Contacts of the helix formed by residues 63 - 73 (chain A) in PDB entry 1CKQ
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 LYS 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE 3.9 0.6 + - - -
62A LYS* 1.3 70.8 - - - +
64A THR* 1.3 57.7 + - - +
66A ILE* 3.4 17.6 + - + +
67A ASN* 3.0 45.4 + - - +
80A THR* 3.3 28.1 + - - +
81A LEU* 3.9 24.7 - - + +
82A PHE* 5.2 3.0 - - - +
86A SER* 2.8 38.2 + - - +
87A SER* 4.0 5.8 - - - +
88A ILE* 5.7 1.1 - - + -
152A GLU* 4.6 21.1 - - - +
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Residues in contact with THR 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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62A LYS* 3.1 30.7 + - - +
63A LYS* 1.3 78.8 - - - +
65A GLU* 1.3 57.5 + - - +
67A ASN* 3.7 8.2 + - + +
68A GLU* 3.1 31.3 + - - +
81A LEU* 4.0 12.6 - - + +
84A SER 3.8 13.7 + - - -
86A SER 4.8 0.4 + - - -
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Residues in contact with GLU 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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56A ARG* 5.6 0.3 + - - -
58A ARG* 2.9 39.5 + - - -
60A SER 4.6 0.3 - - - +
61A ILE* 3.8 10.4 - - + +
62A LYS* 3.1 39.4 + - + +
64A THR* 1.3 76.4 - - - +
66A ILE* 1.3 63.9 + - - +
68A GLU* 3.3 7.2 + - - +
69A ALA* 3.1 22.5 + - - +
156A PHE* 3.8 14.3 - - + -
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Residues in contact with ILE 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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61A ILE* 4.0 13.7 - - + +
62A LYS 3.9 11.9 - - - +
63A LYS* 3.4 17.9 + - + +
65A GLU* 1.3 76.3 - - - +
67A ASN* 1.3 58.5 + - - +
69A ALA* 3.2 5.0 + - - +
70A LEU* 3.0 33.3 + - + +
88A ILE* 4.2 27.4 - - + -
152A GLU* 3.8 44.2 - - + +
153A ILE* 6.0 0.4 - - + -
155A ASN* 4.4 9.6 - - + +
156A PHE* 3.8 26.0 - - + +
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Residues in contact with ASN 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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63A LYS* 3.0 32.7 + - - +
64A THR* 3.9 6.7 - - + +
66A ILE* 1.3 78.4 - - - +
68A GLU* 1.3 56.8 + - - +
70A LEU* 3.3 8.4 + - - +
71A LYS* 3.0 41.1 + - - +
78A GLY* 3.3 35.2 + - - +
80A THR 3.1 26.6 + - - +
81A LEU* 4.1 13.9 - - - +
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Residues in contact with GLU 68 (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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64A THR* 3.1 23.1 + - - +
65A GLU* 3.5 7.9 - - - +
66A ILE 3.3 0.4 - - - -
67A ASN* 1.3 77.1 - - - +
69A ALA* 1.3 61.3 + - - +
71A LYS* 3.4 26.5 + - - +
72A LYS* 3.3 39.2 + - - +
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Residues in contact with ALA 69 (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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65A GLU 3.1 12.2 + - - +
66A ILE 3.5 8.5 - - - +
68A GLU* 1.3 76.0 - - - +
70A LEU* 1.3 62.5 + - - +
72A LYS* 3.5 24.5 + - + +
73A ILE* 3.6 19.4 - - + +
155A ASN 5.2 0.2 - - - -
156A PHE* 3.9 35.7 - - + +
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Residues in contact with LEU 70 (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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66A ILE* 3.0 20.9 + - + +
67A ASN* 3.3 12.5 + - - +
69A ALA* 1.3 76.8 - - - +
71A LYS* 1.3 61.4 + - - +
73A ILE* 3.4 7.8 + - + +
74A ASP 3.2 21.0 + - - +
77A LEU* 3.5 24.9 - - + +
78A GLY* 3.9 23.1 - - - +
155A ASN* 3.2 54.7 - - + +
158A LEU* 4.3 16.6 - - + -
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Residues in contact with LYS 71 (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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67A ASN* 3.0 25.8 + - - +
68A GLU* 3.7 20.5 + - - +
69A ALA 3.3 0.4 - - - -
70A LEU* 1.3 75.2 - - - +
72A LYS* 1.3 62.6 + - + +
74A ASP 3.2 21.9 - - - +
75A PRO* 3.7 15.2 - - + +
77A LEU 3.1 13.9 - - - +
78A GLY 2.8 29.1 + - - -
79A GLY* 4.6 5.8 - - - -
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Residues in contact with LYS 72 (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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68A GLU* 3.3 36.5 + - - +
69A ALA* 3.7 14.4 - - - +
70A LEU 3.3 0.4 - - - -
71A LYS* 1.3 76.7 - - + +
73A ILE* 1.3 63.8 + - + +
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Residues in contact with ILE 73 (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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69A ALA 3.6 16.6 - - - +
70A LEU* 3.7 13.0 - - + +
71A LYS 3.2 0.8 - - - -
72A LYS* 1.3 81.7 - - + +
74A ASP* 1.3 64.8 + - + +
75A PRO* 4.8 1.1 - - - +
77A LEU* 4.7 7.0 - - + -
155A ASN 4.6 2.0 - - - +
156A PHE 6.1 0.2 - - - +
158A LEU* 3.4 45.1 - - + +
159A SER* 3.9 24.5 - - - +
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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