Contacts of the helix formed by residues 73 - 90 (chain E) in PDB entry 1Q0K
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 73 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E TYR* 2.9 38.2 - - - -
72E PRO* 1.3 76.2 - - - +
74E LEU* 1.3 64.2 + - - +
75E HIS 3.4 2.2 - - - -
76E THR* 3.3 12.8 + - - +
77E LEU* 3.0 25.9 + - + +
110E ILE* 4.5 9.6 - - + +
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Residues in contact with LEU 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E PHE* 3.6 38.1 - - + -
67E HIS* 4.6 11.4 - - + +
68E PHE* 3.6 32.1 - - + -
71E TYR* 2.8 19.0 + - + +
72E PRO 3.4 0.4 - - - -
73E GLU* 1.3 80.6 + - - +
75E HIS* 1.3 66.1 + - - +
77E LEU* 3.1 11.4 + - + +
78E VAL* 3.0 38.2 + - + +
107E ILE* 5.2 2.9 - - + -
110E ILE* 3.9 32.1 - - + -
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Residues in contact with HIS 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 3.8 4.7 - - - -
75D HIS* 3.5 52.0 - + + +
76D THR* 4.3 12.6 + - - -
79D ASN* 4.3 4.5 - - + -
59E TRP* 2.9 36.6 + + - +
68E PHE* 3.4 52.8 - + + +
71E TYR 6.1 0.2 - - - -
72E PRO 4.9 8.2 + - - +
73E GLU 3.4 0.6 - - - -
74E LEU* 1.3 78.0 - - - +
76E THR* 1.3 57.0 + - - +
78E VAL* 3.4 0.5 + - - -
79E ASN* 2.9 30.1 + - - +
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Residues in contact with THR 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D HIS* 4.3 12.8 + - - -
72E PRO 5.6 0.9 + - - -
73E GLU* 3.3 13.2 + - - -
74E LEU 3.3 0.4 - - - -
75E HIS* 1.3 78.3 - - - +
77E LEU* 1.3 53.8 + - - +
79E ASN* 3.3 6.6 + - - +
80E GLU* 2.7 66.1 + - + +
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Residues in contact with LEU 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E GLU* 3.0 20.1 + - + +
74E LEU* 3.1 11.2 + - + +
76E THR* 1.3 76.9 - - - +
78E VAL* 1.3 57.9 + - - +
80E GLU* 3.2 10.3 + - - +
81E ALA* 2.9 27.5 + - - +
103E TYR* 3.7 26.9 - - + +
106E GLN* 3.3 33.7 - - + +
107E ILE* 3.6 38.6 - - + +
110E ILE* 4.0 20.4 - - + -
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Residues in contact with VAL 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 3.6 21.5 - - + -
55E LEU* 4.2 22.0 - - + +
58E LEU* 6.4 0.4 - - + -
59E TRP* 3.9 30.7 - - + +
63E PHE* 4.9 5.2 - - + -
74E LEU* 3.0 31.5 + - + +
75E HIS 3.9 2.2 - - - +
77E LEU* 1.3 71.6 - - - +
79E ASN* 1.3 67.2 + - - +
81E ALA* 3.1 2.1 + - - +
82E VAL* 3.0 24.1 + - + +
107E ILE* 3.8 24.0 - - + -
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Residues in contact with ASN 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 3.0 62.6 + - + +
60D SER* 4.1 1.0 - - - +
65D PRO* 5.9 0.3 - - - +
68D PHE* 3.6 17.0 - - - -
75D HIS* 4.3 5.8 - - + -
75E HIS 2.9 17.5 + - - +
76E THR* 3.7 4.7 - - - +
78E VAL* 1.3 76.4 - - - +
80E GLU* 1.3 58.0 + - + +
82E VAL* 3.0 20.7 - - - +
83E LYS* 2.8 43.3 + - - +
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Residues in contact with GLU 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E THR* 2.7 49.8 + - + +
77E LEU* 3.5 13.4 - - - +
79E ASN* 1.3 72.3 - - + +
81E ALA* 1.3 60.4 + - - +
83E LYS* 3.3 8.3 + - + +
84E ALA* 2.8 30.7 + - - +
103E TYR* 3.7 41.2 + - + +
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Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E LEU* 3.8 14.8 - - + -
77E LEU 2.9 13.8 + - - +
78E VAL 3.1 7.2 + - - +
80E GLU* 1.3 77.0 - - - +
82E VAL* 1.3 62.6 + - - +
84E ALA* 3.2 4.1 + - - +
85E LEU* 3.0 26.2 + - - +
100E ALA* 4.6 1.9 - - - +
103E TYR* 3.7 27.7 - - + -
104E ILE* 4.7 4.4 - - + +
107E ILE* 3.7 19.3 - - + -
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Residues in contact with VAL 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP* 4.3 2.9 - - + -
60D SER* 3.4 33.7 - - - -
52E LYS* 3.9 17.9 - - - +
55E LEU* 4.0 24.5 - - + -
56E ASP* 3.6 21.3 - - - +
78E VAL* 3.0 15.8 + - + +
79E ASN* 3.0 25.6 - - - +
81E ALA* 1.3 75.1 - - - +
83E LYS* 1.3 62.0 + - - +
85E LEU* 3.1 11.8 + - - +
86E SER* 3.0 23.4 + - - -
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Residues in contact with LYS 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TRP 3.7 1.4 + - - -
60D SER 2.8 36.0 + - - +
61D ASP* 4.9 1.1 - - - +
63D PHE 2.9 27.6 + - - -
64D LYS* 4.2 9.6 - - - +
65D PRO* 4.2 27.1 - - + -
79E ASN* 2.8 42.2 + - - +
80E GLU* 3.7 9.0 - - + +
82E VAL* 1.3 77.9 - - - +
84E ALA* 1.3 62.1 + - - +
86E SER* 3.3 9.1 + - - -
87E ALA* 3.1 22.5 + - - +
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Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E GLU 2.8 18.3 + - - +
81E ALA 3.4 5.8 - - - +
83E LYS* 1.3 77.8 - - - +
85E LEU* 1.3 58.7 + - - +
87E ALA* 3.4 7.5 + - - +
88E ALA* 3.0 26.0 + - - +
96E THR* 4.2 5.9 - - - +
99E LYS* 4.5 11.0 - - + +
100E ALA* 3.9 25.8 - - + +
103E TYR* 3.9 15.9 - - + -
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ALA* 4.3 14.1 - - + -
21E VAL* 5.0 5.8 - - + -
48E ALA* 4.0 13.0 - - + +
51E ALA* 3.6 34.3 - - + -
52E LYS* 3.6 27.4 - - + +
55E LEU* 3.7 25.4 - - + -
81E ALA 3.0 13.0 + - - +
82E VAL* 3.1 7.4 + - - +
84E ALA* 1.3 76.4 - - - +
86E SER* 1.3 64.8 + - - +
88E ALA* 3.1 9.4 + - + +
89E LYS* 3.0 25.0 + - - +
100E ALA* 3.6 20.9 - - + -
104E ILE* 4.8 3.4 - - + -
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Residues in contact with SER 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ASP* 3.0 32.5 + - - +
60D SER 5.4 0.5 + - - -
61D ASP* 3.8 5.0 + - - -
52E LYS* 3.0 24.1 + - - +
82E VAL 3.0 8.7 + - - -
83E LYS* 3.3 13.0 + - - -
85E LEU* 1.3 75.8 - - - +
87E ALA* 1.3 63.4 + - - +
89E LYS* 3.1 15.8 + - - +
90E ALA* 3.3 12.1 + - - +
39F ARG* 5.0 1.2 + - - -
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Residues in contact with ALA 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E LYS 3.1 13.6 + - - +
84E ALA* 3.7 11.4 - - - +
85E LEU 3.2 0.2 - - - -
86E SER* 1.3 77.1 - - - +
88E ALA* 1.3 61.0 + - - +
90E ALA* 3.3 8.3 + - - +
91E SER* 3.3 23.9 + - - -
96E THR* 4.3 11.2 - - + +
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Residues in contact with ALA 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E VAL* 4.0 23.6 - - + -
25E GLN* 3.3 5.2 + - - +
44E LYS* 3.3 7.3 + - - +
48E ALA* 5.5 0.2 - - + -
84E ALA 3.0 14.1 + - - +
85E LEU* 3.1 15.7 + - + +
87E ALA* 1.3 75.6 - - - +
89E LYS* 1.3 64.1 + - - +
91E SER 3.0 20.8 + - - +
96E THR* 3.6 28.7 - - - +
97E GLY* 4.3 1.8 - - - +
100E ALA* 5.3 0.2 - - + -
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D CYS 5.0 1.0 + - - -
3D ASP* 2.6 40.8 + - - +
44E LYS* 2.7 27.9 + - - +
45E GLU* 3.1 53.6 + - - +
48E ALA* 3.4 20.4 - - + +
49E GLU* 2.6 42.0 + - - +
52E LYS* 4.1 5.5 - - - +
85E LEU 3.0 11.3 + - - +
86E SER* 3.1 6.9 + - - +
88E ALA* 1.3 76.5 - - - +
90E ALA* 1.3 57.9 + - - +
91E SER 3.3 0.2 + - - -
39F ARG* 3.3 19.9 + - - +
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Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LEU 5.0 1.3 - - - +
5D PRO* 6.4 0.2 - - + -
86E SER 3.3 7.3 + - - +
87E ALA* 3.3 10.4 + - - +
88E ALA 3.1 0.6 - - - -
89E LYS* 1.3 80.3 - - - +
91E SER* 1.3 57.7 + - - +
35F HIS* 5.7 4.9 - - - +
39F ARG* 3.6 29.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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