Contacts of the helix formed by residues 53 - 62 (chain A) in PDB entry 1B54
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 ALA 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.2 12.6 - - + -
51A LYS 3.7 1.4 + - - -
52A PRO* 1.3 71.7 - - - +
54A SER* 1.3 54.9 + - - +
55A ASP 3.3 0.4 - - - -
56A ILE* 3.4 13.3 + - - +
57A GLN* 3.0 22.5 + - - +
78A LYS* 4.5 8.5 - - + +
81A LEU* 4.4 20.0 - - + -
82A LEU* 3.4 31.8 - - + +
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 3.6 20.2 - - - +
6A THR 3.6 24.5 - - - -
7A TYR* 3.7 9.9 - - - -
52A PRO* 3.8 16.5 - - - +
53A ALA* 1.3 75.9 - - - +
55A ASP* 1.3 65.0 + - - +
57A GLN* 3.2 4.2 + - - +
58A ILE* 2.9 32.9 + - - +
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 2.8 50.7 + - - +
15A LEU* 3.3 15.0 - - - +
51A LYS* 4.3 3.5 - - + +
52A PRO* 3.1 34.5 + - + +
54A SER* 1.3 84.6 + - - +
56A ILE* 1.3 61.0 + - + +
58A ILE* 3.2 8.7 - - - +
59A LEU* 3.1 19.6 + - - +
245A PHE* 3.5 23.1 - - + -
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Residues in contact with ILE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER* 3.6 34.5 - - - +
51A LYS* 5.4 0.2 - - + -
52A PRO 3.9 9.9 - - - +
53A ALA* 3.4 7.3 + - - +
55A ASP* 1.3 77.4 - - + +
57A GLN* 1.3 53.8 + - - +
59A LEU* 3.4 0.8 + - - -
60A TYR* 2.6 37.8 + - - +
67A PHE* 3.7 37.5 - - + -
69A GLU* 4.1 0.2 - - - +
78A LYS* 3.8 32.3 - - + +
82A LEU* 3.9 23.8 - - + -
86A ILE* 4.1 9.0 - - + -
88A TRP* 4.1 5.6 - - + -
245A PHE* 5.3 1.1 - - + -
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY* 4.0 9.5 - - - +
5A ILE* 3.2 40.1 + - + +
7A TYR* 3.5 19.7 - - + -
53A ALA 3.0 14.7 + - - +
54A SER 3.2 9.6 + - - +
56A ILE* 1.3 73.1 - - - +
58A ILE* 1.3 61.4 + - - +
60A TYR* 3.9 14.6 - - - -
61A ASP* 2.8 59.3 + - - +
81A LEU 5.1 1.4 - - - +
82A LEU* 3.8 10.9 - - + +
83A PRO* 4.5 13.1 - - - +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 3.3 47.7 + - + -
11A ARG* 3.7 24.7 - - + +
12A LYS* 3.7 31.9 - - + +
15A LEU* 3.8 24.0 - - + -
16A ILE* 4.3 12.9 - - + +
54A SER 2.9 12.9 + - - +
55A ASP* 3.2 15.5 - - - +
57A GLN* 1.3 79.1 - - - +
59A LEU* 1.3 65.6 + - + +
61A ASP* 3.4 4.0 + - - +
62A HIS* 3.1 17.5 + - - +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.6 41.3 - - + +
16A ILE* 4.2 18.2 - - + -
19A TYR* 4.1 24.9 - - + -
46A VAL* 4.3 7.9 - - + -
55A ASP 3.1 6.4 + - - +
56A ILE 3.9 2.7 - - - +
58A ILE* 1.3 78.1 - - + +
60A TYR* 1.3 69.0 + - - +
62A HIS* 2.8 19.3 + - + +
64A VAL* 3.1 32.0 + - + +
67A PHE* 3.9 10.3 - - + -
244A ILE* 4.1 14.6 - - + -
245A PHE* 4.1 15.5 - - + -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE 2.6 23.6 + - - +
57A GLN* 3.6 11.0 - - - +
59A LEU* 1.3 71.3 - - - +
61A ASP* 1.3 69.0 + - - +
63A GLY* 2.6 25.1 + - - -
64A VAL 3.4 12.6 - - - -
65A ARG* 2.9 46.5 + - - -
67A PHE* 3.9 4.4 - - + -
83A PRO* 3.4 36.2 - - + +
85A ASP* 2.7 33.3 + - - -
86A ILE* 3.4 30.1 - - + -
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A TYR* 2.6 31.5 + - - +
57A GLN* 2.8 49.9 + - - +
58A ILE 3.6 4.9 - - - +
60A TYR* 1.3 79.9 - - - +
62A HIS* 1.3 59.6 + - - +
63A GLY* 3.3 0.9 + - - -
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Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 3.6 42.3 - - + +
19A TYR* 3.9 21.3 - + - -
20A GLU* 2.5 36.7 + - + +
58A ILE 3.1 12.9 + - - +
59A LEU* 2.8 13.7 + - + +
61A ASP* 1.3 76.0 - - - +
63A GLY* 1.3 58.1 + - - +
64A VAL* 4.3 5.8 - - + -
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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