Contacts of the helix formed by residues 98 - 122 (chain A) in PDB entry 2PGW
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 ILE 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 4.7 1.7 - - - -
91A TYR* 3.7 27.4 - - + -
96A ALA* 2.7 26.6 + - + +
97A ASN* 1.3 72.9 - - - +
99A MSE 1.3 59.2 + - - +
100A ARG 3.4 2.7 - - - -
101A ALA* 3.3 21.7 + - + +
102A ALA* 2.9 24.1 + - - +
55G PRO* 4.9 7.2 - - + -
100G ARG* 3.6 20.2 - - + +
101G ALA* 3.4 33.4 - - + +
104G GLN* 3.8 22.2 - - + +
228G TRP* 4.5 0.2 - - - -
251G PHE* 4.9 4.5 - - + -
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Residues in contact with MSE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 4.0 23.6 - - + -
97A ASN 3.5 5.3 + - - -
98A ILE* 1.3 74.8 - - - +
100A ARG* 1.3 58.1 + - - +
102A ALA* 3.2 1.3 + - - +
103A ASN* 2.7 48.5 + - - +
252A THR* 3.6 35.2 - - + -
253A LEU* 5.2 1.6 - - - -
254A TYR* 4.0 20.0 - - + -
100G ARG* 5.3 1.6 - - - +
228G TRP* 3.4 59.4 - - + +
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE 3.4 0.8 - - - -
99A MSE 1.3 76.0 - - - +
101A ALA* 1.3 63.6 + - - +
103A ASN* 3.2 11.2 + - - +
104A GLN* 3.1 20.8 + - - +
227A SER 5.1 2.4 + - - -
228A TRP* 3.4 23.1 - - - -
248A GLN 4.0 5.9 + - - -
249A ALA* 3.8 13.9 + - - +
251A PHE* 3.3 40.2 - - + +
252A THR* 3.9 11.2 - - + +
255A ASP* 3.1 29.2 + - - -
273A ARG 4.9 1.0 - - - +
274A GLU 4.7 0.7 - - - +
2100A GOL 4.1 16.2 + - - -
97G ASN* 2.9 34.8 + - - +
98G ILE* 3.6 19.5 - - + +
99G MSE 5.3 1.3 - - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 4.8 0.7 - - + -
98A ILE* 3.3 19.6 + - + +
100A ARG* 1.3 78.9 - - - +
102A ALA* 1.3 63.1 + - - +
104A GLN* 3.2 15.1 - - - +
105A ILE* 3.1 22.5 - - + +
98G ILE* 3.4 18.6 - - + +
101G ALA* 3.5 31.4 - - + -
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 3.5 38.6 - - + -
91A TYR* 3.8 25.7 + - + -
98A ILE 2.9 12.9 + - - +
99A MSE 3.2 3.1 + - - +
101A ALA* 1.3 77.2 - - - +
103A ASN* 1.3 65.1 + - - +
105A ILE* 3.1 5.4 + - - +
106A PHE* 2.9 32.7 + - + -
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PHE* 6.2 0.2 - - - -
99A MSE 2.7 44.5 + - - +
100A ARG* 3.4 4.4 - - - +
102A ALA* 1.3 75.7 - - - +
104A GLN* 1.3 57.6 + - - +
106A PHE* 4.5 6.8 - - - +
107A SER* 2.9 33.4 + - - -
251A PHE 4.3 0.2 - - - +
252A THR* 4.0 10.9 - - - +
273A ARG 3.7 1.9 - - - +
274A GLU 3.0 28.2 - - - +
275A ILE* 3.2 22.0 + - - +
276A GLY* 3.4 12.6 - - - +
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Residues in contact with GLN 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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51A CYS* 3.7 17.2 - - - +
52A THR* 3.2 46.4 + - - +
53A VAL 4.0 0.6 - - - -
54A ALA* 2.9 30.9 + - - +
60A THR* 4.5 6.6 - - - +
100A ARG 3.1 11.4 + - - +
101A ALA* 3.2 15.0 - - - +
103A ASN* 1.3 78.0 - - - +
105A ILE* 1.3 63.9 + - + +
107A SER* 3.8 8.7 - - - -
273A ARG* 3.6 21.4 + - + +
96G ALA* 4.1 10.6 - - - +
98G ILE* 3.7 24.6 - - + +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A CYS* 3.2 22.4 - - + -
60A THR* 5.0 12.6 - - + +
63A ILE* 3.8 20.4 - - + -
64A LEU* 3.4 36.1 - - + +
67A LEU* 3.5 24.0 - - + -
91A TYR* 3.2 24.0 - - - +
101A ALA* 3.1 27.6 - - + +
102A ALA 3.1 3.9 + - - +
104A GLN* 1.3 82.6 - - + +
106A PHE* 1.3 64.9 + - - +
107A SER 3.1 3.2 + - - -
108A GLY 3.2 2.4 + - - -
109A ILE* 3.5 8.8 + - + +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.0 15.3 - - + -
83A ILE* 3.5 41.7 - - + +
86A ILE* 3.9 24.7 - - + -
87A PHE* 3.7 52.9 - + + -
91A TYR* 4.2 4.7 - + - -
102A ALA* 2.9 32.3 + - + +
103A ASN* 4.2 9.0 - - - +
105A ILE* 1.3 73.1 - - - +
107A SER* 1.3 57.4 + - - +
109A ILE* 3.7 17.9 - - + +
110A ASP* 2.7 36.7 + - - +
276A GLY* 3.6 10.5 - - - +
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU 4.8 4.6 + - - -
51A CYS* 6.0 0.4 - - - -
103A ASN 2.9 15.4 + - - -
104A GLN 3.8 9.6 - - - -
105A ILE 3.1 0.2 - - - -
106A PHE* 1.3 76.6 - - - +
108A GLY* 1.3 57.8 + - - +
110A ASP* 3.9 2.1 - - - +
111A MSE 3.0 34.6 + - - +
272A PRO* 3.0 41.7 + - - +
273A ARG* 3.5 7.4 + - - +
276A GLY 3.5 13.0 + - - -
277A GLY* 3.6 1.9 - - - +
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Residues in contact with GLY 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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37A ILE* 3.4 16.9 - - - +
49A GLY* 3.7 0.2 - - - -
50A GLU 3.4 28.0 + - - -
51A CYS* 3.6 14.8 - - - -
105A ILE 3.2 4.9 + - - -
107A SER* 1.3 80.6 + - - +
109A ILE* 1.3 61.0 + - - +
111A MSE 3.2 5.1 - - - +
112A ALA 3.1 18.7 + - - -
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 4.2 10.1 - - + +
39A ILE* 3.9 4.9 - - + +
51A CYS* 4.7 0.2 - - - -
64A LEU* 3.8 23.1 - - + -
67A LEU* 3.9 28.7 - - + +
68A ALA* 4.0 14.4 - - + +
71A LEU* 3.7 26.9 - - + -
83A ILE* 4.3 16.4 - - + -
86A ILE* 5.7 2.2 - - + -
105A ILE* 3.5 6.0 + - + +
106A PHE* 3.2 24.6 + - + +
108A GLY* 1.3 73.0 - - - +
110A ASP* 1.3 67.9 + - - +
112A ALA* 3.3 4.2 + - - +
113A MSE 3.0 31.7 + - + +
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.2 18.7 - - - +
83A ILE* 4.0 13.4 - - + +
106A PHE 2.7 21.2 + - - +
107A SER 3.9 2.2 - - - +
109A ILE* 1.3 72.3 - - - +
111A MSE 1.3 65.3 + - - +
113A MSE 3.2 1.4 + - - +
114A TRP* 3.0 45.0 + - - -
276A GLY 3.8 9.6 - - - +
277A GLY* 4.0 2.7 - - - -
278A ILE* 2.7 33.3 + - - +
279A GLN* 3.1 17.1 + - - +
280A PRO* 4.3 5.8 - - - +
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Residues in contact with MSE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE 4.2 2.2 - - - -
49A GLY* 3.8 3.1 - - - -
50A GLU 3.8 25.1 - - - +
107A SER* 3.0 21.5 + - - +
108A GLY 3.2 10.3 - - - +
110A ASP* 1.3 77.7 + - - +
112A ALA* 1.3 57.7 + - - +
114A TRP* 3.2 2.8 + - - +
115A ASP* 3.0 27.2 + - - +
272A PRO* 5.5 5.2 - - + -
278A ILE* 4.0 15.9 - - + +
305A ILE* 3.1 50.3 - - + +
306A THR* 4.4 11.9 - - - -
309A ALA* 3.3 27.8 - - + -
356A LEU* 3.4 19.9 - - + +
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Residues in contact with ALA 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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37A ILE* 3.9 5.2 - - + +
39A ILE* 3.5 25.6 - - + -
47A GLY* 3.4 15.8 - - - +
48A ILE 3.7 14.7 + - - +
49A GLY 3.6 16.4 - - - +
108A GLY 3.1 6.9 + - - +
109A ILE 3.7 2.7 - - - +
111A MSE 1.3 78.8 - - - +
113A MSE 1.3 57.9 + - - +
115A ASP* 3.2 0.6 + - - -
116A LEU* 2.8 30.8 + - - +
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Residues in contact with MSE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 3.6 24.7 - - + -
39A ILE* 3.6 18.8 - - + -
71A LEU* 4.0 10.8 - - + -
76A PRO* 3.5 36.4 - - + +
79A VAL* 3.8 32.3 - - + -
82A LEU* 3.8 27.8 - - + -
83A ILE* 6.5 0.2 - - + -
109A ILE* 3.0 26.6 + - + +
110A ASP 3.6 7.2 - - - +
112A ALA* 1.3 76.9 - - - +
114A TRP* 1.3 56.9 + - - +
116A LEU* 3.3 5.7 + - - +
117A GLN* 2.8 33.4 + - - +
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Residues in contact with TRP 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 3.8 13.8 - - + +
110A ASP* 3.0 56.2 + - - +
113A MSE 1.3 75.5 - - + +
115A ASP* 1.3 61.9 + - - +
117A GLN* 3.5 31.9 - - - +
118A GLY 2.9 24.9 + - - -
125A VAL* 3.7 19.3 - - + +
128A LEU* 4.0 30.6 - - + +
129A LEU* 4.5 20.2 - - + -
278A ILE* 3.9 24.0 - - + -
279A GLN* 3.5 35.9 - - + +
128B LEU 4.3 12.6 - - - -
129B LEU* 4.6 0.4 - - - -
130B GLY* 4.1 17.7 - - - -
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Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLY* 3.2 3.1 - - - -
48A ILE* 2.8 27.6 + - - +
111A MSE 3.0 13.9 + - - +
112A ALA 3.4 7.6 - - - +
114A TRP* 1.3 78.0 - - - +
116A LEU* 1.3 62.9 + - - +
118A GLY 3.3 0.2 + - - -
119A LYS* 2.7 59.1 + - - +
125A VAL* 4.4 0.6 - - - +
355A GLY* 3.5 7.9 - - - -
356A LEU* 2.8 44.3 + - + +
357A GLY 4.4 0.9 + - - -
358A PHE* 4.6 4.7 + - - -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.5 3.4 - - + -
39A ILE* 3.8 30.5 - - + +
41A ALA* 4.1 12.3 - - + -
45A THR* 3.6 43.1 - - + +
47A GLY* 3.8 11.2 - - - +
76A PRO* 3.5 28.9 - - + -
112A ALA 2.8 17.8 + - - +
113A MSE 3.5 5.8 - - - +
115A ASP* 1.3 77.8 - - - +
117A GLN* 1.3 62.8 + - - +
119A LYS* 3.2 4.3 + - - +
120A LEU* 2.9 38.8 + - + +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 3.1 28.7 + - + +
77A HIS* 3.5 32.6 + - + +
79A VAL* 3.7 15.0 - - - +
113A MSE 2.8 20.1 + - - +
114A TRP* 3.3 45.8 + - - +
116A LEU* 1.3 75.3 - - - +
118A GLY* 1.3 57.8 + - - +
120A LEU* 3.4 8.8 + - - +
121A ALA* 3.0 30.3 + - - +
128A LEU* 3.9 11.8 - - + +
127B GLN 4.0 9.9 - - - +
128B LEU* 5.3 1.4 - - - -
130B GLY* 5.5 0.4 + - - -
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TRP 2.9 11.1 + - - -
117A GLN* 1.3 77.6 - - - +
119A LYS* 1.3 51.2 + - - +
121A ALA* 3.2 1.7 + - - -
122A GLY* 2.6 31.9 + - - -
123A LEU 2.9 24.5 + - - -
128A LEU* 3.5 14.1 - - - +
355A GLY* 3.4 16.7 + - - -
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A THR* 3.6 24.3 + - + +
46A VAL 2.9 25.5 + - - +
48A ILE* 4.4 14.1 - - - +
115A ASP* 2.7 48.1 + - - +
116A LEU 3.7 1.3 - - - +
118A GLY* 1.3 75.8 - - - +
120A LEU* 1.3 62.3 + - - +
122A GLY* 3.5 9.2 + - - -
354A PRO* 4.0 27.1 - - + +
355A GLY 3.6 0.2 - - - +
357A GLY 5.9 0.4 - - - +
358A PHE* 4.9 16.5 + - - +
359A GLN* 5.9 3.6 - - - +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A VAL* 4.0 22.7 - - + -
43A ASP* 3.5 18.6 - - - +
45A THR* 3.4 30.7 - - - +
76A PRO* 3.8 28.9 - - + -
77A HIS* 4.4 12.8 - - + +
116A LEU* 2.9 30.7 + - + +
117A GLN* 3.7 4.0 - - - +
119A LYS* 1.3 75.8 - - - +
121A ALA* 1.3 60.3 + - - +
122A GLY 3.8 0.2 + - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A HIS* 6.2 1.6 - - + -
117A GLN 3.0 18.0 + - - +
118A GLY 3.9 1.8 - - - +
120A LEU* 1.3 77.4 - - - +
122A GLY* 1.3 64.0 + - - +
123A LEU* 3.8 26.8 - - + +
128A LEU* 4.5 9.0 - - + -
121B ALA* 5.1 14.4 - - + -
123B LEU* 6.1 3.1 - - + -
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLY 2.6 13.2 + - - -
119A LYS 3.5 8.1 + - - -
120A LEU 3.4 2.8 - - - -
121A ALA* 1.3 76.0 - - - +
123A LEU* 1.3 64.0 + - - +
124A PRO* 4.8 0.3 - - - +
354A PRO* 4.0 21.3 - - - +
----------------------------------------------------------
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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