Contacts of the helix formed by residues 48 - 61 (chain H) in PDB entry 2J28
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 48 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H GLN* 5.5 6.8 + - - +
44H ILE* 2.6 37.4 + - + +
45H GLU* 5.1 0.7 - - - -
47H PHE* 1.3 88.4 - - - +
49H ALA* 1.3 59.1 + - - +
50H ARG* 3.0 1.6 + - - -
51H ARG* 3.3 33.7 + - - +
52H ALA* 4.4 0.9 + - - +
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Residues in contact with ALA 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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44H ILE 3.9 0.8 + - - -
45H GLU 3.9 11.1 + - - +
46H PHE* 2.9 25.8 + - + +
48H GLU* 1.3 79.3 - - - +
50H ARG* 1.3 60.7 + - - +
51H ARG 3.2 0.7 + - - -
52H ALA* 3.5 7.9 + - - +
53H GLU* 3.2 24.6 + - + +
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Residues in contact with ARG 50 (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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15H LEU* 4.5 32.0 + - - +
16H GLY* 5.8 1.6 - - - -
46H PHE 3.6 1.4 + - - +
47H PHE* 2.7 57.5 + - + +
48H GLU* 4.7 0.9 - - - +
49H ALA* 1.3 76.9 - - - +
51H ARG* 1.3 74.7 + - + +
53H GLU* 4.7 4.9 - - - +
54H LEU* 3.0 60.1 + - + +
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Residues in contact with ARG 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLU* 3.3 28.3 + - - +
49H ALA 3.2 0.6 - - - -
50H ARG* 1.3 90.4 - - + +
52H ALA* 1.3 65.5 + - - +
54H LEU* 4.0 1.9 - - - +
55H GLU* 3.3 29.8 + - - +
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Residues in contact with ALA 52 (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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48H GLU 4.4 0.8 + - - +
49H ALA* 3.5 9.0 + - - +
50H ARG 3.4 0.2 - - - -
51H ARG* 1.3 83.3 - - + +
53H GLU* 1.3 63.7 + - - +
55H GLU* 3.4 21.1 + - - +
56H ALA* 3.8 4.5 + - - +
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Residues in contact with GLU 53 (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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49H ALA* 3.2 15.1 + - + +
50H ARG* 4.4 3.9 - - - +
52H ALA* 1.3 78.6 - - - +
54H LEU* 1.3 85.6 + - - +
56H ALA* 3.2 22.2 + - + +
57H LYS* 3.2 35.7 - - + +
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Residues in contact with LEU 54 (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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50H ARG* 3.0 68.9 + - + +
51H ARG* 4.0 2.0 - - - +
53H GLU* 1.3 89.1 + - - +
55H GLU* 1.3 62.8 + - - +
56H ALA 2.9 6.8 + - - -
57H LYS* 3.3 20.0 + - + +
58H LEU* 3.0 38.0 + - + +
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Residues in contact with GLU 55 (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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51H ARG* 3.3 24.4 + - - +
52H ALA* 3.5 16.4 - - - +
53H GLU 3.2 0.2 - - - -
54H LEU* 1.3 76.8 - - - +
56H ALA* 1.3 58.0 + - - +
58H LEU* 3.7 6.8 - - + +
59H ALA* 2.9 31.0 + - + +
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Residues in contact with ALA 56 (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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52H ALA 3.8 3.7 + - - +
53H GLU* 3.2 17.1 + - + +
54H LEU 2.9 0.6 + - - -
55H GLU* 1.3 75.6 - - - +
57H LYS* 1.3 59.0 + - + +
58H LEU 2.9 3.8 - - - -
59H ALA* 2.7 23.4 + - - -
60H GLU* 2.8 25.9 + - - +
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Residues in contact with LYS 57 (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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53H GLU* 3.2 51.1 - - + +
54H LEU* 3.3 25.5 + - + +
56H ALA* 1.3 75.1 - - + +
58H LEU* 1.3 66.2 + - + +
60H GLU* 4.1 16.2 + - - +
61H VAL* 4.3 12.1 - - - +
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Residues in contact with LEU 58 (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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54H LEU* 3.0 40.9 + - + +
55H GLU* 3.7 7.9 - - + +
56H ALA 2.9 0.8 - - - -
57H LYS* 1.3 88.4 - - + +
59H ALA* 1.3 58.6 + - - +
60H GLU 3.5 0.2 - - - -
61H VAL* 3.0 27.6 - - + +
62H LEU* 4.3 8.1 + - - +
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Residues in contact with ALA 59 (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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55H GLU* 2.9 21.6 + - + +
56H ALA* 2.7 8.5 + - - +
58H LEU* 1.3 78.2 - - - +
60H GLU* 1.3 59.6 + - - +
61H VAL 3.2 0.4 - - - -
62H LEU* 2.7 29.5 + - - +
63H ALA* 2.7 18.7 + - + +
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Residues in contact with GLU 60 (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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56H ALA* 2.8 31.4 + - + +
57H LYS* 4.2 9.6 - - - +
59H ALA* 1.3 85.0 - - - +
61H VAL* 1.3 60.0 + - + +
63H ALA* 2.8 29.5 + - - +
64H ALA* 3.1 18.5 + - + +
65H ALA 4.0 2.4 + - - -
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Residues in contact with VAL 61 (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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57H LYS 4.3 9.8 + - - +
58H LEU* 3.0 34.3 - - + +
60H GLU* 1.3 77.9 - - + +
62H LEU* 1.3 60.6 + - + +
65H ALA* 3.8 20.5 - - - +
66H ASN 4.1 1.7 + - - -
135H HIS* 3.8 41.7 - - + +
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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