Contacts of the helix formed by residues 97 - 128 (chain B) in PDB entry 3OMA
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 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 3.7 11.2 - - + -
3B DMU 2.9 50.9 + - - +
96B HIS* 1.3 76.6 - - - +
98B SER* 1.3 53.7 + - - +
99B PRO* 3.5 11.3 - - - +
100B LEU* 2.8 52.2 + - + +
101B GLU* 3.0 19.3 + - - +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B HIS* 5.0 3.8 - - - +
97B ASN* 1.3 72.1 - - - +
99B PRO* 1.4 71.3 - - - +
101B GLU* 3.3 13.4 + - - +
102B ILE* 3.0 25.5 + - - +
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Residues in contact with PRO 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN* 3.5 12.1 - - - +
98B SER* 1.4 94.5 - - - +
100B LEU* 1.3 56.2 + - - +
102B ILE* 3.6 6.1 + - + +
103B ALA* 3.1 26.5 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 5.8 1.1 - - + -
3B DMU 3.8 61.7 - - + -
97B ASN* 2.8 38.0 + - + +
99B PRO* 1.3 72.4 - - - +
101B GLU* 1.3 58.9 + - + +
102B ILE 3.2 0.4 - - - -
103B ALA* 3.3 9.7 + - + +
104B TRP* 2.8 52.0 + - + +
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 3.9 13.7 - - + -
315A PRO* 4.1 17.3 - - - +
9B CD 2.1 31.3 - - - -
96B HIS* 3.5 2.8 - - - -
97B ASN 3.0 32.1 + - - +
98B SER* 3.3 9.4 + - - +
100B LEU* 1.3 74.6 - - + +
102B ILE* 1.3 60.0 + - - +
104B TRP* 3.3 35.0 + - + +
105B THR* 2.8 25.8 + - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER 3.0 17.1 + - - +
99B PRO* 3.9 7.2 - - + +
101B GLU* 1.3 76.9 - - - +
103B ALA* 1.3 64.4 + - - +
104B TRP 3.2 0.2 - - - -
105B THR* 3.3 2.7 + - - -
106B ILE* 3.1 38.1 + - + +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B DMU 6.4 0.4 - - + -
99B PRO 3.1 18.2 + - - +
100B LEU* 3.6 13.0 - - + +
102B ILE* 1.3 78.6 - - - +
104B TRP* 1.3 56.4 + - - +
105B THR 3.2 0.4 - - - -
106B ILE* 4.9 3.1 - - - -
107B VAL* 3.1 38.6 + - + +
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Residues in contact with TRP 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A PHE* 3.6 24.9 - + - -
357A VAL 5.6 0.9 - - - +
361A ILE* 4.1 25.8 + - + +
364A PHE* 3.5 56.5 - + + -
365A SER* 3.8 20.2 - - - -
368A ALA* 4.2 2.2 - - + -
3B DMU 3.9 39.5 - - + -
100B LEU* 2.8 36.1 + - + +
101B GLU* 3.3 36.6 + - + +
102B ILE 3.2 0.4 - - - -
103B ALA* 1.3 76.3 - - + +
105B THR* 1.3 64.2 + - - +
107B VAL* 5.1 0.2 - - - -
108B PRO* 3.4 22.0 - - - +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 4.1 22.4 - - + +
361A ILE* 3.9 17.9 - - + +
101B GLU 2.8 20.8 + - - -
102B ILE* 3.3 5.3 + - - -
103B ALA 3.2 0.4 - - - -
104B TRP* 1.3 84.7 + - - +
106B ILE* 1.3 69.9 + - + +
107B VAL 3.5 0.2 - - - -
108B PRO* 3.9 3.3 - - - +
109B ILE* 3.3 30.4 + - + +
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 3.1 29.2 + - + +
103B ALA* 4.5 2.5 - - - +
105B THR* 1.3 91.2 - - + +
107B VAL* 1.3 72.6 + - + +
109B ILE* 3.2 14.7 + - + +
110B VAL* 3.0 32.2 + - + +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA* 3.1 23.0 + - + +
104B TRP* 5.1 0.2 - - - -
106B ILE* 1.3 80.4 - - + +
108B PRO* 1.3 72.5 - - + +
110B VAL* 3.2 9.8 + - + +
111B ILE* 3.0 39.6 + - + +
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Residues in contact with PRO 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 4.0 30.9 - - + +
356A ALA 5.4 0.4 - - - +
357A VAL* 4.6 20.2 - - + +
360A GLY* 5.7 2.0 - - - -
364A PHE* 4.6 15.9 - - + -
104B TRP* 3.4 28.0 - - - +
105B THR* 3.9 4.3 - - - +
106B ILE 3.8 1.3 - - - -
107B VAL* 1.3 96.1 - - + +
109B ILE* 1.3 55.5 + - - +
111B ILE* 3.2 6.5 + - + +
112B LEU* 2.9 36.3 + - + +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A VAL* 3.8 24.9 - - + -
4B TRD 5.4 4.2 - - + +
105B THR* 3.3 31.0 - - + +
106B ILE* 3.2 19.3 + - + +
108B PRO* 1.3 75.2 - - - +
110B VAL* 1.3 58.7 + - + +
112B LEU* 3.5 4.4 + - - +
113B VAL* 3.0 45.2 + - + +
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 3.0 27.4 + - + +
107B VAL* 3.5 13.2 - - + +
109B ILE* 1.3 73.4 - - + +
111B ILE* 1.3 63.8 + - + +
113B VAL* 3.3 6.2 + - - +
114B ALA* 2.9 31.9 + - + +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 4.1 20.2 - - + -
64B ILE* 3.6 32.9 - - + +
68B ILE* 4.5 13.7 - - + -
107B VAL* 3.0 38.7 + - + +
108B PRO* 3.4 12.1 - - + +
110B VAL* 1.3 78.2 - - + +
112B LEU* 1.3 62.8 + - - +
114B ALA* 3.3 8.3 + - - +
115B ILE* 3.1 30.5 + - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 4.1 27.8 - - + -
353A MET* 3.3 41.3 - - + +
354A VAL* 4.9 0.9 - - - -
356A ALA* 4.0 7.9 - - + -
357A VAL* 3.9 23.3 - - + -
399A ILE* 4.3 15.9 - - + -
4B TRD 4.1 21.2 - - + +
108B PRO* 2.9 21.2 + - + +
109B ILE* 3.9 4.7 - - - +
111B ILE* 1.3 70.8 - - - +
113B VAL* 1.3 56.3 + - - +
115B ILE* 3.2 11.7 + - + +
116B GLY* 2.8 32.7 + - - -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRD 3.7 43.0 - - + +
109B ILE* 3.0 34.8 + - + +
110B VAL* 3.3 5.8 + - - +
112B LEU* 1.3 74.6 - - - +
114B ALA* 1.3 56.9 + - - +
116B GLY* 3.3 1.2 + - - -
117B ALA* 2.9 28.5 + - + +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 4.7 9.9 - - + -
64B ILE* 5.8 2.2 - - + -
110B VAL* 2.9 16.8 + - + +
111B ILE* 3.4 12.1 - - - +
112B LEU 3.2 0.2 - - - -
113B VAL* 1.3 76.8 - - - +
115B ILE* 1.3 62.2 + - + +
117B ALA* 3.3 11.8 + - - +
118B PHE* 3.2 29.7 + - + -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A HEA 5.8 1.8 - - + -
353A MET* 4.9 2.5 - - - -
399A ILE* 4.9 9.4 - - + -
403A GLN* 3.5 30.5 - - + +
57B LEU* 4.7 1.1 - - + +
60B PHE* 4.2 8.5 - - + -
61B ILE* 3.9 35.0 - - + -
64B ILE* 4.0 26.2 - - + -
65B ILE* 5.7 2.0 - - + -
111B ILE* 3.1 37.1 + - + +
112B LEU* 3.5 17.7 - - + +
114B ALA* 1.3 73.3 - - - +
116B GLY* 1.3 57.7 + - - +
117B ALA 3.2 0.3 + - - -
118B PHE* 3.3 3.5 + - - +
119B SER* 2.9 31.3 + - - -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A MET* 4.6 9.6 - - - -
350A MET* 6.2 0.2 - - - -
353A MET* 4.7 3.6 - - - -
4B TRD 3.7 21.5 - - - -
112B LEU 2.8 18.3 + - - -
113B VAL 3.6 4.0 - - - -
115B ILE* 1.3 73.6 - - - +
117B ALA* 1.3 56.4 + - - +
119B SER* 4.3 5.6 - - - -
120B LEU* 3.1 36.3 + - - +
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TRD 3.9 21.0 - - + +
113B VAL* 2.9 14.6 + - + +
114B ALA* 3.5 12.3 - - - +
115B ILE 3.2 0.2 - - - -
116B GLY* 1.3 77.1 - - - +
118B PHE* 1.3 63.5 + - + +
121B PRO* 3.1 23.9 - - - +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 4.2 15.4 - - + +
60B PHE* 4.0 31.6 - + + -
114B ALA* 3.2 25.9 + - + -
115B ILE 3.3 5.6 + - - +
117B ALA* 1.3 81.2 - - + +
119B SER* 1.3 62.1 + - - +
121B PRO* 3.6 9.1 - - - +
122B VAL* 3.4 21.0 - - - +
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A MET* 3.2 13.2 - - - +
403A GLN* 2.7 31.8 + - - +
405A SER* 3.4 15.8 + - - -
57B LEU* 3.5 19.0 - - - +
115B ILE* 2.9 16.0 + - - -
117B ALA 3.4 0.4 - - - -
118B PHE* 1.3 78.3 - - - +
120B LEU* 1.3 61.8 + - - +
121B PRO 3.5 0.2 - - - -
122B VAL* 3.3 4.3 + - - +
123B LEU* 3.0 26.3 + - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A SER* 3.4 35.0 - - - +
349A MET* 4.1 11.9 - - + -
350A MET* 3.9 27.6 - - + -
4B TRD 4.4 15.7 - - + -
6B DMU 4.1 18.6 - - - +
116B GLY* 3.1 18.7 + - - +
119B SER* 1.3 73.6 - - - +
121B PRO* 1.4 70.7 - - + +
123B LEU* 3.3 13.3 + - + +
124B PHE* 2.9 41.3 + - + -
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Residues in contact with PRO 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B DMU 3.7 47.6 - - - +
53B GLN* 5.2 2.2 - - - +
117B ALA 3.1 25.8 - - - +
118B PHE* 3.6 7.9 - - - +
119B SER 3.5 3.6 - - - -
120B LEU* 1.4 90.7 - - + +
122B VAL* 1.3 58.2 + - + +
124B PHE* 2.9 5.7 + - - +
125B ASN* 2.9 30.0 + - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER* 3.6 19.5 - - - +
50B VAL* 6.3 0.4 - - + -
53B GLN* 3.9 54.6 - - + +
54B ILE* 4.7 2.9 - - + +
57B LEU* 4.2 16.2 - - + -
118B PHE 3.4 17.0 - - - +
119B SER 3.3 8.4 + - - +
121B PRO* 1.3 79.9 - - + +
123B LEU* 1.3 60.7 + - - +
125B ASN* 3.5 2.6 + - - +
126B GLN* 3.1 28.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.7 12.3 - - + -
345A GLN* 3.6 13.2 - - + +
346A SER* 3.7 34.8 - - - +
349A MET* 4.3 8.5 - - - -
404A ALA* 3.7 17.7 - - + -
405A SER* 3.9 14.6 - - - +
408A ARG* 3.3 30.1 - - - +
119B SER 3.0 14.6 + - - +
120B LEU* 3.6 17.3 - - + +
121B PRO 3.2 0.2 - - - -
122B VAL* 1.3 76.3 - - - +
124B PHE* 1.3 57.3 + - - +
126B GLN* 3.2 4.5 + - - +
127B GLN* 3.0 29.0 + - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 3.6 29.8 - - + -
343A THR* 6.3 0.7 - - - -
346A SER* 3.7 22.4 - - - -
6B DMU 3.6 65.7 - - - +
120B LEU* 2.9 33.8 + - + +
121B PRO 2.9 8.7 + - - +
123B LEU* 1.3 74.5 - - - +
125B ASN* 1.3 65.2 + - - +
128B GLU* 3.0 52.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B DMU 3.7 13.5 + - - +
49B PRO* 5.5 3.6 + - - +
50B VAL* 4.0 14.5 - - - +
53B GLN* 2.7 37.6 + - - +
121B PRO 2.9 14.3 + - - +
122B VAL 3.8 0.7 - - - +
124B PHE* 1.3 77.6 - - - +
126B GLN* 1.3 61.9 + - - +
128B GLU* 3.9 7.1 - - - +
239B TRP* 3.1 28.5 + - - -
----------------------------------------------------------
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A SER* 2.9 40.1 + - - +
408A ARG* 2.6 43.7 + - + +
50B VAL* 3.8 25.0 - - + +
53B GLN* 5.7 0.2 - - - +
54B ILE* 3.6 21.8 - - - +
122B VAL* 3.1 18.1 + - - +
123B LEU* 3.3 6.2 - - - +
124B PHE 3.1 0.2 - - - -
125B ASN* 1.3 78.3 - - - +
127B GLN* 1.3 69.5 + - - +
128B GLU 3.6 0.2 - - - -
129B ILE* 5.8 0.2 - - - +
225B GLY 4.9 1.3 - - - +
238B LEU* 6.0 0.9 - - - -
239B TRP* 3.4 21.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU 4.6 0.9 - - - +
342A LEU* 4.0 23.3 - - + +
345A GLN* 3.3 24.7 + - - +
408A ARG* 3.2 48.0 + - - +
123B LEU* 3.0 21.5 + - + +
126B GLN* 1.3 90.2 + - - +
128B GLU* 1.3 62.0 + - - +
129B ILE* 3.4 17.7 + - - +
228B GLN* 4.8 12.2 + - - +
237B GLN 5.5 1.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 4.0 12.3 - - + -
6B DMU 2.8 35.1 + - - -
124B PHE* 3.0 45.2 + - - +
125B ASN* 3.9 4.3 - - - +
127B GLN* 1.3 73.0 - - - +
129B ILE* 1.3 61.9 + - - +
130B PRO* 3.2 13.7 - - - +
239B TRP* 3.7 10.4 + - - -
----------------------------------------------------------
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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