Contacts of the helix formed by residues 52 - 63 (chain B) in PDB entry 1JS6
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 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 4.5 3.1 - - - +
51B ASP* 1.3 74.5 - - - +
53B PHE* 1.3 64.9 + - - +
54B GLU* 2.7 51.4 - - + +
55B ASP* 2.8 26.5 + - - +
56B ILE* 2.8 15.6 + - - +
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Residues in contact with PHE 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.9 20.2 - - + -
364A PHE* 4.4 6.1 - + - -
368A MET* 3.8 28.4 - - + -
9B ARG* 3.5 54.6 - - + +
12B GLU* 3.3 33.4 - - + -
13B MET* 4.0 31.2 - - + -
51B ASP 3.8 2.6 + - - -
52B THR* 1.3 72.0 - - - +
54B GLU* 1.3 59.7 + - - +
56B ILE* 3.1 11.0 + - + +
57B LEU* 2.8 52.7 + - + +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 4.1 9.9 + - - -
9B ARG* 2.7 45.2 + - - +
12B GLU* 5.3 4.0 - - - +
52B THR* 2.7 26.1 - - + +
53B PHE* 1.3 78.5 - - - +
55B ASP* 1.3 58.1 + - - +
57B LEU* 3.4 6.6 + - - +
58B GLN* 3.1 32.2 + - - +
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ARG* 3.3 17.6 + - - +
51B ASP* 4.1 9.4 - - - +
52B THR* 2.8 30.3 + - - +
54B GLU* 1.3 73.4 - - - +
56B ILE* 1.3 62.1 + - - +
58B GLN* 3.2 22.4 + - - +
59B ASP* 3.1 29.2 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TRP* 4.6 2.6 - - + -
364A PHE* 3.7 42.8 - - + +
367A ARG* 3.3 50.0 - - + +
368A MET* 3.3 39.9 - - + +
51B ASP* 4.4 5.4 - - + -
52B THR 2.8 17.3 + - - +
53B PHE* 3.5 8.1 - - + +
55B ASP* 1.3 75.0 - - - +
57B LEU* 1.3 64.2 + - - +
59B ASP* 3.3 3.8 + - - +
60B VAL* 3.1 22.3 + - + +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 5.4 0.4 - - + -
364A PHE* 5.0 2.7 - - + -
12B GLU* 5.5 6.5 - - + +
13B MET* 3.8 28.3 - - + -
16B TYR* 4.2 44.0 + - + -
53B PHE* 2.8 42.6 + - + +
54B GLU* 3.8 6.3 - - - +
55B ASP 3.2 0.2 - - - -
56B ILE* 1.3 79.1 - - - +
58B GLN* 1.3 60.5 + - - +
60B VAL* 3.2 25.7 - - + +
61B GLU* 3.4 6.8 + - - +
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLU* 3.1 23.0 + - - +
55B ASP* 3.2 30.3 + - - +
57B LEU* 1.3 70.8 - - - +
59B ASP* 1.3 62.4 + - - +
60B VAL 3.0 1.8 - - - -
61B GLU* 3.1 7.0 + - - +
62B LYS* 2.8 55.2 + - + +
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Residues in contact with ASP 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TRP* 3.8 12.9 - - + -
367A ARG* 2.7 38.1 + - - +
55B ASP* 3.1 20.8 + - - +
56B ILE 3.4 9.6 - - - +
57B LEU 3.2 0.2 - - - -
58B GLN* 1.3 78.5 - - - +
60B VAL* 1.3 56.9 + - - +
62B LYS* 4.8 3.1 - - - +
63B ILE* 2.7 57.0 + - + +
64B ILE* 3.3 1.6 + - - +
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Residues in contact with VAL 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 3.8 34.8 - - + -
98A ILE* 5.2 1.3 - - + -
360A LEU* 5.8 0.2 - - + -
363A TRP* 4.0 17.5 - - + -
364A PHE* 4.3 8.3 - - + -
16B TYR* 3.4 24.9 - - + +
56B ILE 3.1 19.7 + - - +
57B LEU* 3.2 15.7 - - + +
58B GLN 3.0 0.4 - - - -
59B ASP* 1.3 75.8 - - - +
61B GLU* 1.3 57.6 + - - +
64B ILE* 3.2 19.5 + - + +
65B MET* 2.9 35.4 + - + +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TYR* 3.3 29.5 + - + +
20B TYR* 5.9 0.2 - - - +
27B ARG* 2.5 41.7 + - - -
57B LEU 3.4 5.1 + - - +
58B GLN* 3.1 10.8 + - - +
60B VAL* 1.3 79.6 - - - +
62B LYS* 1.3 69.8 + - + +
65B MET* 3.4 22.6 - - - +
66B PRO* 3.6 4.7 - - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 5.8 1.0 - - - +
58B GLN* 2.8 45.0 + - + +
59B ASP* 4.5 2.5 - - - +
61B GLU* 1.3 81.2 - - + +
63B ILE* 1.3 66.9 + - + +
66B PRO* 3.3 17.4 - - - +
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A TRP* 5.5 2.2 - - + -
37B TYR* 3.0 24.6 + - - -
38B LEU* 3.2 31.0 - - + -
41B LEU* 3.6 42.2 - - + +
42B ILE* 4.7 7.9 - - + -
59B ASP* 2.7 42.5 + - + +
62B LYS* 1.3 83.4 - - + +
64B ILE* 1.3 65.6 + - + +
66B PRO* 3.4 8.2 - - - +
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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