Contacts of the helix formed by residues 67 - 87 (chain E) in PDB entry 1XK4
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 ASN 67 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E TYR* 3.3 9.2 - - - -
27E HIS 3.8 12.6 - - - +
28E ALA* 5.4 0.2 - - - -
63E ASP* 6.0 0.4 + - - -
65E ALA* 4.0 1.0 - - + -
66E VAL* 1.3 75.4 - - - +
68E PHE* 1.3 59.0 + - - +
69E GLN* 3.0 10.5 - - - +
70E GLU* 2.9 37.2 + - - +
71E PHE* 2.9 24.8 + - - +
68H THR* 5.6 8.5 - - + -
81H MET* 3.4 30.5 - - - +
85H ARG* 3.1 30.5 - - - +
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Residues in contact with PHE 68 (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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12E ILE* 4.9 0.2 - - + -
13E ILE* 3.6 32.8 - - + -
16E TYR* 3.5 44.8 + + + -
27E HIS 4.7 1.0 + - - -
67E ASN* 1.3 74.5 - - - +
69E GLN* 1.3 64.1 + - - +
71E PHE* 3.1 24.6 + + - +
72E LEU* 3.0 41.7 + - + +
87G THR* 3.8 18.6 - - + -
88G TRP* 3.8 17.9 - + + -
91G HIS* 3.6 48.9 - + + +
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Residues in contact with GLN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E ASN* 3.0 19.3 - - - +
68E PHE* 1.3 79.3 - - - +
70E GLU* 1.3 63.9 + - + +
72E LEU* 3.3 22.7 + - + +
73E ILE* 3.7 9.2 + - - +
76F ILE* 6.1 0.8 - - - +
88G TRP* 3.8 29.9 - - + -
81H MET* 3.0 23.7 - - + +
84H ALA* 5.6 3.2 - - - +
85H ARG* 2.7 46.4 + - - +
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E LEU* 3.2 31.8 - - - +
59E ASP* 4.0 0.4 - - - -
60E ILE* 2.9 30.1 + - + +
61E ASN* 3.1 9.8 + - - +
65E ALA 3.1 3.8 - - - +
66E VAL* 3.3 9.3 - - + -
67E ASN* 2.9 42.4 + - - +
69E GLN* 1.3 76.8 - - + +
71E PHE* 1.3 67.2 + - - +
73E ILE* 3.0 28.7 + - + +
1511E CA 2.4 30.6 - - - -
81H MET* 4.6 4.4 - - - +
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Residues in contact with PHE 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 3.8 19.3 - - + -
15E VAL* 4.3 20.2 - - + -
16E TYR* 3.5 42.2 - + + -
34E LEU* 5.6 2.5 - - + -
37E LEU* 3.6 28.0 - - + -
58E LEU* 5.2 1.3 - - + -
66E VAL* 3.7 10.4 - - + +
67E ASN 2.9 13.6 + - - +
68E PHE* 3.1 20.2 + + - +
70E GLU* 1.3 75.6 - - - +
72E LEU* 1.3 63.3 + - + +
74E LEU* 3.0 33.7 + - + +
75E VAL* 3.0 36.8 + - + +
8G LEU* 4.3 7.4 - - + -
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 4.5 4.0 - - + -
68E PHE* 3.0 50.4 + - + +
69E GLN* 3.5 15.9 - - + +
70E GLU 3.1 0.6 - - - -
71E PHE* 1.3 77.1 - - - +
73E ILE* 1.3 57.0 + - - +
75E VAL* 3.6 21.1 - - + +
76E ILE* 2.8 38.2 + - + +
84G ALA* 3.7 35.2 - - + +
87G THR* 4.2 16.2 - - + -
88G TRP* 4.1 13.0 - - + +
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Residues in contact with ILE 73 (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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57E GLU* 4.9 4.9 - - + +
58E LEU* 3.7 15.9 - - + +
60E ILE* 3.9 32.5 - - + -
69E GLN 4.0 8.3 - - - +
70E GLU* 3.0 19.2 + - - +
72E LEU* 1.3 79.4 - - - +
74E LEU* 1.3 63.2 + - - +
76E ILE* 3.4 2.5 + - + +
77E LYS* 3.0 37.7 + - + +
60F ILE* 4.1 37.0 - - + +
73F ILE* 4.5 13.9 - - + -
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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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34E LEU* 4.5 4.3 - - + -
37E LEU* 4.0 26.9 - - + -
38E LEU* 4.1 12.1 - - + -
46E ILE* 4.3 4.9 - - + -
54E TRP* 3.7 38.4 - - + -
58E LEU* 3.4 31.4 - - + +
71E PHE* 3.0 23.1 + - + +
73E ILE* 1.3 78.0 - - - +
75E VAL* 1.3 59.1 + - - +
77E LYS* 3.2 1.1 + - - +
78E MET* 2.8 60.3 + - + +
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Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ILE* 4.1 32.8 - - + -
71E PHE* 3.0 47.9 + - + +
72E LEU* 3.6 16.6 - - + +
73E ILE 3.2 0.2 - - - -
74E LEU* 1.3 78.8 - - - +
76E ILE* 1.3 58.3 + - + +
78E MET* 3.5 7.2 + - - +
79E GLY* 3.0 26.0 + - - -
8G LEU* 4.5 12.6 - - + -
12G ILE* 4.4 7.7 - - + +
15G ILE* 5.8 2.0 - - + -
80G ILE* 4.1 5.9 - - + +
84G ALA* 6.3 1.6 - - + -
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Residues in contact with ILE 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU* 2.8 25.2 + - + +
73E ILE* 3.7 5.2 - - + +
75E VAL* 1.3 77.3 - - + +
77E LYS* 1.3 64.2 + - - +
79E GLY* 3.3 1.6 + - - -
80E VAL* 3.0 29.6 + - + +
60F ILE* 3.6 31.4 - - + +
61F ASN* 3.7 26.9 - - + -
69F GLN* 6.0 1.8 - - - +
80G ILE* 3.9 22.9 - - + +
81G MET* 4.3 18.2 - - + -
84G ALA* 3.8 29.8 - - + -
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Residues in contact with LYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E ILE* 4.8 3.4 - - + +
49E LYS* 5.2 2.2 - - - +
54E TRP* 3.9 23.8 - - + -
57E GLU* 2.4 36.3 + - - +
73E ILE* 3.0 24.9 + - + +
74E LEU 3.8 3.4 - - - +
76E ILE* 1.3 76.4 - - - +
78E MET* 1.3 56.4 + - - +
80E VAL* 3.6 5.8 + - - +
81E ALA* 3.0 29.3 + - - +
56F LYS 5.6 3.9 + - - -
57F GLU 5.1 3.0 + - - -
59F ASP 5.3 1.1 - - - -
60F ILE* 3.8 45.0 - - + +
62F THR* 5.9 3.8 - - + -
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Residues in contact with MET 78 (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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41E GLU 4.0 5.8 - - - +
42E SER* 3.9 14.4 - - - -
43E PRO* 3.8 28.0 - - + -
45E TYR* 4.6 1.9 + - - -
46E ILE* 4.1 21.5 - - + -
74E LEU* 2.8 46.1 + - + +
75E VAL* 3.8 5.2 - - - +
77E LYS* 1.3 76.5 - - - +
79E GLY* 1.3 53.0 + - - +
81E ALA* 3.3 1.6 + - - +
82E ALA* 2.8 36.2 + - - +
8G LEU* 3.8 28.9 - - + -
9G GLU* 4.9 4.3 - - + -
12G ILE* 3.8 21.5 - - + +
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Residues in contact with GLY 79 (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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75E VAL 3.0 16.3 + - - -
76E ILE 3.8 0.9 - - - -
77E LYS 3.3 0.2 - - - -
78E MET* 1.3 74.2 - - - +
80E VAL* 1.3 58.6 + - - +
82E ALA* 3.4 1.6 + - - +
83E HIS* 2.9 25.3 + - - +
12G ILE* 3.9 20.5 - - - +
16G ILE* 4.0 1.2 - - - +
76G PHE* 3.3 18.7 - - - -
80G ILE* 3.9 11.0 - - - -
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Residues in contact with VAL 80 (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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76E ILE* 3.0 25.1 + - + +
77E LYS* 3.9 6.1 - - - +
79E GLY* 1.3 75.2 - - - +
81E ALA* 1.3 63.3 + - - +
83E HIS* 3.4 3.3 + - - +
84E LYS* 3.1 29.0 + - + +
60F ILE 5.4 0.7 - - - +
61F ASN* 4.0 16.8 - - - +
62F THR* 3.7 19.7 - - + +
76G PHE* 3.9 8.0 - - + -
77G GLU* 3.9 25.5 - - + +
80G ILE* 4.1 20.6 - - + +
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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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45E TYR* 3.7 26.0 - - + -
46E ILE* 4.3 9.2 - - + -
77E LYS 3.0 18.9 + - - +
78E MET 3.8 2.5 - - - +
80E VAL* 1.3 77.0 - - - +
82E ALA* 1.3 62.6 + - - +
83E HIS 3.2 0.2 + - - -
84E LYS* 3.3 11.6 + - - +
85E LYS* 3.0 27.6 + - + +
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Residues in contact with ALA 82 (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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45E TYR* 3.4 18.5 + - - +
78E MET 2.8 21.4 + - - +
79E GLY 3.9 0.4 - - - +
81E ALA* 1.3 74.2 - - - +
83E HIS* 1.3 56.4 + - - +
85E LYS* 3.4 4.4 + - - +
86E SER* 2.9 29.3 + - - -
12G ILE* 3.9 12.8 - - + -
16G ILE* 3.6 19.3 - - + +
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Residues in contact with HIS 83 (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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79E GLY 2.9 18.8 + - - +
80E VAL 3.7 3.9 + - - +
81E ALA 3.1 0.2 - - - -
82E ALA* 1.3 74.0 - - - +
84E LYS* 1.3 70.8 + - - +
86E SER* 3.3 19.6 + - - -
87E HIS* 3.3 22.1 + + - -
16G ILE* 3.5 23.3 - - + +
19G PHE* 4.4 4.7 - + - -
30G ASP* 2.7 44.4 + - - -
76G PHE* 3.5 50.9 - + + +
77G GLU* 4.9 9.9 + - - -
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Residues in contact with LYS 84 (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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80E VAL* 3.1 17.3 + - + +
81E ALA* 3.4 13.0 - - - +
83E HIS* 1.3 84.7 + - - +
85E LYS* 1.3 62.3 + - + +
87E HIS* 3.3 14.1 + - + +
88E GLU* 3.2 35.3 + - + +
77G GLU* 5.3 7.6 - - - +
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Residues in contact with LYS 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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45E TYR* 3.9 53.0 - - + +
48E LYS* 5.8 1.2 - - - +
81E ALA* 3.0 15.8 + - - +
82E ALA* 3.7 7.2 - - - +
83E HIS 3.3 0.2 - - - -
84E LYS* 1.3 74.2 - - + +
86E SER* 1.3 62.7 + - - +
87E HIS 2.9 6.9 + - - -
88E GLU* 3.0 38.1 + - - +
89E GLU* 3.4 16.7 - - - +
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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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82E ALA 2.9 15.8 + - - -
83E HIS* 3.3 13.6 + - - -
85E LYS* 1.3 75.5 - - - +
87E HIS* 1.3 60.8 + - - +
89E GLU* 3.5 21.2 - - - +
16G ILE* 3.8 24.5 - - - +
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Residues in contact with HIS 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 HIS* 3.3 25.9 + + - -
84E LYS* 3.3 13.3 + - + +
85E LYS 3.0 0.6 - - - -
86E SER* 1.3 82.5 + - - +
88E GLU* 1.3 57.0 + - - +
89E GLU 2.7 22.0 + - - +
30G ASP* 3.2 36.8 + - + +
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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