Contacts of the helix formed by residues 40 - 49 (chain H) in PDB entry 3DBL
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 GLU 40 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H SER* 3.0 9.8 + - - +
39H THR* 1.3 86.9 - - + +
41H SER* 1.3 62.1 + - - +
42H LEU 3.4 3.3 + - - -
43H GLN* 3.6 12.9 + - + +
44H PHE* 3.4 30.2 + - + +
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Residues in contact with SER 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 3.8 22.7 + - - +
35H PHE* 6.1 0.2 - - - -
36H GLU 4.8 1.8 + - - -
38H SER* 2.9 37.4 + - - -
39H THR 3.6 0.2 - - - -
40H GLU* 1.3 73.5 - - - +
42H LEU* 1.3 65.3 + - - +
44H PHE* 3.2 10.0 - - - +
45H LEU* 3.0 22.3 + - - +
312H THR* 6.4 0.4 - - - -
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Residues in contact with LEU 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H TRP* 3.7 40.6 - - + -
20H VAL* 4.5 19.7 - - + -
21H LYS* 4.0 28.9 - - + -
24H LEU* 4.0 18.1 - - + +
38H SER 5.3 0.2 + - - -
39H THR 4.8 6.4 + - - +
40H GLU 3.4 0.6 - - - -
41H SER* 1.3 77.2 + - - +
43H GLN* 1.3 65.8 + - - +
45H LEU* 3.1 15.6 + - + +
46H LEU* 3.1 32.5 + - + +
71H GLY* 4.7 8.1 - - - +
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Residues in contact with GLN 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H THR 5.4 0.8 + - - +
40H GLU* 3.6 17.5 + - + +
42H LEU* 1.3 79.8 - - - +
44H PHE* 1.3 63.6 + - - +
46H LEU* 3.3 16.2 + - - +
47H ASP* 3.0 64.3 + - - +
73H ARG* 4.8 5.7 - - - +
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Residues in contact with PHE 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H GLU* 3.4 21.5 + - + +
41H SER* 3.2 14.1 - - - +
43H GLN* 1.3 79.3 - - - +
45H LEU* 1.3 54.9 + - - +
47H ASP* 4.6 3.1 - - + -
48H THR* 2.6 71.0 + - + -
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Residues in contact with LEU 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H LEU* 4.7 8.5 - - + -
41H SER 3.0 12.6 + - - +
42H LEU* 3.1 11.0 + - + +
44H PHE* 1.3 78.0 - - - +
46H LEU* 1.3 60.8 + - - +
48H THR* 4.9 0.2 - - - -
49H CYS* 3.4 40.0 + - + +
70H SER 4.6 0.2 - - - +
71H GLY* 3.8 25.4 - - - +
72H PHE* 3.4 35.3 - - + -
73H ARG 4.5 0.7 + - - -
74H GLN* 5.3 0.2 - - - +
308H PHE* 4.2 14.8 - - + -
311H ALA* 3.9 14.1 - - + +
312H THR* 3.9 24.0 - - + -
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Residues in contact with LEU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H ASP* 5.0 1.3 - - - +
17H TRP* 3.9 31.0 - - + +
42H LEU* 3.1 40.2 + - + +
43H GLN* 3.8 15.3 - - - +
45H LEU* 1.3 76.8 - - - +
47H ASP* 1.3 68.5 + - - +
71H GLY* 2.8 32.5 - - - +
72H PHE 4.7 0.7 - - - +
73H ARG* 3.2 53.1 - - + +
74H GLN* 3.2 20.6 - - - +
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Residues in contact with ASP 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43H GLN* 3.0 45.4 + - - +
44H PHE* 3.8 2.7 - - - +
46H LEU* 1.3 86.5 - - - +
48H THR* 1.3 68.3 + - + +
49H CYS 3.8 0.7 - - - -
73H ARG* 4.4 6.2 + - - -
74H GLN* 3.6 18.4 - - - +
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Residues in contact with THR 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44H PHE* 2.6 62.8 + - + +
47H ASP* 1.3 84.3 - - + +
49H CYS* 1.3 59.6 + - - +
50H LYS* 3.4 10.3 + - - +
74H GLN* 4.8 1.6 - - - -
139H HIS* 3.6 19.8 + - - -
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Residues in contact with CYS 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 3.4 46.1 + - + +
47H ASP 3.8 1.2 - - - -
48H THR* 1.3 77.7 + - - +
50H LYS* 1.3 61.9 + - - +
51H VAL* 3.5 11.2 + - - +
72H PHE* 3.9 19.1 - - + +
73H ARG 5.2 0.2 + - - -
74H GLN* 3.1 25.5 + - - +
139H HIS* 4.3 21.8 - - + -
140H ILE* 5.1 1.8 - - - -
311H ALA* 4.1 11.0 - - - -
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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