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Residues in contact with TYR 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 ILE* 2.9 40.1 + - + +
29C SER* 4.7 1.6 - - - +
31C ILE* 1.3 75.0 - - - +
33C LYS* 1.3 61.0 + - + +
34C LEU 4.1 1.4 - - - +
69C ILE* 3.6 36.8 - - + -
72C ALA* 3.7 4.7 - - - +
73C LYS* 3.2 47.7 + - + +
76C GLN* 3.4 29.5 + - - -
82C SER 4.1 2.6 + - - -
83C LYS* 4.3 5.8 - - + +
84C PRO* 3.5 26.5 - - + +
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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