Contacts of the helix formed by residues 20 - 32 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D GLN 3.6 2.0 + - - -
19D GLU* 1.3 75.1 - - - +
21D LYS* 1.3 57.0 + - - +
23D ALA* 3.7 5.8 - - - +
24D THR* 2.9 44.5 + - - -
58D THR* 4.2 6.7 - - + -
61D LYS* 3.9 24.7 - - + -
62D LEU* 3.5 40.6 - - + -
65D LYS* 4.3 11.0 - - + -
88D ARG* 3.9 20.0 - - - -
11F G 3.3 63.9 - - - +
12F C 3.4 11.4 - - - +
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Residues in contact with LYS 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D GLU* 3.3 4.9 - - + +
20D PHE* 1.3 76.4 - - - +
22D GLN* 1.3 61.5 + - - +
24D THR* 3.5 7.8 + - - -
25D ASN* 3.1 25.1 + - - +
86D GLU* 3.0 34.3 + - - +
12F C 3.0 54.1 + - - +
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ASN 5.1 1.0 + - - -
18D GLN* 3.6 37.8 + - - +
19D GLU* 3.0 21.5 + - + +
21D LYS* 1.3 76.0 - - - +
23D ALA* 1.3 65.3 + - - +
25D ASN* 3.0 16.3 + - + +
26D SER* 3.1 17.4 + - - +
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Residues in contact with ALA 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D LEU* 3.6 26.8 - - + +
18D GLN* 3.7 19.5 - - + +
19D GLU 2.8 19.1 + - - +
20D PHE* 3.7 6.1 - - - +
22D GLN* 1.3 72.7 - - - +
24D THR* 1.3 61.3 + - - +
26D SER* 3.4 1.4 + - - -
27D LEU* 3.1 25.3 + - - +
62D LEU* 3.6 27.6 - - + -
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Residues in contact with THR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 2.9 43.7 + - - -
21D LYS* 3.6 8.7 - - - -
22D GLN 3.2 0.2 - - - -
23D ALA* 1.3 72.3 - - - +
25D ASN* 1.3 62.6 + - - +
27D LEU* 3.1 11.3 + - - +
28D ILE* 2.9 43.6 + - + +
62D LEU* 4.6 1.0 - - - +
65D LYS* 3.8 34.0 - - + +
69D ILE* 4.4 3.1 - - + -
84D PRO* 6.0 1.1 - - + -
12F C 5.2 0.5 + - - -
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Residues in contact with ASN 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS 3.1 13.8 + - - +
22D GLN* 3.0 11.9 + - + +
24D THR* 1.3 79.1 - - - +
26D SER* 1.3 56.4 + - - +
28D ILE* 3.2 23.0 + - - +
29D SER* 2.9 34.8 + - - -
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.0 10.1 - - - +
15D LEU* 3.7 19.9 - - - +
18D GLN* 3.3 14.2 + - - -
22D GLN* 3.1 13.5 + - - +
23D ALA 3.7 8.5 - - - -
24D THR 3.3 0.2 - - - -
25D ASN* 1.3 75.6 - - - +
27D LEU* 1.3 63.2 + - - +
29D SER* 3.4 7.1 + - - -
30D PHE* 3.0 23.6 + - - +
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.6 30.7 - - + -
11D LEU* 4.0 16.4 - - + -
12D ILE* 4.2 9.0 - - + -
15D LEU* 4.1 10.3 - - + -
23D ALA 3.1 20.0 + - - +
24D THR* 3.1 9.6 + - - +
26D SER* 1.3 77.3 - - - +
28D ILE* 1.3 56.6 + - - +
30D PHE* 3.3 2.5 + - + +
31D ILE* 2.8 36.3 + - + +
62D LEU* 3.7 42.4 - - + +
65D LYS* 4.6 2.9 - - + -
66D ALA* 4.2 10.3 - - + +
69D ILE* 3.6 15.0 - - + -
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Residues in contact with ILE 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D THR* 2.9 31.5 + - + +
25D ASN* 3.6 28.5 - - - +
27D LEU* 1.3 75.9 - - - +
29D SER* 1.3 64.5 + - - +
32D TYR* 2.9 54.9 + - + +
69D ILE* 3.7 28.0 - - + -
84D PRO* 4.7 14.4 - - + -
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ASN* 2.9 22.4 + - - -
26D SER* 3.7 7.1 - - - -
28D ILE* 1.3 78.8 - - - +
30D PHE* 1.3 65.6 + - - +
32D TYR* 4.4 1.3 - - - -
33D LYS* 3.1 46.6 + - - +
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Residues in contact with PHE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ALA* 3.9 6.5 - - - -
7D LYS* 3.7 27.8 - - + -
8D LEU* 3.7 45.1 - - + -
11D LEU* 3.5 33.0 - - + -
26D SER 3.0 10.1 + - - +
27D LEU 3.5 2.7 - - - +
29D SER* 1.3 78.9 - - - +
31D ILE* 1.3 78.9 + - + +
33D LYS* 3.5 9.9 + - - +
34D LEU* 3.5 39.8 + - + +
42D LEU* 4.3 6.5 - - + -
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.5 8.7 - - + -
27D LEU* 2.8 26.3 + - + +
30D PHE* 1.3 85.8 - - + +
32D TYR* 1.3 63.8 + - - +
34D LEU* 3.1 27.2 + - + +
39D VAL* 4.4 3.3 - - + +
42D LEU* 3.9 13.7 - - + -
66D ALA* 3.8 33.0 - - + +
69D ILE* 3.7 30.5 - - + -
70D VAL* 3.8 18.6 - - + -
73D LYS* 4.1 25.9 - - + +
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Residues in contact with TYR 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ILE* 2.9 34.6 + - + +
29D SER* 4.6 1.3 - - - +
31D ILE* 1.3 77.7 - - - +
33D LYS* 1.3 61.2 + - + +
34D LEU 3.3 0.7 - - - +
69D ILE* 3.6 37.9 - - + -
72D ALA* 3.7 4.0 - - - +
73D LYS* 3.0 49.7 + - + +
76D GLN* 3.4 29.6 + - - -
82D SER 4.0 2.4 + - - -
83D LYS* 4.1 1.7 - - - +
84D PRO* 3.4 26.9 - - + +
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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