Contacts of the helix formed by residues 55 - 81 (chain H) in PDB entry 1KYO
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 GLN 55 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 4.5 6.0 + - - -
323C LYS* 2.7 39.8 + - - +
327C PHE* 5.6 4.4 - - - -
51H ARG* 5.8 1.3 - - + -
52H PHE* 4.1 23.6 - - + +
53H LYS 3.9 1.0 - - - +
54H SER* 1.3 83.4 - - - +
56H PHE* 1.3 53.3 + - - +
57H LEU 2.7 19.0 + - - -
58H TYR* 2.9 41.4 + - - +
59H VAL* 3.4 11.1 + - + +
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Residues in contact with PHE 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H PHE* 3.0 46.7 - - + +
53H LYS* 3.2 34.3 - - + -
54H SER 4.4 1.1 - - - -
55H GLN* 1.3 76.5 - - - +
57H LEU* 1.3 84.7 + - + +
59H VAL* 3.8 1.6 - - - -
60H LEU* 2.7 55.5 + - + +
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Residues in contact with LEU 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PHE* 5.2 0.4 - - - -
54H SER 4.6 7.6 - - - +
55H GLN 2.7 7.1 + - - -
56H PHE* 1.3 104.5 - - + +
58H TYR* 1.3 67.8 + - + +
59H VAL 3.0 1.8 - - - -
60H LEU* 4.2 5.6 - - + +
61H ILE* 3.0 52.5 + - + +
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Residues in contact with TYR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C VAL* 3.3 49.3 - - + +
323C LYS* 3.8 35.7 + - + -
324C PHE* 3.9 19.8 - + + +
327C PHE* 3.2 19.7 - - + +
35G LEU* 4.5 17.2 + - - +
54H SER 3.8 17.0 - - - -
55H GLN* 2.9 44.4 + - - +
57H LEU* 1.3 81.0 - - + +
59H VAL* 1.3 58.7 + - - +
62H PRO* 2.9 25.5 - - - +
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Residues in contact with VAL 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C PHE* 3.8 34.8 - - + -
331C PHE* 3.9 18.7 - - + -
52H PHE* 3.9 35.0 - - + -
55H GLN* 3.4 12.5 + - + +
56H PHE* 3.8 5.8 - - - +
57H LEU 3.0 0.4 - - - -
58H TYR* 1.3 78.5 - - + +
60H LEU* 1.3 71.4 + - + +
62H PRO* 3.2 4.0 - - - +
63H ALA* 3.1 22.0 + - + +
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Residues in contact with LEU 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H PHE* 5.2 6.3 - - + -
56H PHE* 2.7 44.2 + - + +
57H LEU* 4.3 8.7 - - + +
59H VAL* 1.3 82.3 - - + +
61H ILE* 1.3 57.9 + - + +
63H ALA* 3.0 9.6 + - + +
64H GLY* 2.7 34.0 + - - -
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Residues in contact with ILE 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PHE* 3.6 26.2 - - + -
57H LEU* 3.0 37.0 + - + +
60H LEU* 1.3 72.7 - - + +
62H PRO* 1.3 66.8 - - + +
64H GLY* 3.9 1.4 - - - -
65H ILE* 2.9 47.9 + - + +
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Residues in contact with PRO 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PHE* 3.9 22.4 - - + +
327C PHE* 3.8 30.7 - - + +
328C ILE* 4.0 15.0 - - + -
331C PHE* 4.1 4.5 - - + -
57H LEU 3.6 0.2 - - - +
58H TYR 2.9 31.2 - - - +
59H VAL 3.2 7.2 - - - +
61H ILE* 1.3 93.2 - - + +
63H ALA* 1.3 64.7 + - - +
65H ILE* 3.3 2.6 + - + +
66H TYR* 3.0 29.5 + - - -
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Residues in contact with ALA 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C PHE* 3.8 31.9 - - + -
59H VAL* 3.1 13.0 + - + +
60H LEU* 3.0 14.9 + - + +
62H PRO* 1.3 77.2 - - - +
64H GLY* 1.3 54.4 + - - +
66H TYR* 3.0 3.3 + - - +
67H TRP* 2.7 39.5 + - + +
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Residues in contact with GLY 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H LEU* 2.7 20.7 + - - +
61H ILE* 3.9 2.0 - - - -
63H ALA* 1.3 72.8 - - - +
65H ILE* 1.3 61.6 + - - +
67H TRP* 4.6 7.4 - - - -
68H TYR* 2.9 33.8 + - - +
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Residues in contact with ILE 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C PHE* 4.5 6.5 - - + -
328C ILE* 4.5 16.6 - - + -
61H ILE* 2.9 45.5 + - + +
62H PRO* 3.3 5.4 + - + +
64H GLY* 1.3 73.4 - - - +
66H TYR* 1.3 71.7 + - + +
68H TYR* 3.8 3.4 - - - +
69H TRP* 3.2 31.4 + - + +
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Residues in contact with TYR 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ILE* 3.7 33.9 + - + +
331C PHE* 4.0 22.0 - - + +
332C ASN* 3.0 40.7 + - + +
335C LEU* 3.8 26.2 - - + +
358C ILE* 3.4 19.2 - - - +
62H PRO* 3.0 26.1 + - + +
63H ALA* 3.8 2.0 - - - +
65H ILE* 1.3 82.6 - - + +
67H TRP* 1.3 60.2 + - - +
68H TYR 3.1 1.6 - - - -
69H TRP* 3.3 35.3 + + - +
70H TRP* 2.9 30.2 + - - +
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Residues in contact with TRP 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63H ALA* 2.7 22.5 + - + +
64H GLY* 4.2 5.4 - - - +
66H TYR* 1.3 74.8 - - - +
68H TYR* 1.3 95.0 + + - +
70H TRP* 3.7 14.1 - + - +
71H LYS* 3.0 58.0 + - + +
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Residues in contact with TYR 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLY* 2.9 20.9 + - - +
65H ILE* 3.8 4.9 - - - +
67H TRP* 1.3 108.9 - + - +
69H TRP* 1.3 57.8 + - - +
70H TRP 3.2 0.5 + - - -
71H LYS* 3.6 2.7 - - + +
72H ASN* 2.9 40.4 + - + +
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Residues in contact with TRP 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ASN* 4.8 0.9 - - - -
335C LEU* 4.4 9.6 - - + -
350C LEU* 6.0 0.2 - - + -
351C MET* 3.5 50.6 - - + +
354C ILE* 3.7 38.4 - - + -
355C ALA 4.5 3.1 - - - -
358C ILE* 4.6 6.3 - - + -
65H ILE* 3.2 20.2 + - + +
66H TYR* 3.5 44.9 - + - +
68H TYR* 1.3 79.4 - - - +
70H TRP* 1.3 61.8 + - - +
72H ASN* 4.6 5.2 - - + -
73H GLY* 3.1 16.9 + - - -
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Residues in contact with TRP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LEU* 3.9 22.4 - - + +
338C GLN* 3.5 38.5 + - + +
339C ILE* 4.0 9.0 - - + -
342C CYS* 3.2 29.6 - - - -
348C TYR* 3.4 34.1 - + - -
351C MET* 4.0 9.9 - - + -
66H TYR 2.9 16.6 + - - +
67H TRP* 3.7 16.8 - + - +
68H TYR 3.2 0.2 - - - -
69H TRP* 1.3 74.1 - - - +
71H LYS* 1.3 60.4 + - + +
73H GLY* 3.0 4.2 + - - -
74H ASN* 2.7 55.5 + - + +
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Residues in contact with LYS 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H TRP* 3.0 51.6 + - + +
68H TYR* 3.6 5.4 - - - +
70H TRP* 1.3 81.0 - - + +
72H ASN* 1.3 66.7 + - - +
74H ASN* 2.9 18.7 + - - +
75H GLU* 2.9 47.6 + - + +
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Residues in contact with ASN 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H TYR* 2.9 26.1 + - + +
69H TRP* 4.0 6.5 - - + +
71H LYS* 1.3 77.7 - - - +
73H GLY* 1.3 65.1 + - - +
75H GLU* 3.1 23.1 + - - +
76H TYR* 3.3 12.4 + - - +
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Residues in contact with GLY 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C PRO* 3.3 29.0 - - - +
348C TYR* 4.5 4.9 - - - -
351C MET* 4.5 12.3 - - - -
69H TRP* 3.1 12.1 + - - -
70H TRP 3.0 7.1 + - - -
72H ASN* 1.3 81.6 - - - +
74H ASN* 1.3 59.7 + - - +
76H TYR* 3.6 6.1 + - - +
77H ASN 3.4 6.6 + - - -
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Residues in contact with ASN 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C TYR* 2.4 33.4 + - - +
70H TRP* 2.7 39.4 + - + +
71H LYS* 2.9 12.9 + - - +
73H GLY* 1.3 72.0 - - - +
75H GLU* 1.3 67.0 + - - +
77H ASN* 3.3 3.6 - - - +
78H GLU* 3.1 30.3 + - - +
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Residues in contact with GLU 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H LYS* 2.9 54.4 + - + +
72H ASN* 3.1 15.8 + - - +
74H ASN* 1.3 76.9 - - + +
76H TYR* 1.3 60.6 + - - +
78H GLU* 3.1 12.4 + - - +
79H PHE* 2.9 30.5 + - - +
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Residues in contact with TYR 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C VAL* 4.6 9.4 - - + -
347C PRO* 4.0 18.4 - - + -
72H ASN* 3.3 8.8 + - - +
73H GLY* 3.7 11.7 - - - +
75H GLU* 1.3 78.0 - - - +
77H ASN* 1.3 62.3 + - - +
79H PHE* 4.2 12.3 - + + -
80H LEU* 3.0 59.6 + - + +
88H GLU* 3.6 33.5 + - - +
92H VAL* 3.9 15.3 - - + +
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Residues in contact with ASN 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU* 3.0 33.8 + - - +
347C PRO* 3.3 37.7 - - + +
348C TYR* 3.4 25.5 + - + +
62D MET 4.1 6.8 + - - -
73H GLY 3.4 3.1 + - - +
74H ASN* 3.3 11.1 + - - +
75H GLU 3.1 0.4 - - - -
76H TYR* 1.3 77.6 - - - +
78H GLU* 1.3 64.5 + - - +
79H PHE 3.0 1.4 + - - -
80H LEU* 3.1 14.3 + - - +
81H TYR* 3.2 21.1 + - - +
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Residues in contact with GLU 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ASN* 3.1 18.7 + - - +
75H GLU* 3.1 14.6 + - - +
77H ASN* 1.3 82.6 - - - +
79H PHE* 1.3 62.4 + - - +
81H TYR* 4.0 3.3 + - - +
82H SER* 3.5 18.5 + - - -
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Residues in contact with PHE 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H GLU 2.9 15.1 + - - +
76H TYR* 3.7 20.4 - + - +
77H ASN 3.0 0.2 + - - -
78H GLU* 1.3 74.7 - - - +
80H LEU* 1.3 72.6 + - + +
82H SER* 2.5 31.5 + - - -
84H ALA* 3.8 13.9 - - + -
85H GLY* 3.3 36.4 + - - -
88H GLU* 3.6 26.2 - - + -
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Residues in contact with LEU 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C VAL* 3.8 36.3 - - + -
347C PRO* 4.2 9.6 - - + -
76H TYR* 3.0 55.7 + - + +
77H ASN 3.1 3.3 + - - +
79H PHE* 1.3 80.9 - - + +
81H TYR* 1.3 61.8 + - + +
82H SER 3.3 3.1 + - - +
85H GLY* 4.4 2.2 - - - -
86H ARG* 3.5 12.6 + - - -
88H GLU* 3.8 19.3 - - + -
89H LEU* 3.4 48.5 - - + +
92H VAL* 4.3 2.5 - - + -
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Residues in contact with TYR 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU* 3.7 40.5 - - + +
346C VAL 4.6 2.5 + - - -
62D MET* 3.2 39.9 - - - +
63D THR* 3.7 36.2 - - + +
64D ALA 4.8 1.0 + - - -
125F GLU* 5.2 0.3 - - - +
77H ASN* 3.2 26.0 + - - +
78H GLU* 4.2 4.7 - - - +
79H PHE 3.2 1.0 - - - -
80H LEU* 1.3 78.9 - - + +
82H SER* 1.3 60.7 + - - +
86H ARG* 6.0 0.2 - - - -
89H LEU* 3.8 32.4 - - + +
93H ASN* 4.1 13.0 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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