Contacts of the helix formed by residues 56 - 67 (chain A) in PDB entry 5AJ1
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU 5.3 1.8 - - - +
55A ALA* 1.3 72.8 - - - +
57A VAL* 1.3 56.2 + - - +
58A GLU* 3.4 9.6 + - - +
59A GLU* 2.7 41.7 + - - +
60A ARG* 2.7 34.7 + - - +
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Residues in contact with VAL 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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56A THR* 1.3 73.3 - - - +
58A GLU* 1.3 64.0 + - + +
60A ARG* 3.5 26.9 + - - +
61A LYS* 3.1 45.3 + - + +
85A ALA 5.6 2.7 - - - +
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Residues in contact with GLU 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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56A THR* 3.1 7.9 + - - +
57A VAL* 1.3 79.9 - - + +
59A GLU* 1.3 65.4 + - + +
61A LYS* 3.2 22.8 + - + +
62A LYS* 3.0 54.1 + - - +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.0 28.5 - - + +
53A ARG* 2.6 33.6 + - - -
54A LEU 3.8 4.3 - - - +
55A ALA* 3.1 16.9 - - + -
56A THR* 2.7 54.0 + - - +
58A GLU* 1.3 77.4 - - + +
60A ARG* 1.3 50.6 + - - +
62A LYS* 3.2 13.6 + - + +
63A ILE* 2.7 42.8 + - + +
90A LEU* 4.8 0.2 - - - -
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Residues in contact with ARG 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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54A LEU* 4.6 8.1 - - - +
55A ALA* 2.6 32.9 + - + +
56A THR* 2.7 25.6 + - - +
57A VAL* 3.7 23.9 - - - +
59A GLU* 1.3 70.8 - - - +
61A LYS* 1.3 63.5 + - - +
63A ILE* 3.0 10.7 + - - +
64A VAL* 2.9 31.8 + - + +
85A ALA* 2.6 38.5 + - + +
86A THR* 3.0 24.2 + - - +
87A SER* 3.7 9.1 - - - +
88A VAL* 3.1 37.1 - - + +
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Residues in contact with LYS 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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57A VAL* 3.1 40.3 + - + +
58A GLU* 3.4 24.5 + - - +
60A ARG* 1.3 77.8 - - - +
62A LYS* 1.3 62.9 + - + +
64A VAL* 3.5 6.5 + - - +
65A ALA* 3.2 23.9 + - - +
85A ALA* 6.1 3.6 - - + -
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Residues in contact with LYS 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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18A GLN 5.9 2.9 - - - +
19A LEU* 5.1 13.2 - - + -
58A GLU* 3.0 52.0 + - - +
59A GLU* 3.5 10.3 - - + +
61A LYS* 1.3 74.4 - - + +
63A ILE* 1.3 55.0 + - + +
65A ALA* 4.7 3.4 - - - -
66A SER* 2.5 48.7 + - - +
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Residues in contact with ILE 63 (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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17A PHE* 3.5 28.3 - - + -
19A LEU* 5.5 1.8 - - + -
28A ILE* 3.6 31.2 - - + -
55A ALA* 3.4 32.3 - - + -
59A GLU* 2.7 30.1 + - + +
60A ARG* 3.0 11.8 + - - +
62A LYS* 1.3 73.2 - - - +
64A VAL* 1.3 60.2 + - + +
66A SER* 3.7 4.9 - - - -
67A SER* 2.6 38.2 + - - -
68A HIS* 4.7 2.0 - - + -
84A LEU* 4.9 0.7 - - + -
88A VAL* 3.5 19.1 - - + -
90A LEU* 3.9 9.2 - - + -
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Residues in contact with VAL 64 (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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60A ARG 2.9 18.9 + - - +
61A LYS* 3.9 5.6 - - - +
63A ILE* 1.3 76.4 - - - +
65A ALA* 1.3 51.7 + - - +
68A HIS* 2.5 56.9 + - + +
69A GLY* 4.3 2.9 - - - +
80A GLY* 6.1 0.2 - - - -
81A TYR* 3.9 36.3 - - + +
84A LEU* 3.8 31.9 - - + -
85A ALA* 4.8 8.3 - - + -
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Residues in contact with ALA 65 (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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61A LYS 3.2 14.7 + - - +
62A LYS* 4.2 3.1 - - - +
64A VAL* 1.3 80.1 - - - +
66A SER* 1.3 61.2 + - - +
68A HIS 2.9 13.4 - - - +
69A GLY* 5.0 1.4 - - - -
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Residues in contact with SER 66 (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 LYS 5.1 0.3 - - - +
17A PHE* 3.4 22.3 - - - +
18A GLN 4.7 9.0 + - - -
62A LYS* 2.5 33.6 + - - +
63A ILE* 3.6 0.3 + - - -
65A ALA* 1.3 75.3 - - - +
67A SER* 1.3 70.8 + - - +
68A HIS 4.2 0.7 - - - +
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Residues in contact with SER 67 (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 VAL* 3.3 25.0 - - - +
16A LYS 3.2 23.3 + - - +
17A PHE* 3.3 25.8 - - - -
63A ILE* 2.6 27.5 + - - -
66A SER* 1.3 77.8 + - - +
68A HIS* 1.3 64.4 + - - +
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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