Contacts of the helix formed by residues 67 - 87 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F TYR* 3.3 9.6 - - - -
27F HIS* 3.7 13.5 - - + +
61F ASN* 5.5 0.4 - - - +
63F ASP* 5.7 2.2 + - - -
65F ALA* 3.9 0.6 - - - +
66F VAL* 1.3 74.5 - - - +
68F PHE* 1.3 60.4 + - - +
69F GLN* 2.9 25.7 + - - +
70F GLU* 2.8 24.6 + - - +
71F PHE* 2.8 27.4 + - - +
68G THR* 5.5 8.3 - - + -
81G MET* 3.5 32.9 - - - +
85G ARG* 3.5 26.3 - - - +
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 4.2 1.3 - - + -
13F ILE* 3.7 20.9 - - + -
16F TYR* 3.6 44.4 + + + -
27F HIS 4.7 0.6 + - - -
67F ASN* 1.3 76.0 - - - +
69F GLN* 1.3 57.2 + - - +
71F PHE* 3.0 25.8 + + - +
72F LEU* 2.9 49.0 + - + +
87H THR* 3.7 27.4 - - + -
88H TRP* 3.8 17.7 - + + -
91H HIS* 3.8 47.8 - + + +
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Residues in contact with GLN 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ILE* 6.0 1.6 - - - +
67F ASN* 2.9 20.1 + - - +
68F PHE* 1.3 78.6 - - - +
70F GLU* 1.3 63.0 + - + +
72F LEU* 3.3 22.1 + - + +
73F ILE* 3.8 6.8 + - - +
81G MET* 4.0 18.2 - - + +
84G ALA* 5.7 3.8 - - - +
85G ARG* 2.7 49.7 + - - +
88H TRP* 3.5 33.4 - - + -
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F LEU* 3.2 29.9 - - - +
60F ILE* 2.9 26.4 + - + -
61F ASN* 3.1 7.3 - - - +
65F ALA 3.1 4.3 - - - +
66F VAL* 3.2 8.3 - - + -
67F ASN* 2.8 42.4 + - - +
69F GLN* 1.3 75.6 - - + +
71F PHE* 1.3 65.0 + - - +
73F ILE* 3.1 28.2 + - - +
2511F CA 2.4 30.7 - - - -
81G MET* 3.3 19.9 - - + +
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Residues in contact with PHE 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 3.6 28.5 - - + -
15F VAL* 4.2 17.5 - - + -
16F TYR* 3.6 31.6 - + + -
34F LEU* 5.7 1.6 - - + -
37F LEU* 3.7 31.6 - - + -
58F LEU* 5.1 1.8 - - + -
66F VAL* 3.5 10.9 - - + +
67F ASN 2.8 16.9 + - - +
68F PHE* 3.0 20.2 + + - +
70F GLU* 1.3 72.3 - - - +
72F LEU* 1.3 61.3 + - - +
73F ILE 3.0 1.6 + - - -
74F LEU* 3.0 34.4 + - + +
75F VAL* 3.1 33.7 + - + +
8H LEU* 4.3 8.1 - - + -
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ILE* 4.2 17.5 - - + -
68F PHE* 2.9 54.5 + - + +
69F GLN* 3.5 15.9 - - + +
70F GLU 3.2 0.4 - - - -
71F PHE* 1.3 75.5 - - - +
73F ILE* 1.3 55.6 + - - +
75F VAL* 3.7 13.9 - - + +
76F ILE* 2.9 36.4 + - + +
84H ALA* 3.7 34.8 - - + +
87H THR* 4.3 10.3 - - - +
88H TRP* 4.1 12.3 - - + +
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Residues in contact with ILE 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ILE* 4.0 40.2 - - + -
73E ILE* 4.5 7.9 - - + -
57F GLU* 4.7 6.1 - - + +
58F LEU* 3.5 19.1 - - + +
60F ILE* 4.0 33.7 - - + -
69F GLN 3.8 5.8 + - - +
70F GLU* 3.1 18.2 + - - +
71F PHE 3.0 0.2 + - - -
72F LEU* 1.3 78.1 - - - +
74F LEU* 1.3 59.2 + - - +
76F ILE* 3.4 2.8 + - + +
77F LYS* 2.9 49.0 + - + +
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Residues in contact with LEU 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F LEU* 4.7 3.4 - - + -
37F LEU* 3.9 21.5 - - + -
38F LEU* 3.9 21.1 - - + -
46F ILE* 4.0 7.6 - - + -
54F TRP* 3.9 37.7 - - + -
58F LEU* 3.7 26.3 - - + +
71F PHE* 3.0 24.3 + - + +
73F ILE* 1.3 79.2 - - - +
75F VAL* 1.3 58.0 + - - +
77F LYS* 3.3 0.6 + - - -
78F MET* 2.9 59.3 + - + +
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Residues in contact with VAL 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F ILE* 4.0 33.0 - - + -
71F PHE* 3.1 47.8 + - + +
72F LEU* 3.7 16.8 - - + +
73F ILE 3.3 0.2 - - - -
74F LEU* 1.3 74.9 - - - +
76F ILE* 1.3 68.0 + - + +
78F MET* 3.4 7.2 + - - +
79F GLY* 2.9 21.7 + - - -
8H LEU* 4.4 12.8 - - + -
12H ILE* 4.4 8.5 - - + +
15H ILE* 5.8 1.3 - - + -
80H ILE* 5.1 8.4 - - + +
84H ALA* 6.3 1.6 - - + -
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Residues in contact with ILE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ILE* 3.8 22.4 - - + +
61E ASN* 3.7 35.0 - - + -
69E GLN* 6.1 0.9 - - - +
72F LEU* 2.9 25.6 + - + +
73F ILE* 3.7 4.3 - - + +
75F VAL* 1.3 75.8 - - + +
77F LYS* 1.3 64.9 + - - +
79F GLY* 3.2 1.7 + - - -
80F VAL* 3.0 24.1 + - + +
80H ILE* 4.0 23.8 - - + +
81H MET* 4.2 19.5 - - + -
84H ALA* 3.8 30.3 - - + -
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Residues in contact with LYS 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E LYS 5.4 4.4 + - - -
57E GLU* 5.2 3.4 + - - +
59E ASP 5.2 1.3 - - - -
60E ILE* 3.6 42.2 - - - +
62E THR* 5.7 4.9 - - + -
46F ILE* 4.6 3.1 - - + +
49F LYS* 5.4 1.1 - - - +
54F TRP* 4.1 20.6 - - + -
57F GLU* 2.5 40.6 + - - +
73F ILE* 2.9 31.9 + - + +
74F LEU 3.9 2.7 - - - +
76F ILE* 1.3 78.9 - - - +
78F MET* 1.3 55.4 + - - +
80F VAL* 3.6 5.8 + - - +
81F ALA* 3.0 28.8 + - - +
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Residues in contact with MET 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F LEU* 6.0 0.2 - - - -
41F GLU 4.1 8.3 - - - +
42F SER* 4.0 11.7 - - - -
43F PRO* 4.0 23.8 - - + -
45F TYR* 4.6 1.7 + - - -
46F ILE* 3.8 26.5 - - + -
74F LEU* 2.9 45.7 + - + +
75F VAL* 3.7 2.0 - - - +
77F LYS* 1.3 72.1 - - - +
79F GLY* 1.3 58.3 + - - +
81F ALA* 3.4 1.0 + - - +
82F ALA* 2.8 32.6 + - - +
8H LEU* 3.7 30.5 - - + -
9H GLU* 4.8 4.5 - - + -
12H ILE* 3.6 26.4 - - + +
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F VAL 2.9 15.0 + - - -
76F ILE 3.2 2.9 + - - -
78F MET* 1.3 73.8 - - - +
80F VAL* 1.3 55.1 + - - +
82F ALA* 3.4 1.0 + - - +
83F HIS* 2.8 37.1 + - - +
12H ILE* 3.8 21.9 - - - +
16H ILE* 4.2 0.7 - - - +
76H PHE* 3.4 15.9 - - - -
80H ILE* 4.9 6.1 - - - -
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ILE 5.5 0.4 - - - +
61E ASN 4.0 17.3 - - - +
62E THR* 3.7 20.2 - - + +
76F ILE* 3.0 24.6 + - + +
77F LYS* 3.9 5.6 - - - +
79F GLY* 1.3 74.8 - - - +
81F ALA* 1.3 63.0 + - - +
83F HIS* 3.4 2.8 + - - +
84F LYS* 3.1 29.8 + - + +
76H PHE* 4.0 8.0 - - + -
77H GLU* 3.9 25.2 - - + +
80H ILE* 4.0 19.7 - - + -
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F TYR* 3.6 26.5 - - + -
46F ILE* 4.5 6.5 - - + -
77F LYS 3.0 18.4 + - - +
78F MET 4.0 1.8 - - - +
80F VAL* 1.3 78.0 - - - +
82F ALA* 1.3 65.2 + - - +
84F LYS* 3.3 12.3 + - + +
85F LYS* 3.0 28.3 + - + +
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Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F TYR* 3.5 17.4 + - - +
78F MET 2.8 23.1 + - - +
79F GLY 3.9 0.9 - - - +
81F ALA* 1.3 72.0 - - - +
83F HIS* 1.3 58.8 + - - +
85F LYS* 3.2 5.1 + - - +
86F SER* 2.9 30.7 + - - -
12H ILE* 3.9 11.2 - - + -
16H ILE* 3.8 18.3 - - + +
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Residues in contact with HIS 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F GLY 2.8 22.2 + - - +
80F VAL 3.8 3.5 + - - +
82F ALA* 1.3 74.8 - - - +
84F LYS* 1.3 65.3 + - - +
86F SER* 3.2 17.7 + - - -
87F HIS* 3.3 22.5 + + - -
16H ILE* 3.6 23.6 - - + +
19H PHE* 4.1 8.0 - + - -
20H HIS* 6.5 0.4 - - + -
30H ASP* 2.9 41.4 + - - -
76H PHE* 3.5 53.2 - + + +
77H GLU* 5.0 8.7 + - - -
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Residues in contact with LYS 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F VAL* 3.1 20.2 + - + +
81F ALA* 3.3 14.6 + - - +
83F HIS* 1.3 79.0 + - - +
85F LYS* 1.3 64.9 + - + +
87F HIS* 3.3 30.8 + - + +
77H GLU* 5.3 8.1 - - - +
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Residues in contact with LYS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F TYR* 3.9 53.1 - - + +
48F LYS* 5.9 0.6 - - - +
81F ALA* 3.0 21.2 + - - +
82F ALA* 3.2 7.6 + - - +
84F LYS* 1.3 72.8 - - + +
86F SER* 1.3 60.2 + - - +
87F HIS* 2.9 15.5 + - - -
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Residues in contact with SER 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F ALA 2.9 14.4 + - - -
83F HIS* 3.2 14.3 + - - -
85F LYS* 1.3 75.7 - - - +
87F HIS* 1.3 60.8 + - - +
16H ILE* 3.8 24.8 - - - +
17H ASN* 6.1 0.2 - - - -
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Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F HIS* 3.3 27.4 + + - -
84F LYS* 3.3 23.0 + - + +
85F LYS 3.0 6.2 - - - -
86F SER* 1.3 83.1 + - - +
30H ASP* 3.1 36.2 + - + +
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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