Contacts of the helix formed by residues 96 - 118 (chain U) in PDB entry 3MQT
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 96 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93Q GLY 4.7 6.1 - - - -
95Q ARG* 3.7 15.9 - - - +
95U ARG* 1.3 72.0 - - - +
97U LEU* 1.3 56.3 + - - -
98U GLY 3.1 2.2 - - - -
99U LEU* 2.7 35.2 + - - +
100U PHE* 3.6 13.6 + - - -
262U THR* 3.1 21.1 + - - -
285U ARG* 6.2 0.2 - - - -
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Residues in contact with LEU 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Q CYS* 5.5 0.4 - - - -
53Q PHE* 4.2 20.9 - - + -
92Q ILE* 4.0 20.6 + - + +
95Q ARG 4.6 1.8 + - - -
97Q LEU* 4.6 23.4 - - + +
98Q GLY 5.3 0.4 - - - +
46U PRO* 4.3 11.2 - - + -
49U CYS* 4.2 18.8 - - - -
50U MET* 3.4 34.0 - - + +
53U PHE* 3.9 24.9 - - + -
95U ARG 3.9 1.0 + - - -
96U GLY* 1.3 71.3 - - - -
98U GLY* 1.3 63.8 + - - +
100U PHE* 3.0 34.2 + - + +
101U ALA 3.6 3.6 + - - -
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Residues in contact with GLY 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q LEU* 5.1 1.6 - - - +
53U PHE* 3.8 28.0 - - - -
89U THR* 5.6 0.8 + - - -
92U ILE 4.4 4.6 + - - -
93U GLY* 4.0 17.3 - - - -
95U ARG 4.4 2.2 + - - -
96U GLY 2.9 1.4 + - - -
97U LEU* 1.3 79.4 - - - +
99U LEU* 1.3 62.5 + - - +
101U ALA* 3.5 7.4 + - - +
102U ILE* 3.4 24.5 + - - +
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Residues in contact with LEU 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82U TYR* 3.8 18.4 - - - +
86U TYR* 4.3 7.9 - - + -
93U GLY* 4.5 0.2 - - - -
94U MET* 3.1 45.5 - - - +
95U ARG* 3.4 9.6 - - - +
96U GLY 2.7 15.3 + - - +
98U GLY* 1.3 70.1 - - - -
100U PHE* 1.3 53.0 + - - -
102U ILE* 3.6 15.9 + - + +
103U SER* 2.6 37.1 + - - -
262U THR* 4.1 6.3 - - - -
263U THR* 3.4 26.2 - - + -
285U ARG 3.3 14.1 - - - +
286U CYS 3.8 10.3 - - - +
287U GLY* 3.9 4.7 + - - -
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Residues in contact with PHE 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91Q TRP 3.7 10.1 - - - -
92Q ILE* 4.2 12.3 - - + -
93Q GLY 6.0 0.2 - - - -
43U ALA* 3.2 11.3 - - - +
44U ASP* 3.3 33.4 - - + +
45U GLY* 3.9 11.7 - - - -
50U MET* 3.7 2.5 - - + -
96U GLY* 3.6 15.7 - - - -
97U LEU* 3.0 34.3 + - + +
99U LEU* 1.3 76.6 - - - +
101U ALA* 1.3 61.7 - - - +
103U SER* 3.2 4.0 + - - -
104U GLY 3.1 18.4 + - - -
262U THR* 4.1 4.5 - - + -
284U ASN 3.6 11.4 - - - +
285U ARG* 3.2 62.8 - - + -
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Residues in contact with ALA 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12U PHE* 3.7 27.4 - - + -
43U ALA* 4.3 0.9 - - - -
50U MET* 3.8 7.4 - - + +
53U PHE* 3.7 31.2 - - + -
66U ILE* 3.8 10.3 - - + -
97U LEU 3.6 1.8 + - - -
98U GLY 3.5 11.6 + - - +
100U PHE* 1.3 77.8 - - - +
102U ILE* 1.3 62.1 + - - +
104U GLY 3.4 1.6 + - - -
105U ILE* 3.3 26.5 + - - +
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Residues in contact with ILE 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U ILE* 3.5 22.9 - - + -
82U TYR* 3.7 22.9 - - + +
85U MET* 3.9 21.7 - - + +
86U TYR* 4.0 33.0 - - + +
89U THR* 4.2 10.5 - - - +
94U MET 5.9 1.3 - - - +
98U GLY 3.4 13.3 + - - +
99U LEU* 3.8 22.9 - - + +
100U PHE 3.4 0.4 - - - -
101U ALA* 1.3 75.1 - - - +
103U SER* 1.3 66.3 + - - +
105U ILE* 3.2 2.4 + - - +
106U ASP* 2.8 23.0 + - - +
287U GLY* 3.7 16.4 - - - +
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Residues in contact with SER 103 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42U GLU 4.6 1.1 - - - -
99U LEU 2.6 21.6 + - - -
100U PHE 3.2 8.3 + - - -
102U ILE* 1.3 75.7 - - - +
104U GLY* 1.3 58.5 + - - +
106U ASP* 3.4 2.1 + - - +
107U MET* 2.9 29.5 + - - +
283U TYR 3.4 20.9 - - - +
284U ASN* 3.4 12.1 - - - -
285U ARG 3.1 7.6 - - - -
287U GLY 2.8 32.2 + - - -
288U GLY* 3.7 5.2 - - - +
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Residues in contact with GLY 104 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U VAL* 3.8 14.7 - - - +
41U GLY* 3.7 4.5 - - - -
42U GLU 3.5 30.6 + - - -
43U ALA* 4.0 0.9 - - - -
100U PHE 3.1 11.6 + - - -
101U ALA 3.4 1.8 + - - -
102U ILE 3.2 0.4 - - - -
103U SER* 1.3 77.3 - - - +
105U ILE* 1.3 60.8 + - - +
107U MET* 3.4 4.3 + - - +
108U ALA* 3.1 22.5 + - - +
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Residues in contact with ILE 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10U VAL* 4.0 11.7 - - + -
12U PHE* 3.8 15.5 - - + -
29U VAL* 3.7 22.9 - - + +
31U VAL* 4.4 7.2 - - + -
66U ILE* 3.7 35.4 - - + -
67U LYS 5.3 0.2 - - - +
70U VAL* 4.5 12.8 - - + -
85U MET* 3.7 25.6 - - + -
101U ALA 3.3 17.5 + - - +
102U ILE 3.2 2.5 + - - +
104U GLY* 1.3 73.8 - - - +
106U ASP* 1.3 64.2 + - - +
108U ALA* 3.1 4.9 + - - +
109U LEU* 2.9 41.4 + - + +
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Residues in contact with ASP 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78U PHE* 4.7 3.6 - - - +
82U TYR* 4.2 9.5 - - - +
85U MET* 4.2 7.7 - - + +
102U ILE* 2.8 22.1 + - + +
103U SER 3.5 4.5 - - - +
105U ILE* 1.3 73.3 - - - +
107U MET* 1.3 61.8 + - - +
109U LEU* 3.2 19.5 + - - +
110U TYR* 3.0 27.5 + - - -
287U GLY 3.8 12.3 - - - +
289U VAL 2.9 14.7 + - - -
290U THR* 2.5 50.6 + - - -
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Residues in contact with MET 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U LEU 4.2 0.2 - - - -
41U GLY* 3.6 9.0 - - - -
42U GLU 3.6 30.5 - - - +
103U SER 2.9 11.0 + - - +
104U GLY 3.5 9.2 - - - +
105U ILE 3.3 0.2 - - - -
106U ASP* 1.3 76.2 + - - +
108U ALA* 1.3 63.4 + - - +
110U TYR* 3.1 19.9 + - - +
111U ASP* 3.2 11.1 + - - +
283U TYR* 4.0 34.1 - - + +
284U ASN* 4.3 0.4 - - + -
289U VAL* 4.9 11.0 - - + +
315U ILE* 4.0 14.1 - - - +
316U THR* 3.8 21.8 - - - +
319U ALA* 4.0 21.1 - - + -
369U LEU* 3.8 17.0 - - + +
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Residues in contact with ALA 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29U VAL* 3.9 4.7 - - + +
31U VAL* 3.7 18.4 - - + -
39U GLY* 3.5 18.2 - - - +
40U LEU 3.6 12.3 - - - +
41U GLY* 3.5 17.0 - - - +
104U GLY 3.1 7.4 + - - +
105U ILE* 3.1 9.7 + - - +
107U MET* 1.3 79.0 - - - +
109U LEU* 1.3 52.9 + - - +
111U ASP 3.2 0.5 + - - -
112U LEU* 2.7 36.1 + - - +
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Residues in contact with LEU 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U ILE* 3.6 29.2 - - + -
31U VAL* 4.0 19.7 - - + -
70U VAL* 4.2 7.4 - - + -
75U PRO* 4.0 18.0 - - + +
78U PHE* 3.8 10.0 - - + +
81U ASN* 4.1 30.7 - - + +
85U MET* 4.2 7.9 - - + -
105U ILE* 2.9 33.0 + - + +
106U ASP* 3.6 12.8 - - - +
107U MET 3.2 0.4 - - - -
108U ALA* 1.3 75.6 - - - +
110U TYR* 1.3 57.6 + - - +
112U LEU* 3.8 3.0 - - + +
113U ALA* 2.8 34.0 + - - +
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Residues in contact with TYR 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78U PHE* 3.5 49.1 - + - +
106U ASP* 3.0 33.5 + - - -
107U MET* 3.1 9.0 + - - +
109U LEU* 1.3 75.9 - - - +
111U ASP* 1.3 63.5 + - - +
114U GLY* 3.1 19.8 + - - -
121U ALA* 4.1 17.0 - - + +
124U LEU* 4.1 20.3 - - + +
125U MET* 4.2 29.4 - - + -
289U VAL* 3.6 21.5 - - + -
290U THR* 2.7 37.7 + - - +
293U LEU* 3.8 9.7 - - - +
368U GLY* 4.1 3.5 - - - -
369U LEU* 4.8 3.1 - - + -
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Residues in contact with ASP 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U TYR 4.4 0.3 - - - +
39U GLY* 3.3 4.4 - - - -
40U LEU* 2.7 44.8 + - - +
107U MET 3.2 2.2 + - - +
108U ALA 3.2 9.1 + - - +
110U TYR* 1.3 78.6 - - - +
112U LEU* 1.3 63.6 + - - +
115U LYS* 3.1 40.4 + - - +
368U GLY* 3.5 2.1 - - - -
369U LEU* 2.9 43.2 + - + +
370U GLY 4.2 2.8 + - - -
371U ILE* 4.2 7.9 + - - +
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Residues in contact with LEU 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7U ILE* 4.3 6.5 - - + -
31U VAL* 3.6 35.9 - - + +
33U ASP* 4.1 9.9 - - + +
37U VAL* 3.7 28.7 - - + +
38U TYR* 3.9 11.4 - - - +
39U GLY* 3.6 9.6 - - - +
75U PRO* 3.9 26.2 - - + -
108U ALA 2.7 20.5 + - - +
109U LEU* 3.8 4.0 - - + +
111U ASP* 1.3 71.2 - - - +
113U ALA* 1.3 60.4 + - - +
115U LYS* 3.0 4.4 + - - -
116U GLN* 2.8 47.8 + - + +
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Residues in contact with ALA 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75U PRO* 4.0 11.6 - - - +
76U LEU* 4.1 14.1 - - + +
78U PHE* 3.7 24.9 - - + -
109U LEU 2.8 22.3 + - - +
110U TYR 4.3 0.2 - - - +
112U LEU* 1.3 72.8 - - - +
114U GLY* 1.3 61.3 + - - +
116U GLN* 3.4 12.1 + - - +
117U LEU* 3.0 30.4 + - - +
124U LEU* 3.8 8.5 - - + -
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Residues in contact with GLY 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U TYR 3.1 12.9 + - - -
113U ALA* 1.3 75.7 - - - +
115U LYS* 1.3 53.1 + - - +
118U GLY* 2.7 30.1 + - - -
119U VAL* 2.8 31.5 + - - -
121U ALA 5.1 0.4 - - - -
124U LEU* 3.6 12.0 - - - +
367U PRO* 3.7 0.5 - - - +
368U GLY* 3.6 13.5 - - - -
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Residues in contact with LYS 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U VAL* 4.0 22.1 - - + +
38U TYR* 2.7 49.0 + - - +
111U ASP* 3.1 34.2 + - - +
112U LEU 3.0 5.2 + - - +
114U GLY* 1.3 73.4 - - - +
116U GLN* 1.3 66.3 + - - +
118U GLY* 3.2 9.9 + - - -
367U PRO* 4.0 26.5 - - + +
371U ILE 5.9 1.0 + - - -
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Residues in contact with GLN 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U ALA* 3.0 34.6 + - + +
33U ASP* 3.2 34.7 + - - +
37U VAL* 5.0 5.3 - - + +
74U ASP* 4.3 4.5 - - - +
75U PRO* 3.2 33.1 - - - +
76U LEU* 5.1 1.0 + - - +
112U LEU* 2.8 27.8 + - + +
113U ALA* 3.8 6.9 - - - +
115U LYS* 1.3 73.3 - - - +
117U LEU* 1.3 64.4 + - + +
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Residues in contact with LEU 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R LEU* 4.0 43.9 - - + +
119R VAL* 5.0 4.9 - - + -
76U LEU* 3.9 30.7 - - + -
113U ALA* 3.0 19.2 + - + +
116U GLN* 1.3 80.6 - - + +
118U GLY* 1.3 63.6 + - - +
119U VAL* 3.7 19.5 + - + +
124U LEU* 3.7 30.3 - - + -
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Residues in contact with GLY 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114U GLY 2.7 10.8 + - - -
115U LYS 3.2 10.8 + - - -
116U GLN 3.3 0.4 + - - -
117U LEU* 1.3 78.5 - - - +
119U VAL* 1.3 60.7 + - - +
120U PRO* 4.8 0.7 - - - +
365U ASP 5.5 0.9 - - - +
367U PRO* 4.0 20.6 - - - +
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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