Contacts of the helix formed by residues 97 - 119 (chain A) in PDB entry 3SJN
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 GLY 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ARG* 1.3 72.7 - - - +
98A ALA* 1.3 66.8 + - - -
100A ILE* 2.9 13.9 + - - +
101A HIS* 3.2 20.7 + - - -
254A THR* 2.9 21.5 + - - -
94B GLY 4.2 8.3 - - - -
95B ARG* 4.6 3.6 - - - +
96B ARG* 3.6 17.8 - - - +
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Residues in contact with ALA 98 (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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46A SER* 4.7 4.3 - - - +
50A VAL* 3.6 29.8 - - + -
51A VAL* 4.8 3.8 - - + +
54A CYS* 4.2 4.3 - - - -
96A ARG 3.6 1.2 + - - -
97A GLY* 1.3 70.8 - - - -
99A GLY* 1.3 62.4 + - - +
101A HIS* 3.1 17.8 + - - +
102A ALA* 3.1 20.4 + - - +
93B MET* 3.4 23.0 + - - +
96B ARG 4.4 2.4 + - - -
98B ALA* 4.5 15.9 - - + +
99B GLY 5.3 0.2 - - - +
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A CYS* 3.9 19.0 - - - -
67A LEU* 4.5 1.6 - - - +
90A SER* 5.2 1.0 + - - -
93A MET* 4.6 6.3 + - - -
94A GLY* 3.9 21.8 - - - -
96A ARG 4.2 3.2 + - - -
97A GLY 3.3 1.0 - - - -
98A ALA* 1.3 77.5 - - - +
100A ILE* 1.3 59.8 + - - +
102A ALA* 3.4 5.0 + - - +
103A ILE* 3.1 31.1 + - - +
98B ALA* 5.2 1.0 - - - +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TRP* 5.1 4.0 - - + -
87A TYR* 3.9 16.6 - - + -
95A ARG 3.4 45.3 - - - +
96A ARG* 3.7 9.4 - - - -
97A GLY 2.9 7.0 + - - +
99A GLY* 1.3 72.6 - - - +
101A HIS* 1.3 61.3 + - - +
103A ILE* 3.3 15.8 + - + +
104A SER* 2.9 30.5 + - - -
254A THR* 3.7 10.5 - - - +
255A THR* 3.9 15.3 - - + -
277A ARG 3.5 13.9 - - - +
278A CYS 3.6 8.3 - - - +
279A GLY* 3.6 18.8 - - - +
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Residues in contact with HIS 101 (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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44A ALA* 3.4 13.2 - - + +
46A SER* 2.7 36.4 + - - -
51A VAL* 4.5 0.9 - - + -
97A GLY* 3.4 20.8 + - - -
98A ALA* 3.1 13.6 + - - +
100A ILE* 1.3 77.2 - - - +
102A ALA* 1.3 61.7 + - - +
104A SER* 3.2 17.1 + - - -
105A ALA 3.3 10.0 + - - -
254A THR* 3.5 13.6 - - + +
276A THR 4.0 7.9 - - - +
277A ARG* 3.2 62.6 + - + -
92B TYR 3.3 11.9 - - - -
93B MET* 4.4 4.7 - - - -
94B GLY 5.6 0.2 - - - -
95B ARG* 5.7 0.2 + - - -
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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
----------------------------------------------------------
51A VAL* 4.2 19.2 - - + +
54A CYS* 3.6 28.9 - - + -
55A ILE* 4.1 10.4 - - + +
67A LEU* 3.7 12.8 - - + -
98A ALA 3.1 9.1 + - - +
99A GLY 3.5 9.6 - - - +
100A ILE 3.2 0.2 - - - -
101A HIS* 1.3 76.8 - - - +
103A ILE* 1.3 61.5 + - - +
105A ALA* 3.4 6.6 + - - +
106A ILE* 3.3 24.1 + - - +
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Residues in contact with ILE 103 (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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67A LEU* 3.8 18.2 - - + -
83A TRP* 3.5 39.0 - - + +
86A MET* 3.9 39.4 - - + +
87A TYR* 3.9 20.9 - - + +
90A SER* 4.1 6.5 - - - +
95A ARG 5.9 0.4 - - - +
99A GLY 3.1 16.6 + - - +
100A ILE* 3.3 24.9 + - + +
102A ALA* 1.3 71.2 - - - +
104A SER* 1.3 68.2 + - - +
106A ILE* 3.2 3.6 + - - +
107A ASP* 2.9 20.4 + - - +
279A GLY* 4.1 1.8 - - - +
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Residues in contact with SER 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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100A ILE 2.9 12.5 + - - -
101A HIS 3.2 8.3 + - - -
103A ILE* 1.3 76.6 - - - +
105A ALA* 1.3 56.9 + - - +
107A ASP* 3.2 1.4 + - - +
108A ILE* 2.9 35.9 + - - +
275A ILE 3.6 3.1 - - - -
276A THR 3.5 20.6 - - - -
277A ARG 3.3 8.5 - - - -
279A GLY 2.8 27.3 + - - -
280A GLY* 3.5 18.8 - - - +
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Residues in contact with ALA 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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30A VAL* 3.4 28.9 - - + +
42A GLY* 3.4 11.6 - - - -
43A GLU* 3.4 34.6 + - - +
44A ALA* 3.9 5.8 - - + +
51A VAL* 5.2 0.9 - - + -
55A ILE* 5.2 0.4 - - + -
101A HIS 3.3 6.6 + - - +
102A ALA* 3.6 10.3 - - - +
103A ILE 3.3 0.2 - - - -
104A SER* 1.3 77.7 - - - +
106A ILE* 1.3 64.0 + - - +
108A ILE* 3.5 0.8 + - - -
109A ALA 3.1 16.8 + - - -
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Residues in contact with ILE 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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7A ILE* 4.2 20.6 - - + -
30A VAL* 4.1 14.8 - - + -
32A VAL* 4.4 9.4 - - + -
55A ILE* 4.0 16.8 - - + -
67A LEU* 3.7 41.7 - - + -
71A LEU* 3.6 24.5 - - + -
86A MET* 3.8 14.4 - - + -
102A ALA 3.3 4.0 + - - +
103A ILE 3.2 7.2 + - - +
105A ALA* 1.3 76.0 - - - +
107A ASP* 1.3 59.7 + - - +
109A ALA* 3.1 5.1 + - - +
110A LEU* 2.9 35.0 + - + +
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Residues in contact with ASP 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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79A ILE* 3.4 11.8 - - - +
83A TRP* 3.5 12.2 - - + +
86A MET* 4.7 2.8 - - + +
103A ILE* 2.9 17.3 + - + +
104A SER 3.6 4.3 - - - +
106A ILE* 1.3 76.4 - - - +
108A ILE* 1.3 64.6 + - - +
110A LEU* 3.1 10.9 + - - +
111A TRP* 3.1 31.4 + - - -
279A GLY 3.9 12.3 - - - +
280A GLY* 4.2 0.2 - - - -
281A ILE 2.8 28.4 + - - -
282A THR* 2.5 35.8 + - - -
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Residues in contact with ILE 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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41A VAL 3.6 15.0 - - - +
42A GLY* 3.7 7.0 - - - -
43A GLU 3.9 9.2 - - - +
104A SER 2.9 19.3 + - - +
105A ALA 3.7 4.0 - - - +
107A ASP* 1.3 75.4 - - - +
109A ALA* 1.3 62.1 + - - +
111A TRP* 3.2 5.4 + - - +
112A ASP* 3.1 20.1 + - - +
275A ILE* 3.5 32.3 - - + +
276A THR* 3.8 23.3 - - + -
280A GLY* 4.3 6.7 - - - -
281A ILE* 4.3 20.4 - - + +
307A ILE* 4.5 5.4 - - + -
311A ALA* 4.1 12.1 - - + -
358A LEU* 3.7 17.9 - - + +
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Residues in contact with ALA 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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30A VAL* 4.2 2.7 - - + -
32A VAL* 3.7 19.3 - - + -
40A GLY* 3.4 29.4 - - - +
41A VAL 3.6 11.2 - - - +
42A GLY 3.7 11.4 - - - +
105A ALA 3.1 9.1 + - - +
106A ILE 3.1 9.4 + - - +
108A ILE* 1.3 77.5 - - - +
110A LEU* 1.3 57.4 + - - +
112A ASP* 3.3 3.9 - - - +
113A ILE* 2.9 26.5 + - - +
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Residues in contact with LEU 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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4A ILE* 4.1 15.0 - - + -
32A VAL* 4.2 15.9 - - + -
71A LEU* 4.6 2.0 - - + -
76A ALA* 3.7 32.6 - - + +
79A ILE* 3.5 33.6 - - + +
82A LEU* 3.9 29.6 - - + -
86A MET* 4.7 3.6 - - + -
106A ILE* 2.9 32.8 + - + +
107A ASP* 3.1 11.6 + - - +
109A ALA* 1.3 75.2 - - - +
111A TRP* 1.3 56.8 + - - +
113A ILE* 3.3 7.6 + - + +
114A ALA* 2.9 23.6 + - - +
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Residues in contact with TRP 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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79A ILE* 3.7 26.0 - - + +
107A ASP* 3.1 38.9 + - - -
108A ILE 3.2 6.9 + - - +
110A LEU* 1.3 73.7 - - - +
112A ASP* 1.3 58.8 + - - +
114A ALA* 3.3 1.9 + - - +
115A GLY 2.9 24.8 + - - -
122A VAL* 3.2 31.4 - - + +
125A LEU* 3.8 40.1 - - + +
126A LEU* 3.7 22.9 - - + -
281A ILE* 3.6 31.6 - - + -
282A THR* 3.0 36.2 + - + +
285A LYS* 5.7 2.9 - - + -
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Residues in contact with ASP 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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39A VAL 4.0 1.0 - - - +
40A GLY* 3.5 4.9 - - - -
41A VAL* 2.9 31.8 + - - +
108A ILE 3.1 11.9 + - - +
109A ALA 3.3 9.9 - - - +
111A TRP* 1.3 75.6 - - - +
113A ILE* 1.3 62.4 + - - +
115A GLY 3.4 0.2 + - - -
116A GLN* 3.1 48.1 + - - +
122A VAL* 4.1 1.0 - - - +
356A PRO 4.7 0.2 - - - +
357A GLY* 3.5 3.1 - - - -
358A LEU* 2.9 45.4 + - + +
359A GLY 4.3 2.3 + - - -
360A ILE* 4.7 9.3 + - - +
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Residues in contact with ILE 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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2A LEU* 3.6 29.8 - - + -
32A VAL* 3.5 42.6 - - + +
34A THR* 3.8 15.9 - - + -
38A ILE* 3.9 17.5 - - + +
39A VAL 4.0 2.9 - - - -
40A GLY 3.4 19.1 - - - +
76A ALA* 4.2 8.5 - - + -
77A LEU* 4.9 1.1 - - + -
109A ALA 2.9 14.8 + - - +
110A LEU* 3.4 16.8 - - + +
112A ASP* 1.3 76.3 - - - +
114A ALA* 1.3 59.0 + - - +
116A GLN* 3.3 2.9 + - - +
117A PHE* 2.9 28.1 + - - +
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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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77A LEU* 4.0 20.2 - - + +
79A ILE* 4.1 17.0 - - + -
110A LEU 2.9 15.2 + - - +
111A TRP* 3.3 4.9 + - + +
113A ILE* 1.3 77.5 - - - +
115A GLY* 1.3 64.7 + - - +
117A PHE 3.3 0.2 + - - -
118A TYR* 2.9 44.2 + - + -
125A LEU* 3.8 14.6 - - + -
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Residues in contact with GLY 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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111A TRP 2.9 13.3 + - - -
114A ALA* 1.3 77.6 - - - +
116A GLN* 1.3 50.7 + - - +
118A TYR 3.7 0.2 - - - -
119A GLY* 2.8 29.8 + - - -
120A VAL* 2.9 30.1 + - - -
122A VAL* 4.7 1.6 - - - -
125A LEU* 3.7 12.5 - - - +
357A GLY* 3.4 14.9 + - - -
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Residues in contact with GLN 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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38A ILE* 3.6 25.7 - - + +
39A VAL 2.9 29.2 + - - +
112A ASP* 3.1 38.0 + - - +
113A ILE 3.6 5.2 - - - +
115A GLY* 1.3 72.9 - - - +
117A PHE* 1.3 66.4 + - - +
119A GLY* 3.3 11.6 + - - -
356A PRO* 4.1 24.9 - - + +
357A GLY 3.6 0.2 - - - +
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Residues in contact with PHE 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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2A LEU* 4.0 27.6 - - + -
36A LYS* 3.7 37.0 - - + -
38A ILE* 3.7 16.0 - - + +
77A LEU* 3.7 25.6 - - + -
113A ILE 2.9 20.8 + - - +
114A ALA 3.8 2.7 - - - +
116A GLN* 1.3 74.9 - - - +
118A TYR* 1.3 85.3 + + - +
119A GLY 3.5 0.3 + - - -
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Residues in contact with TYR 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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77A LEU* 3.6 30.9 + - + +
114A ALA* 2.9 40.7 + - + +
117A PHE* 1.3 96.4 - + - +
119A GLY* 1.3 61.9 + - - +
120A VAL* 3.7 20.1 + - + +
125A LEU* 3.7 24.7 - - + -
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Residues in contact with GLY 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 GLY 2.8 10.5 + - - -
116A GLN 3.3 7.8 + - - -
117A PHE 3.3 4.2 + - - -
118A TYR* 1.3 78.1 - - - +
120A VAL* 1.3 61.0 + - - +
121A PRO* 4.8 0.3 - - - +
356A PRO* 4.1 20.0 - - - +
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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