Contacts of the helix formed by residues 103 - 123 (chain A) in PDB entry 1XS2
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLU* 4.5 7.5 + - - -
65A GLU* 3.4 29.6 + - - +
69A GLY* 5.2 7.5 + - - -
70A ALA* 5.4 0.6 - - - +
73A LEU* 3.6 33.5 - - + +
78A PHE* 5.1 1.1 - - + -
100A TYR* 6.5 0.4 - - + -
101A ARG 3.0 16.6 - - - +
102A GLY* 1.3 72.0 - - - +
104A ARG* 1.3 64.8 + - - +
105A MET 3.3 2.7 - - - -
106A ALA* 3.3 3.0 + - + +
107A ARG* 3.1 24.0 + - + +
60C PRO* 3.6 8.4 - - + +
64C GLU* 2.9 29.1 + - - +
66C THR* 5.0 6.5 - - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 5.2 1.2 + - - +
65A GLU* 3.3 5.1 + - - +
102A GLY* 4.1 16.9 - - - +
103A ASN* 1.3 77.1 - - - +
105A MET* 1.3 58.4 + - - +
107A ARG* 3.3 11.8 + - - +
108A ALA* 2.8 28.9 + - - +
249A ALA* 3.2 32.3 + - - +
250A SER* 3.8 15.6 - - - -
271A ALA 3.7 2.0 - - - -
272A ARG 3.6 19.5 - - - +
273A VAL 2.6 30.7 + - - -
274A GLY* 3.6 12.1 - - - +
278A GLU* 3.9 15.8 + - - +
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Residues in contact with MET 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLY* 5.4 0.5 - - - -
55A THR* 3.3 27.8 - - - +
56A MET* 3.8 34.0 - - + +
62A TYR* 3.9 33.7 - - + -
63A ARG* 4.5 13.2 - - + -
65A GLU* 2.9 25.1 + - - +
104A ARG* 1.3 77.2 - - - +
106A ALA* 1.3 62.3 + - - +
108A ALA* 3.0 13.6 + - - +
109A MET* 3.2 16.5 + - - +
271A ALA* 3.4 19.1 - - + +
272A ARG* 4.0 21.3 - - + +
298A MET* 4.6 4.0 - - + -
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Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A MET* 3.8 8.4 - - - +
65A GLU* 3.0 16.5 + - - +
70A ALA* 4.0 29.2 - - + +
73A LEU* 4.1 18.4 - - + -
74A LEU* 3.8 12.4 - - + +
78A PHE* 4.1 5.6 - - + -
103A ASN* 3.7 5.4 - - - +
104A ARG 3.3 0.2 - - - -
105A MET* 1.3 72.5 - - - +
107A ARG* 1.3 66.8 + - - +
109A MET* 3.2 20.1 + - - +
110A VAL* 3.7 3.3 + - - +
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 3.5 29.2 - - + -
94A SER* 3.1 36.2 + - - +
97A LEU* 3.5 25.2 + - + +
98A GLY* 3.4 22.6 + - - -
100A TYR* 3.6 16.6 + - - +
102A GLY 3.9 17.5 - - - -
103A ASN 3.1 12.6 + - - +
104A ARG* 3.4 14.4 - - - +
106A ALA* 1.3 75.7 - - - +
108A ALA* 1.3 62.6 + - - +
110A VAL* 3.0 15.2 + - - +
111A GLU* 3.1 13.8 + - + +
274A GLY* 4.5 8.1 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 2.8 13.4 + - - +
105A MET 3.0 11.6 + - - +
107A ARG* 1.3 78.0 - - - +
109A MET* 1.3 55.2 + - - +
111A GLU* 4.4 1.3 - - - -
112A MET* 3.0 44.7 + - - +
271A ALA* 3.8 26.0 - - + -
274A GLY 3.7 24.5 - - - -
275A GLY 3.9 1.6 - - - +
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Residues in contact with MET 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 5.7 0.2 - - + -
39A PRO* 3.9 27.4 - - + +
40A LEU 4.0 4.0 - - - +
41A LEU* 3.5 32.3 - - + +
52A ALA* 3.6 9.7 - - + +
53A GLU 4.2 5.2 - - - +
54A GLY* 3.5 31.2 - - - +
56A MET* 3.8 18.2 - - - +
70A ALA* 5.5 0.4 - - - -
71A LEU* 4.7 5.4 - - + -
74A LEU* 3.8 28.0 - - + -
105A MET 3.2 9.7 + - - +
106A ALA* 3.5 9.0 - - - +
107A ARG 3.2 0.4 - - - -
108A ALA* 1.3 76.9 - - - +
110A VAL* 1.3 61.8 + - - +
112A MET* 5.5 0.2 - - - -
113A ALA* 3.2 25.3 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.8 10.8 - - + -
43A LEU* 3.7 4.6 - - + +
74A LEU* 3.4 29.8 - - + -
78A PHE* 4.1 17.5 - - + -
79A LEU* 4.8 4.0 - - + -
82A ILE* 3.4 30.1 - - + -
93A VAL* 3.9 15.7 - - + -
97A LEU* 4.0 14.4 - - + -
106A ALA 4.0 4.5 - - - +
107A ARG 3.0 7.0 + - - +
109A MET* 1.3 75.9 - - - +
111A GLU* 1.3 59.2 + - - +
113A ALA* 3.3 2.6 + - - +
114A ALA* 2.8 30.5 + - - +
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PRO* 4.6 4.8 - - - +
93A VAL* 5.3 3.1 - - - -
94A SER* 3.1 28.7 - - - +
97A LEU* 5.6 1.5 - - + +
107A ARG 3.1 12.2 + - - +
108A ALA 4.1 1.1 - - - +
110A VAL* 1.3 80.5 - - - +
112A MET* 1.3 60.4 + - - +
114A ALA* 3.3 8.7 - - - +
115A TRP* 3.0 54.6 + - + +
274A GLY 3.9 13.7 - - - +
275A GLY* 3.3 9.2 - - - -
276A HIS 2.9 21.9 + - - -
277A ALA* 2.8 35.2 + - - +
278A GLU 4.5 0.5 + - - -
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.8 9.9 - - + -
53A GLU 5.6 6.5 - - - +
108A ALA* 3.0 39.1 + - - +
109A MET* 5.5 0.2 - - - -
111A GLU* 1.3 85.7 - - - +
113A ALA* 1.3 67.2 + - - +
114A ALA 3.1 1.1 - - - -
115A TRP* 3.0 11.8 + - - +
116A ASP 3.0 10.2 + - - -
270A VAL* 3.6 36.8 - - + -
271A ALA* 4.6 6.1 - - + -
275A GLY* 4.0 4.3 - - - -
276A HIS* 3.7 17.7 - - + +
304A GLY* 5.9 2.2 - - - -
307A HIS* 3.4 51.2 - - + +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.1 6.5 - - + +
43A LEU* 3.7 23.1 - - + +
50A GLY* 3.4 19.6 - - - +
51A VAL 4.1 8.3 - - - +
52A ALA* 3.6 17.5 - - + +
109A MET 3.2 19.6 + - - +
110A VAL 3.3 3.1 + - - +
112A MET* 1.3 76.8 - - - +
114A ALA* 1.3 56.7 + - - +
116A ASP 3.3 1.0 + - - -
117A LEU* 3.0 26.2 + - - +
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Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.7 6.0 - - + -
10A ILE* 5.5 0.4 - - + -
43A LEU* 3.8 9.3 - - + +
90A PRO* 4.1 8.9 - - + +
93A VAL* 4.3 29.2 - - + -
110A VAL 2.8 14.4 + - - +
111A GLU* 3.3 13.9 - - - +
112A MET 3.1 0.2 - - - -
113A ALA* 1.3 74.7 - - - +
115A TRP* 1.3 59.2 + - - +
117A LEU* 3.8 7.4 - - - +
118A TRP* 2.9 31.7 + - - +
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Residues in contact with TRP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A PRO* 3.5 30.8 - - + +
91A GLU* 3.6 27.4 - - - -
111A GLU* 3.0 54.7 + - - -
112A MET 3.0 7.8 + - - +
114A ALA* 1.3 76.0 - - - +
116A ASP* 1.3 58.0 + - - +
118A TRP* 3.7 20.9 - + - +
119A ALA* 2.9 32.6 + - - +
126A LEU* 3.7 28.4 - - + +
129A LEU* 4.2 23.1 - - + -
130A LEU* 3.8 26.0 - - + -
276A HIS* 3.8 16.6 - + + -
277A ALA* 3.8 11.5 - - + +
280A ARG* 4.8 6.3 - - - -
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLN 4.1 0.3 - - - +
50A GLY* 3.5 3.1 - - - -
51A VAL* 3.0 30.5 + - - +
112A MET 3.0 11.6 + - - +
113A ALA 3.5 8.5 - - - +
114A ALA 3.2 0.2 - - - -
115A TRP* 1.3 78.8 - - - +
117A LEU* 1.3 57.6 + - - +
119A ALA* 3.3 4.6 + - - +
120A ARG* 2.6 67.4 + - - +
126A LEU* 5.2 2.0 - - - -
307A HIS* 4.3 2.7 - - + -
353A GLY* 3.3 2.0 - - - -
354A THR* 3.0 40.8 + - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.1 26.7 - - + -
9A LYS 5.1 0.4 - - - +
10A ILE* 4.2 16.4 - - + -
43A LEU* 4.3 16.4 - - + +
45A GLY* 3.7 21.5 - - - +
48A VAL* 3.2 38.8 - - + +
49A GLN* 3.8 11.9 - - - -
50A GLY* 3.6 8.8 - - - +
113A ALA 3.0 16.8 + - - +
114A ALA* 3.8 4.9 - - - +
116A ASP* 1.3 74.2 - - - +
118A TRP* 1.3 64.9 - - - +
120A ARG* 3.0 5.5 + - - +
121A THR* 2.9 28.9 + - + +
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Residues in contact with TRP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG 3.5 25.4 - - - -
8A PHE* 3.6 25.8 - + + -
88A ALA 3.4 21.1 - - - -
89A ASN* 4.4 5.4 - - + +
90A PRO* 3.1 37.9 - - + +
114A ALA 2.9 22.9 + - - +
115A TRP* 3.7 19.6 - + - +
117A LEU* 1.3 72.4 - - - +
119A ALA* 1.3 60.9 + - - +
121A THR* 2.5 36.0 + - - -
122A LEU* 3.2 36.3 + - + +
129A LEU* 3.9 19.3 - - + +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A TRP 2.9 19.6 + - - +
116A ASP* 3.5 4.5 - - - +
118A TRP* 1.3 76.8 - - - +
120A ARG* 1.3 57.5 + - - +
122A LEU* 3.2 3.0 + - - +
123A GLY 2.9 8.1 + - - -
124A VAL 2.9 44.9 + - - +
126A LEU* 4.5 7.6 - - + -
129A LEU* 3.8 23.6 - - + -
353A GLY* 3.7 12.3 - - - -
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Residues in contact with ARG 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.0 25.3 - - + +
49A GLN* 3.2 25.6 + - - +
116A ASP* 2.6 37.3 + - - +
117A LEU 3.0 5.1 + - - +
119A ALA* 1.3 74.1 - - - +
121A THR* 1.3 62.9 + - - +
122A LEU 3.1 2.3 + - - -
123A GLY* 3.4 9.6 + - - +
352A PRO* 3.3 51.0 + - + +
354A THR* 3.2 16.8 + - - -
355A GLY* 3.6 4.2 - - - +
356A VAL 2.9 28.2 + - - +
357A THR* 5.6 5.1 + - - +
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG 5.1 2.2 + - - -
8A PHE* 4.4 11.2 - - + -
46A GLU* 4.3 25.1 - - + -
48A VAL* 3.9 18.4 - - + -
117A LEU* 2.9 19.6 + - + +
118A TRP* 2.5 33.4 + - - +
120A ARG* 1.3 75.5 - - - +
122A LEU* 1.3 65.0 + - - +
123A GLY 3.5 0.2 - - - -
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG 5.2 10.1 - - - +
118A TRP* 3.2 48.7 + - + +
119A ALA 3.2 9.1 + - - +
120A ARG 3.1 0.6 - - - -
121A THR* 1.3 91.4 + - - +
123A GLY* 1.3 59.1 + - - +
124A VAL* 3.7 17.6 + - + +
129A LEU* 4.3 24.7 - - + -
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 2.9 4.7 + - - -
120A ARG 3.4 11.2 + - - -
121A THR 3.5 0.2 - - - -
122A LEU* 1.3 78.9 - - - +
124A VAL* 1.3 60.5 + - - +
125A PRO* 4.1 4.9 - - - +
352A PRO* 4.1 17.4 - - - +
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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
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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