Contacts of the helix formed by residues 83 - 118 (chain o) in PDB entry 5XTD
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 THR 83 (chain o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PLX 5.5 0.4 - - - -
68c ASP* 4.5 15.3 - - - +
69c GLY 4.2 10.8 - - - +
81o ARG* 3.1 20.3 + - + +
82o PRO* 1.3 74.3 - - - +
84o PRO* 1.3 63.2 - - + -
85o LYS* 3.5 9.0 + - - +
86o ASN* 2.9 35.5 + - - +
87o SER* 2.7 38.3 + - - -
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Residues in contact with PRO 84 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203V PLX 4.2 67.0 - - + +
83o THR* 1.3 88.1 - - + +
85o LYS* 1.3 58.6 + - + +
87o SER* 3.7 8.9 - - - +
88o LEU* 2.9 31.5 + - - +
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Residues in contact with LYS 85 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68c ASP* 4.8 15.0 + - - +
70c MET* 6.2 3.6 - - - -
83o THR* 3.1 8.9 + - - +
84o PRO* 1.3 78.7 - - + +
86o ASN* 1.3 63.3 + - - +
88o LEU* 4.3 2.1 - - - +
89o MET* 2.9 36.7 + - + +
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Residues in contact with ASN 86 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68c ASP* 5.1 1.2 - - - +
69c GLY* 3.4 19.5 + - - +
70c MET* 3.9 24.1 - - - +
552l LEU* 4.5 6.2 - - + +
557l TRP* 3.8 19.3 + - + +
80o PHE* 4.1 10.7 - - + -
81o ARG 2.6 29.1 + - - -
82o PRO* 4.0 0.9 - - + +
83o THR* 2.9 30.7 + - - +
85o LYS* 1.3 75.7 - - - +
87o SER* 1.3 67.7 + - - +
89o MET* 4.0 3.1 - - - +
90o GLY* 2.9 23.7 + - - -
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Residues in contact with SER 87 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203V PLX 3.8 45.1 + - - +
557l TRP* 3.5 25.6 - - - -
82o PRO* 3.9 4.7 + - - +
83o THR 2.7 27.4 + - - -
84o PRO* 3.7 8.5 - - - -
85o LYS 3.3 0.2 - - - -
86o ASN* 1.3 73.8 - - - +
88o LEU* 1.3 57.2 + - - +
90o GLY* 3.9 0.3 - - - -
91o ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 88 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203V PLX 4.4 20.2 - - + +
84o PRO 2.9 17.2 + - - +
85o LYS* 4.3 2.2 - - - +
87o SER* 1.3 76.4 - - - +
89o MET* 1.3 66.2 + - - +
91o ALA* 3.1 5.5 + - + -
92o LEU* 2.9 42.9 + - + +
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Residues in contact with MET 89 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547l ASN* 5.9 5.4 - - + +
548l LEU* 3.8 15.9 - - + -
552l LEU* 4.3 12.3 - - + -
85o LYS* 2.9 25.1 + - + +
86o ASN* 4.0 3.4 - - - +
88o LEU* 1.3 78.4 - - - +
90o GLY* 1.3 57.9 + - - +
92o LEU* 5.2 1.1 - - - -
93o CYS* 2.9 64.4 + - - +
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Residues in contact with GLY 90 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PLX 4.1 11.6 - - - +
552l LEU* 3.6 26.6 - - - +
553l LEU* 4.1 3.9 - - - +
557l TRP* 4.6 6.3 - - - -
86o ASN 2.9 15.1 + - - -
87o SER 4.0 0.2 - - - -
89o MET* 1.3 77.7 - - - +
91o ALA* 1.3 59.0 + - - +
93o CYS 4.5 0.2 - - - -
94o GLY* 2.9 27.0 + - - -
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Residues in contact with ALA 91 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203V PLX 3.6 52.6 - - + +
87o SER 2.9 20.1 + - - +
88o LEU* 3.1 5.8 + - + +
90o GLY* 1.3 76.9 - - - +
92o LEU* 1.3 58.6 + - + +
95o PHE* 2.9 37.0 + - + +
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Residues in contact with LEU 92 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88o LEU* 2.9 31.8 + - + +
89o MET* 4.4 2.0 - - - +
91o ALA* 1.3 76.9 - - - +
93o CYS* 1.3 67.2 + - - +
94o GLY 3.1 4.7 - - - -
95o PHE 5.1 0.2 - - - -
96o GLY* 2.9 33.8 + - - +
97o PRO* 3.6 1.9 - - - +
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Residues in contact with CYS 93 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548l LEU* 3.5 34.8 - - + +
552l LEU* 4.5 4.0 - - + -
553l LEU* 4.2 8.7 - - - +
89o MET* 2.9 52.3 + - - +
90o GLY* 3.8 0.7 - - - -
92o LEU* 1.3 87.5 - - - +
94o GLY* 1.3 57.4 + - - +
97o PRO* 3.8 17.0 - - - +
267r TRP* 5.3 3.3 + - - -
271r MET* 5.6 2.1 - - - +
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Residues in contact with GLY 94 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PLX 4.6 5.2 - - - +
553l LEU* 3.7 24.1 - - - +
90o GLY 2.9 17.0 + - - -
93o CYS* 1.3 79.7 - - - +
95o PHE* 1.3 66.2 + - - +
96o GLY 3.3 1.5 + - - -
97o PRO* 4.0 5.5 - - - +
98o LEU* 3.7 21.8 - - - +
267r TRP* 5.1 3.7 + - - -
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Residues in contact with PHE 95 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PLX 3.4 105.4 - - + -
561l LEU* 5.4 2.7 - - + -
91o ALA* 2.9 24.3 + - + +
94o GLY* 1.3 73.4 - - - +
96o GLY* 1.3 63.0 + - - +
98o LEU* 4.1 14.1 - - + -
99o ILE* 3.2 37.1 + - + +
501r PLX 6.6 0.2 - - + -
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Residues in contact with GLY 96 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92o LEU* 2.9 24.1 + - - +
95o PHE* 1.3 76.5 - - - +
97o PRO* 1.3 72.2 - - - +
99o ILE* 3.1 6.8 + - - +
100o PHE* 3.0 23.7 + - - +
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Residues in contact with PRO 97 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548l LEU* 6.6 0.2 - - + -
92o LEU 3.6 9.0 - - - +
93o CYS* 3.8 19.7 - - - +
94o GLY 4.0 3.1 - - - +
96o GLY* 1.3 88.5 - - - +
98o LEU* 1.3 63.1 + - - +
100o PHE* 3.6 8.2 - - + +
101o ILE* 2.9 31.9 + - + +
267r TRP* 3.8 41.7 - - + +
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Residues in contact with LEU 98 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PLX 4.8 13.5 - - + -
94o GLY 3.7 18.2 - - - +
95o PHE* 4.3 18.8 - - + +
96o GLY 3.1 1.2 - - - -
97o PRO* 1.3 80.2 - - - +
99o ILE* 1.3 64.5 + - + +
101o ILE* 3.2 2.5 + - - +
102o TYR* 2.9 24.8 + - - +
210r TYR* 6.0 3.6 - - + -
263r VAL* 3.8 13.0 - - + +
264r LEU* 3.8 31.6 - - + +
267r TRP* 3.8 35.9 - - + -
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Residues in contact with ILE 99 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203V PLX 5.3 10.5 - - + -
95o PHE* 3.2 27.6 + - + +
96o GLY* 3.1 4.9 + - - +
98o LEU* 1.3 76.7 - - + +
100o PHE* 1.3 64.3 + - - +
102o TYR* 3.7 8.7 - - + +
103o TYR* 3.0 27.3 + - + +
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Residues in contact with PHE 100 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96o GLY 3.0 16.7 + - - +
97o PRO* 3.6 9.9 - - + +
99o ILE* 1.3 79.3 - - - +
101o ILE* 1.3 70.1 + - + +
103o TYR* 3.8 6.6 - + - +
104o ILE* 3.0 55.9 + - + +
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Residues in contact with ILE 101 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97o PRO* 2.9 23.2 + - + +
98o LEU* 3.6 3.8 - - - +
100o PHE* 1.3 86.2 - - + +
102o TYR* 1.3 63.7 + - - +
104o ILE* 3.0 8.6 + - + +
105o ILE* 2.9 44.6 + - + +
263r VAL* 4.3 15.3 - - + +
266r LEU* 5.6 0.9 - - + -
267r TRP* 3.7 46.0 - - + +
395r LEU* 4.2 24.9 - - + -
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Residues in contact with TYR 102 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98o LEU 2.9 17.8 + - - +
99o ILE* 3.7 9.2 - - + +
101o ILE* 1.3 75.7 - - - +
103o TYR* 1.3 69.2 + - + +
105o ILE* 4.0 1.8 - - + +
106o LYS* 2.9 48.2 + - + +
259r TYR* 3.6 32.3 - + + +
260r PRO* 4.9 4.3 - - + -
263r VAL* 3.7 30.7 - - + +
501r PLX 3.1 23.7 + - - -
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Residues in contact with TYR 103 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99o ILE* 3.0 19.7 + - + +
100o PHE* 3.8 5.6 - + - +
102o TYR* 1.3 85.6 - - + +
104o ILE* 1.3 75.1 + - + +
106o LYS* 3.8 3.3 - - + +
107o THR* 3.0 51.7 + - + +
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Residues in contact with ILE 104 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100o PHE* 3.0 57.6 + - + +
101o ILE* 3.0 8.4 + - + +
103o TYR* 1.3 87.3 - - + +
105o ILE* 1.3 59.1 + - + +
107o THR* 2.7 21.6 + - - +
108o GLU 3.7 2.6 + - - -
391r ILE* 3.4 39.4 - - + +
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Residues in contact with ILE 105 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101o ILE* 2.9 35.7 + - + +
102o TYR* 4.0 3.6 - - + +
104o ILE* 1.3 76.9 - - + +
106o LYS* 1.3 67.4 + - - +
107o THR 3.1 2.1 + - - -
108o GLU* 3.3 4.1 + - - +
109o ARG* 3.0 34.9 + - + +
259r TYR* 4.7 8.7 - - + -
262r LEU* 6.4 0.4 - - + -
263r VAL* 4.8 10.5 - - + -
266r LEU* 4.1 13.5 - - + -
388r TRP* 4.2 21.1 - - + -
389r SER* 4.4 7.5 - - - +
391r ILE* 5.2 11.7 - - + -
392r THR* 3.9 26.0 - - + -
395r LEU* 5.4 2.2 - - + -
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Residues in contact with LYS 106 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102o TYR* 2.9 44.9 + - + +
103o TYR* 3.9 4.3 - - + +
105o ILE* 1.3 78.7 - - - +
107o THR* 1.3 63.6 + - + +
109o ARG* 3.4 3.8 + - + +
110o ASP* 2.9 55.6 + - - +
113o GLU* 4.6 8.3 + - - -
259r TYR* 3.7 38.9 + - + +
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Residues in contact with THR 107 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103o TYR* 3.0 47.4 + - + +
104o ILE* 2.7 25.3 + - - +
106o LYS* 1.3 77.9 - - + +
108o GLU* 1.3 62.9 + - - +
110o ASP* 2.8 25.3 + - - +
111o ARG* 2.9 26.0 + - - +
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Residues in contact with GLU 108 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704l CDL 4.5 10.7 - - - +
104o ILE 4.4 1.1 - - - +
105o ILE* 3.3 6.7 + - - +
107o THR* 1.3 86.5 + - - +
109o ARG* 1.3 63.5 + - + +
111o ARG* 3.8 24.2 + - - +
112o LYS* 2.9 37.3 + - + +
389r SER* 4.7 4.8 - - - -
390r ASN* 4.0 16.2 + - - +
391r ILE* 3.2 50.5 + - + +
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Residues in contact with ARG 109 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119g ARG* 3.2 32.5 + - - +
105o ILE* 3.0 34.8 + - + +
106o LYS* 3.7 7.0 - - + +
108o GLU* 1.3 76.8 - - - +
110o ASP* 1.3 61.3 + - - +
112o LYS* 3.5 15.8 + - - +
113o GLU* 2.9 54.6 + - - +
116o ILE* 6.2 1.6 - - - +
255r LYS* 5.8 7.5 - - - +
259r TYR* 3.6 27.3 + - + +
388r TRP* 3.1 54.8 + - + +
389r SER* 4.1 8.5 - - - -
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Residues in contact with ASP 110 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106o LYS* 2.9 53.9 + - - +
107o THR* 2.8 13.4 + - - +
109o ARG* 1.3 75.5 - - - +
111o ARG* 1.3 64.4 + - + +
113o GLU* 3.0 14.1 + - - +
114o LYS* 2.9 40.1 + - - +
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Residues in contact with ARG 111 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107o THR* 2.9 25.7 + - - +
108o GLU* 3.3 25.6 + - - +
110o ASP* 1.3 75.8 - - + +
112o LYS* 1.3 64.1 + - + +
114o LYS* 3.2 13.5 + - + +
115o LEU* 2.9 38.7 + - + +
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Residues in contact with LYS 112 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108o GLU* 2.9 28.8 + - + +
109o ARG* 3.9 15.0 - - - +
111o ARG* 1.3 76.0 - - + +
113o GLU* 1.3 65.0 + - + +
114o LYS 3.1 0.2 + - - -
115o LEU* 3.1 7.4 + - + -
116o ILE* 2.9 43.5 + - + +
121o LEU* 5.3 9.9 - - + -
123o ARG* 5.4 7.4 - - - +
387r SER 3.6 15.7 + - - +
388r TRP 3.7 7.1 + - - +
389r SER* 3.3 27.5 - - - +
390r ASN* 2.9 33.2 - - - +
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Residues in contact with GLU 113 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119g ARG* 6.0 7.6 - - + +
106o LYS* 4.6 6.0 + - - -
109o ARG* 2.9 50.1 + - - +
110o ASP* 3.0 17.7 + - - +
112o LYS* 1.3 76.9 - - + +
114o LYS* 1.3 62.3 + - + +
116o ILE* 4.5 8.3 - - + +
117o GLN* 3.7 24.1 + - - +
259r TYR* 4.1 10.0 + - - -
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Residues in contact with LYS 114 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110o ASP* 2.9 30.0 + - - +
111o ARG* 3.6 12.1 - - + +
112o LYS 3.1 0.2 - - - -
113o GLU* 1.3 77.1 - - + +
115o LEU* 1.3 69.6 + - + +
116o ILE 3.2 0.9 + - - -
117o GLN* 3.5 6.0 + - - +
118o GLU* 3.4 39.3 + - - +
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Residues in contact with LEU 115 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111o ARG* 2.9 31.0 + - + +
112o LYS* 3.9 6.3 - - + +
114o LYS* 1.3 81.4 - - + +
116o ILE* 1.3 62.8 + - + +
118o GLU* 5.1 0.2 - - - -
119o GLY* 3.4 12.8 + - - +
120o LYS* 3.2 27.4 + - - -
121o LEU* 3.9 27.6 + - + -
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Residues in contact with ILE 116 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119g ARG* 3.5 49.8 - - + +
109o ARG* 6.2 1.6 - - - +
112o LYS* 2.9 34.8 + - + +
113o GLU* 4.5 7.6 - - + +
114o LYS 3.2 0.2 - - - -
115o LEU* 1.3 79.7 - - - +
117o GLN* 1.3 62.2 + - - +
118o GLU 3.3 1.0 + - - +
120o LYS* 4.5 8.1 + - - +
121o LEU* 4.1 18.6 + - + -
123o ARG* 3.6 37.7 - - + +
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Residues in contact with GLN 117 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119g ARG* 5.4 10.9 + - - +
113o GLU 3.7 19.0 + - - +
114o LYS* 3.5 6.5 + - - +
116o ILE* 1.3 81.0 - - + +
118o GLU* 1.3 78.1 + - + +
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Residues in contact with GLU 118 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114o LYS* 3.4 27.2 + - - +
115o LEU* 5.1 0.2 - - - -
116o ILE 3.2 1.8 - - - -
117o GLN* 1.3 100.7 + - + +
119o GLY* 1.3 62.8 + - - +
120o LYS* 2.9 19.4 + - - +
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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