Contacts of the helix formed by residues 46 - 54 (chain D) in PDB entry 3E4U
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 HIS 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C THR* 3.9 19.9 - - + +
22D LEU* 4.3 6.3 - - + -
25D LEU* 3.8 7.7 - - + +
26D ARG* 3.6 23.5 + - + -
30D ILE 3.2 26.9 - - - -
31D LEU 3.4 16.4 + - - -
32D THR* 3.4 19.0 - - + -
33D ASP* 3.4 5.6 - - - +
34D VAL* 4.3 2.2 - - - -
45D ALA* 1.3 76.0 - - - +
47D LYS* 1.3 66.6 + - - +
48D THR* 3.9 15.9 - - - +
49D VAL* 3.4 13.7 + - + -
50D LEU* 3.4 15.1 + - - +
91D TYR* 2.9 36.8 + + - +
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Residues in contact with LYS 47 (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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12A THR* 5.9 0.2 - - - -
31C LEU* 4.1 30.6 - - + +
33D ASP* 2.7 47.9 + - - +
34D VAL* 3.7 18.1 - - + +
46D HIS* 1.3 71.0 - - - +
48D THR* 1.3 64.2 + - + +
50D LEU* 3.2 8.1 + - - +
51D MET* 3.2 27.5 + - - +
61D PHE* 3.6 28.6 - - + -
67D CYS 2.8 22.0 + - - +
68D ASN* 3.3 14.1 + - - +
69D LEU 2.7 29.9 + - - -
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Residues in contact with THR 48 (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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22C LEU* 3.4 26.6 - - - +
25C LEU* 3.9 14.4 - - + +
31C LEU* 4.4 14.1 - - + +
46C HIS* 3.4 39.0 - - + +
48C THR* 3.9 15.5 + - - +
49C VAL* 6.5 0.2 - - - -
33D ASP* 5.5 4.3 - - - +
46D HIS* 3.9 10.4 - - - +
47D LYS* 1.3 78.5 - - + +
49D VAL* 1.3 67.6 + - - +
51D MET* 3.7 3.2 + - - -
52D ALA* 3.4 14.9 + - - +
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Residues in contact with VAL 49 (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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18C VAL* 5.0 7.6 - - + -
22C LEU* 4.7 5.2 - - + -
19D LEU* 5.2 1.6 - - + -
22D LEU* 4.4 24.5 - - + -
46D HIS* 3.4 8.8 + - + +
47D LYS 3.3 0.8 - - - -
48D THR* 1.3 87.5 + - - +
50D LEU* 1.3 69.0 + - - +
52D ALA* 3.0 15.9 + - - +
53D CYS* 3.2 25.5 + - - -
90D MET* 4.4 9.6 - - + +
91D TYR* 3.7 52.9 - - + +
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Residues in contact with LEU 50 (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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34D VAL* 4.4 8.5 - - + -
36D ILE* 3.7 35.4 - - + -
45D ALA* 3.9 11.7 - - + -
46D HIS 3.4 12.3 + - - +
47D LYS 3.2 6.0 + - - +
49D VAL* 1.3 78.7 - - - +
51D MET* 1.3 56.8 + - - +
53D CYS* 3.2 1.7 + - - -
54D SER* 3.0 35.0 + - - +
57D PHE* 3.7 32.5 - - + -
61D PHE* 4.1 9.2 - - + -
83D PHE* 5.8 0.7 - - + -
87D LEU* 3.8 28.3 - - + -
90D MET* 3.9 19.5 - - + -
91D TYR* 4.6 3.8 - - + -
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Residues in contact with MET 51 (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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21C ASN* 5.3 0.5 - - - +
24C ARG* 5.7 1.7 + - - -
25C LEU* 4.1 20.4 - - + -
30C ILE* 3.6 17.7 - - + -
31C LEU* 3.6 23.1 - - + -
47D LYS 3.2 17.0 + - - +
48D THR* 3.9 4.0 - - - +
49D VAL 3.2 0.8 - - - -
50D LEU* 1.3 75.9 - - - +
52D ALA* 1.3 61.5 + - - +
53D CYS 3.5 0.2 + - - -
54D SER 3.8 4.2 + - - +
58D TYR* 3.6 47.4 - - + +
61D PHE* 3.7 32.3 - - + -
62D THR* 3.5 31.6 - - + -
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Residues in contact with ALA 52 (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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17C ASP* 5.7 0.7 - - - +
18C VAL* 3.8 27.3 - - + +
21C ASN* 2.8 50.9 + - + -
22C LEU* 4.4 6.1 - - + +
25C LEU* 5.4 1.7 - - + +
48D THR 3.4 10.8 + - - +
49D VAL 3.0 10.6 + - - +
51D MET* 1.3 78.4 - - - +
53D CYS* 1.3 61.9 + - - +
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Residues in contact with CYS 53 (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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14C HIS* 3.6 11.4 - - - +
18C VAL* 3.5 30.3 - - - -
49D VAL* 3.2 17.5 + - - +
50D LEU 3.2 3.5 + - - +
52D ALA* 1.3 78.8 - - - +
54D SER* 1.3 56.6 + - - +
55D GLY 4.4 0.2 - - - -
90D MET* 3.5 46.7 - - + -
113D GLN 5.0 0.5 - - - +
114D MET* 3.4 21.9 - - + +
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Residues in contact with SER 54 (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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50D LEU 3.0 13.1 + - - +
51D MET 3.8 1.6 + - - +
52D ALA 3.7 1.4 - - - -
53D CYS* 1.3 80.5 - - - +
55D GLY* 1.3 57.4 + - - +
56D LEU* 3.9 0.5 - - - +
57D PHE* 3.3 24.0 + - - -
58D TYR* 2.9 28.6 + - - +
90D MET* 4.0 17.7 - - - -
112D LEU* 2.8 25.1 + - - +
113D GLN 4.8 0.4 - - - -
114D MET* 4.2 6.7 - - - -
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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