Contacts of the helix formed by residues 48 - 59 (chain E) in PDB entry 2X2D
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 48 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12E HIS* 4.3 19.7 - - + -
46E GLY 4.7 4.0 - - - +
47E ALA* 1.3 76.4 - - - +
49E PRO* 1.3 67.6 - - - +
50E GLN* 3.4 8.0 + - - +
51E ASP* 3.0 33.8 + - - +
52E LEU* 2.9 26.9 + - - +
111E LEU* 4.3 4.7 - - + +
114E GLN* 3.8 7.4 - - - -
115E ILE* 4.5 9.9 - - + -
118E MET* 3.2 27.6 - - + -
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Residues in contact with PRO 49 (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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48E THR* 1.3 86.7 - - - +
50E GLN* 1.3 57.5 + - - +
52E LEU* 3.7 2.0 - - + +
53E ASN* 2.8 37.3 + - - -
103E ASP 4.8 0.2 - - - +
104E ILE 3.2 28.9 - - - +
106E GLY 4.0 9.2 - - - +
114E GLN* 3.9 15.9 - - + +
118E MET* 3.8 13.2 - - + -
126E VAL* 3.9 23.3 - - + +
127E GLY* 3.9 12.8 - - - +
130E TYR* 3.7 14.1 - - + -
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Residues in contact with GLN 50 (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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48E THR* 3.2 0.8 - - - +
49E PRO* 1.3 75.8 - - - +
51E ASP* 1.3 60.5 + - - +
53E ASN* 3.3 7.6 + - - +
54E THR* 3.0 34.9 + - + +
106E GLY* 5.9 0.4 - - - -
111E LEU* 3.1 47.7 - - + +
114E GLN* 2.9 27.7 + - - +
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Residues in contact with ASP 51 (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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12E HIS* 4.7 9.9 + - - -
13E GLN 4.6 7.3 - - - +
14E ALA* 4.9 0.2 - - - -
15E ILE* 3.9 40.5 + - + +
46E GLY 4.8 0.9 - - - +
47E ALA* 3.9 15.6 - - + -
48E THR* 3.0 36.4 + - - +
50E GLN* 1.3 75.3 - - - +
52E LEU* 1.3 61.8 + - - +
54E THR* 2.7 23.7 + - - +
55E MET* 2.9 20.5 + - - +
111E LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 52 (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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40E PHE* 4.0 14.3 - - + -
44E SER* 3.5 23.6 - - - +
47E ALA* 3.4 22.0 - - + -
48E THR 2.9 21.1 + - - +
49E PRO* 3.7 6.7 - - + +
51E ASP* 1.3 76.0 - - - +
53E ASN* 1.3 59.3 + - - +
55E MET* 3.2 9.3 + - - +
56E LEU* 3.0 31.0 + - - +
127E GLY* 3.5 25.4 - - - +
130E TYR* 3.6 24.7 - - + -
131E LYS* 3.8 14.1 - - - +
134E ILE* 3.9 15.0 - - + -
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Residues in contact with ASN 53 (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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49E PRO 2.8 22.0 + - - +
50E GLN* 3.7 6.8 - - - +
52E LEU* 1.3 75.2 - - - +
54E THR* 1.3 59.8 + - + +
56E LEU* 3.2 10.0 + - - +
57E ASN* 2.8 44.0 + - - +
105E ALA 2.8 26.5 + - - -
106E GLY* 4.1 10.9 + - - -
107E THR* 5.5 0.8 - - - +
130E TYR* 2.5 25.2 + - - -
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Residues in contact with THR 54 (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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15E ILE* 3.7 25.1 - - + +
20E LEU* 4.0 10.8 - - - +
50E GLN* 3.0 30.6 + - + +
51E ASP* 2.7 24.6 + - - +
53E ASN* 1.3 75.3 - - + +
55E MET* 1.3 62.4 + - - +
57E ASN* 3.1 24.5 + - - +
58E THR* 3.2 16.6 + - - -
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Residues in contact with MET 55 (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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15E ILE* 4.9 12.3 - - + -
19E THR* 5.7 3.1 - - + +
20E LEU* 3.9 19.5 - - + +
23E TRP* 2.9 57.5 + - + +
40E PHE* 3.8 24.5 - - + -
43E LEU* 3.9 25.8 - - + +
44E SER* 3.7 27.6 - - - -
51E ASP* 2.9 17.4 + - - +
52E LEU* 3.2 13.2 - - - +
53E ASN 3.2 0.2 - - - -
54E THR* 1.3 79.4 + - - +
56E LEU* 1.3 61.2 + - - +
58E THR* 3.6 8.1 + - - +
59E VAL* 4.0 1.4 + - - +
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Residues in contact with LEU 56 (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 TRP* 4.7 10.3 - - + -
40E PHE* 4.2 20.4 - - + -
52E LEU 3.0 19.1 + - - +
53E ASN* 3.2 10.7 + - - +
55E MET* 1.3 78.2 - - - +
57E ASN* 1.3 63.1 + - - +
59E VAL* 3.3 15.2 + - + +
66E MET* 3.5 28.3 - - + +
69E LEU* 3.8 31.6 - - + -
70E LYS* 6.5 0.4 - - + -
73E ILE* 4.3 11.4 - - + -
130E TYR* 4.5 7.2 - - - +
134E ILE* 4.2 27.1 - - + -
138E LEU* 5.9 1.6 - - + -
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Residues in contact with ASN 57 (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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53E ASN* 2.8 34.8 + - - +
54E THR* 3.1 19.3 + - - +
56E LEU* 1.3 72.0 - - - +
58E THR* 1.3 62.5 + - - +
59E VAL 3.4 5.0 + - - +
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Residues in contact with THR 58 (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 LEU* 4.2 18.2 - - + +
23E TRP* 4.2 12.8 - - + -
24E VAL* 2.8 41.7 - - + +
54E THR 3.2 12.2 + - - -
55E MET 3.8 8.7 - - - +
57E ASN* 1.3 81.1 - - - +
59E VAL* 1.3 67.4 + - + +
60E GLY* 3.2 5.4 + - - -
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Residues in contact with VAL 59 (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 TRP* 4.1 18.2 - - + +
24E VAL* 5.7 1.1 - - - +
27E VAL* 4.0 36.3 - - + -
32E PHE* 5.0 1.1 - - + -
55E MET 4.3 0.4 - - - +
56E LEU* 3.3 19.8 + - + +
57E ASN 4.2 5.5 - - - +
58E THR* 1.3 78.2 - - + +
60E GLY* 1.3 60.5 + - - +
61E GLY 4.0 4.6 + - - +
62E HIS* 3.9 25.1 - - + -
66E MET* 3.8 32.3 - - + +
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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