Contacts of the helix formed by residues 55 - 81 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102N TYR* 4.0 9.9 + - - -
323N LYS* 2.9 44.4 + - - +
327N PHE* 5.1 8.1 - - - -
51S ARG 5.4 3.6 - - - +
52S PHE* 4.1 25.8 - - + +
53S LYS 4.1 0.6 - - - +
54S SER* 1.3 86.8 - - - +
56S PHE* 1.3 65.0 + - - +
58S TYR* 2.7 35.1 + - - +
59S VAL* 3.4 9.5 + - + +
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Residues in contact with PHE 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S PHE* 3.1 41.9 + - + +
53S LYS* 3.0 26.5 - - + -
54S SER 3.2 1.0 + - - -
55S GLN* 1.3 76.7 - - - +
57S LEU* 1.3 96.7 + - + +
59S VAL* 3.2 2.8 + - - +
60S LEU* 2.8 58.6 + - + +
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Residues in contact with LEU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N PHE* 5.3 1.2 - - - -
53S LYS 5.6 0.7 - - - +
54S SER 3.7 7.3 + - - +
55S GLN 3.0 1.6 + - - -
56S PHE* 1.3 114.2 - - + +
58S TYR* 1.3 64.2 + - + +
60S LEU* 4.4 3.8 - - + -
61S ILE* 3.4 49.9 + - + +
62S PRO* 4.0 0.2 - - - +
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Residues in contact with TYR 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N VAL* 3.2 56.2 - - + +
323N LYS* 3.9 36.8 + - + +
324N PHE* 3.9 19.9 - + + +
327N PHE* 3.5 25.5 - - + +
35R LEU* 4.3 15.3 + - - +
54S SER* 4.0 12.1 - - - -
55S GLN* 2.7 32.0 + - - +
57S LEU* 1.3 75.9 - - + +
59S VAL* 1.3 58.9 + - - +
62S PRO* 3.1 24.0 - - - +
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Residues in contact with VAL 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327N PHE* 4.0 35.2 - - + -
331N PHE* 3.6 26.6 - - + -
52S PHE* 4.0 29.4 - - + -
55S GLN* 3.8 15.0 - - + +
56S PHE 3.2 3.5 + - - +
58S TYR* 1.3 79.6 - - - +
60S LEU* 1.3 63.7 + - + +
61S ILE 3.4 0.2 - - - -
62S PRO* 3.1 4.9 - - - +
63S ALA* 2.9 29.1 + - + +
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Residues in contact with LEU 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S PHE* 5.8 7.0 - - + -
56S PHE* 2.8 51.6 + - + +
57S LEU* 4.4 4.3 - - + -
59S VAL* 1.3 77.7 - - + +
61S ILE* 1.3 52.9 + - + +
63S ALA* 3.2 8.7 + - + +
64S GLY* 2.5 36.7 + - - +
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Residues in contact with ILE 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N PHE* 4.0 22.7 - - + -
57S LEU* 3.4 34.8 + - + +
60S LEU* 1.3 75.8 - - + +
62S PRO* 1.3 67.9 - - + +
64S GLY* 2.9 2.9 + - - -
65S ILE* 2.7 49.3 + - + +
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Residues in contact with PRO 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N PHE* 4.0 17.0 - - + +
327N PHE* 3.9 6.3 - - + -
328N ILE* 3.8 43.5 - - + +
331N PHE* 3.9 12.3 - - + -
57S LEU 4.0 0.4 - - - +
58S TYR 3.1 23.8 - - - +
59S VAL 3.1 15.3 - - - +
61S ILE* 1.3 90.0 - - + +
63S ALA* 1.3 62.1 + - - +
65S ILE* 3.7 3.0 - - + +
66S TYR* 3.0 29.3 + - - -
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Residues in contact with ALA 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331N PHE* 3.6 34.6 - - + -
59S VAL* 2.9 18.4 + - + +
60S LEU* 3.5 12.1 - - + +
62S PRO* 1.3 76.0 - - - +
64S GLY* 1.3 57.4 + - - +
66S TYR* 3.4 1.7 + - - +
67S TRP* 2.8 32.9 + - - +
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Residues in contact with GLY 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S LEU* 2.5 22.3 + - - +
61S ILE* 2.9 5.7 + - - -
63S ALA* 1.3 70.3 - - - +
65S ILE* 1.3 65.0 + - - -
66S TYR 3.0 0.3 + - - -
67S TRP* 3.1 6.8 + - - +
68S TYR* 3.0 29.7 + - - +
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Residues in contact with ILE 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324N PHE* 4.6 6.3 - - + -
328N ILE* 4.4 19.7 - - + -
61S ILE* 2.7 39.9 + - + +
62S PRO* 3.7 3.8 - - + +
64S GLY* 1.3 69.1 - - - +
66S TYR* 1.3 71.0 + - + +
68S TYR* 3.9 4.8 - - - +
69S TRP* 3.2 28.0 + - + +
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Residues in contact with TYR 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328N ILE* 3.6 34.2 + - + +
331N PHE* 3.9 22.4 - - + +
332N ASN* 2.6 47.1 + - + +
335N LEU* 3.9 25.2 - - + +
358N ILE* 3.3 16.1 - - - +
62S PRO* 3.0 26.4 + - + +
63S ALA 3.9 2.5 - - - +
65S ILE* 1.3 83.6 - - + +
67S TRP* 1.3 63.9 + - - +
69S TRP* 3.3 30.6 + + - +
70S TRP* 3.0 24.8 + - - +
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Residues in contact with TRP 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S ALA 2.8 21.6 + - - +
64S GLY* 3.9 4.0 - - - +
66S TYR* 1.3 73.7 - - - +
68S TYR* 1.3 88.0 + + - +
70S TRP* 3.9 14.3 - + - +
71S LYS* 3.1 66.4 + - + +
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Residues in contact with TYR 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64S GLY* 3.0 17.5 + - - +
65S ILE* 3.9 6.1 - - - +
67S TRP* 1.3 99.6 - + - +
69S TRP* 1.3 55.8 + - - +
71S LYS* 3.9 5.7 - - - +
72S ASN* 2.8 51.7 + - + +
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Residues in contact with TRP 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332N ASN* 4.6 0.9 - - - -
335N LEU* 4.5 10.3 - - + -
351N MET* 3.6 47.3 - - + +
354N ILE* 3.5 44.2 - - + +
355N ALA 4.4 3.6 - - - -
358N ILE* 4.5 5.8 - - + -
65S ILE* 3.2 20.1 + - + +
66S TYR* 3.5 45.1 - + - +
68S TYR* 1.3 80.7 - - - +
70S TRP* 1.3 62.7 + - - +
72S ASN* 3.8 4.1 - - + +
73S GLY* 3.2 17.4 + - - -
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Residues in contact with TRP 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335N LEU* 3.9 26.2 - - + +
338N GLN* 3.6 31.7 + - + +
339N ILE* 3.9 7.0 - - + -
342N CYS* 3.1 32.1 - - - -
348N TYR* 3.5 24.2 - + - -
351N MET* 3.8 13.6 - - + +
66S TYR 3.0 16.3 + - - +
67S TRP* 3.9 16.6 - + - +
69S TRP* 1.3 76.5 - - - +
71S LYS* 1.3 83.2 + - + +
72S ASN 3.1 0.2 + - - -
73S GLY* 3.9 0.3 - - - -
74S ASN* 2.8 54.1 + - - +
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Residues in contact with LYS 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67S TRP* 3.1 61.9 + - + +
68S TYR* 3.9 7.0 - - - +
70S TRP* 1.3 83.5 - - + +
72S ASN* 1.3 65.9 + - - +
74S ASN* 3.3 8.9 + - - +
75S GLU* 3.1 51.2 + - + +
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Residues in contact with ASN 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68S TYR* 2.8 35.2 + - + +
69S TRP* 3.8 6.3 - - + +
71S LYS* 1.3 75.7 - - - +
73S GLY* 1.3 59.8 + - - +
75S GLU* 2.9 34.0 + - - +
76S TYR* 3.3 9.5 + - - +
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Residues in contact with GLY 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347N PRO* 3.3 36.4 - - - +
348N TYR* 4.5 4.0 - - - -
351N MET* 4.6 8.1 - - - -
69S TRP* 3.2 12.9 + - - -
70S TRP 3.8 1.6 - - - -
72S ASN* 1.3 79.9 + - - +
74S ASN* 1.3 59.9 + - - +
75S GLU 3.3 0.2 - - - -
76S TYR* 3.4 9.4 + - - +
77S ASN 3.3 6.4 + - - -
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Residues in contact with ASN 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348N TYR* 3.0 25.0 + - - +
70S TRP* 2.8 52.4 + - + +
71S LYS* 3.3 11.4 + - - +
73S GLY* 1.3 75.9 - - - +
75S GLU* 1.3 68.4 + - - +
77S ASN* 3.4 5.0 + - - +
78S GLU* 3.3 26.4 + - - +
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Residues in contact with GLU 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71S LYS* 3.1 46.7 + - + +
72S ASN* 2.9 16.1 + - - +
74S ASN* 1.3 80.2 - - - +
76S TYR* 1.3 60.3 + - - +
78S GLU* 3.2 16.3 + - - +
79S PHE* 2.9 28.8 + - - +
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Residues in contact with TYR 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346N VAL* 4.1 11.0 - - + -
347N PRO* 4.0 17.7 - - + -
72S ASN* 3.3 5.2 + - - +
73S GLY* 3.5 16.4 - - - +
74S ASN 3.3 0.6 - - - -
75S GLU* 1.3 76.8 - - - +
77S ASN* 1.3 63.3 + - - +
79S PHE* 3.4 12.5 + + + +
80S LEU* 3.0 64.7 + - + +
88S GLU* 3.8 17.7 - - + -
92S VAL* 3.5 28.8 - - + +
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Residues in contact with ASN 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343N HIS* 5.8 1.0 - - - -
345N GLU* 3.2 36.4 + - - +
347N PRO* 3.8 16.9 - - + +
348N TYR* 3.5 39.5 + - + +
62O MET 4.1 7.1 + - - -
73S GLY 3.3 4.0 + - - -
74S ASN 3.5 3.1 - - - +
75S GLU 3.2 0.2 - - - -
76S TYR* 1.3 77.1 - - - +
78S GLU* 1.3 67.3 + - - +
80S LEU* 3.0 5.3 + - - -
81S TYR* 3.0 46.5 + - - +
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Residues in contact with GLU 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S ASN* 3.3 16.0 + - - +
75S GLU* 3.2 18.1 + - - +
77S ASN* 1.3 83.1 + - - +
79S PHE* 1.3 64.2 + - - +
81S TYR* 3.4 16.2 + - - +
82S SER* 3.8 6.1 + - - -
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Residues in contact with PHE 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S GLU 2.9 15.2 + - - +
76S TYR* 3.7 13.5 - + + +
78S GLU* 1.3 75.0 - - - +
80S LEU* 1.3 77.1 + - + +
81S TYR 2.9 0.7 + - - -
82S SER* 2.5 28.1 + - - +
84S ALA* 3.5 42.6 - - + -
85S GLY* 3.5 13.6 + - - -
88S GLU* 3.8 28.7 - - + -
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Residues in contact with LEU 80 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346N VAL* 3.7 26.5 - - + -
347N PRO* 4.5 2.9 - - + -
76S TYR* 3.0 58.7 + - + +
77S ASN 3.0 4.5 + - - +
79S PHE* 1.3 82.5 - - + +
81S TYR* 1.3 63.0 + - + +
82S SER 3.3 4.5 + - - +
85S GLY 3.4 10.6 - - - +
86S ARG* 4.2 1.6 + - - -
88S GLU* 3.4 34.1 - - + -
89S LEU* 3.3 39.3 - - + +
92S VAL* 3.8 9.9 - - + -
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Residues in contact with TYR 81 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345N GLU* 3.6 33.3 + - + +
346N VAL* 4.3 4.3 - - + +
62O MET* 3.7 32.5 - - - +
63O THR* 3.9 31.3 - - + +
64O ALA* 4.3 5.9 + - - +
66O GLU* 5.6 0.9 - - - -
125Q GLU* 4.9 0.7 - - - +
77S ASN* 3.0 43.4 + - - +
78S GLU* 3.7 6.1 - - - +
79S PHE 2.9 0.4 + - - -
80S LEU* 1.3 82.7 - - + +
82S SER* 1.3 58.8 + - - +
89S LEU* 3.8 28.6 - - + +
93S ASN* 3.6 21.6 + - - -
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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