Contacts of the helix formed by residues 96 - 118 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95K ARG* 1.3 73.9 - - - +
97K LEU* 1.3 54.2 + - - -
98K GLY 3.3 0.2 - - - -
99K LEU* 2.8 30.5 + - - +
100K PHE* 3.4 15.4 - - - -
262K THR* 3.1 21.1 + - - +
285K ARG* 6.2 0.2 - - - -
93N GLY 4.6 7.0 - - - -
95N ARG* 3.6 17.2 - - - +
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Residues in contact with LEU 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K PRO* 4.5 9.6 - - + -
49K CYS* 4.1 11.0 - - - -
50K MET* 3.6 33.3 - - + +
53K PHE* 3.7 29.2 - - + -
95K ARG 3.6 2.0 + - - -
96K GLY* 1.3 71.3 - - - -
98K GLY* 1.3 66.5 + - - +
100K PHE* 2.9 35.9 + - + +
101K ALA 3.5 2.8 + - - -
53N PHE* 3.9 33.0 - - + -
92N ILE* 4.0 19.3 + - + +
95N ARG 4.6 1.8 + - - -
97N LEU* 4.3 22.0 - - + +
98N GLY 5.2 1.1 - - - +
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Residues in contact with GLY 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53K PHE* 3.4 32.6 - - - -
89K THR* 5.6 0.4 + - - -
92K ILE 4.4 4.4 + - - -
93K GLY* 4.2 13.7 - - - -
95K ARG 4.4 2.4 + - - -
96K GLY 3.2 1.0 + - - -
97K LEU* 1.3 78.2 - - - +
99K LEU* 1.3 61.5 + - - +
101K ALA* 3.3 7.3 - - - +
102K ILE* 3.3 25.8 + - - +
97N LEU* 5.1 1.2 - - - +
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Residues in contact with LEU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82K TYR* 3.7 22.9 - - - +
86K TYR* 4.2 5.2 - - + -
93K GLY* 4.9 0.2 - - - -
94K MET* 2.9 46.9 - - - +
95K ARG* 3.4 8.4 + - - +
96K GLY 2.8 13.2 + - - +
98K GLY* 1.3 76.0 - - - +
100K PHE* 1.3 57.0 + - - -
102K ILE* 3.4 23.1 + - + +
103K SER* 2.8 32.1 + - - -
262K THR* 4.0 4.9 - - - +
263K THR* 3.4 14.4 - - + -
285K ARG 3.5 12.6 - - - +
286K CYS 3.7 15.0 - - - +
287K GLY* 3.8 8.7 - - - -
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Residues in contact with PHE 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K ALA* 3.3 10.6 - - - +
44K ASP* 3.3 35.9 - - + +
45K GLY* 4.0 5.4 - - - -
50K MET* 3.7 1.6 - - + -
96K GLY* 3.4 19.5 - - - -
97K LEU* 2.9 29.1 + - + +
99K LEU* 1.3 74.6 - - - +
101K ALA* 1.3 62.3 + - - +
103K SER* 3.1 4.2 + - - -
104K GLY 3.1 19.2 + - - -
262K THR* 4.0 10.8 - - + -
284K ASN 3.5 12.3 - - - +
285K ARG* 3.4 57.4 - - + -
91N TRP 3.6 10.1 - - - -
92N ILE* 4.1 21.1 - - + -
93N GLY 5.9 0.4 - - - -
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Residues in contact with ALA 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12K PHE* 3.7 26.3 - - + -
43K ALA* 4.3 0.9 - - - -
50K MET* 3.8 8.7 - - + +
53K PHE* 3.6 31.0 - - + -
66K ILE* 4.0 9.6 - - + -
97K LEU 3.5 1.6 + - - -
98K GLY 3.3 11.6 + - - +
100K PHE* 1.3 78.6 - - - +
102K ILE* 1.3 61.3 + - - +
104K GLY* 3.4 1.9 + - - -
105K ILE* 3.3 25.5 + - - +
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Residues in contact with ILE 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66K ILE* 3.5 22.7 - - + -
82K TYR* 3.7 34.8 - - + +
85K MET* 4.0 22.4 - - + +
86K TYR* 4.0 30.1 - - + -
89K THR* 4.1 11.9 - - - +
94K MET 5.7 2.5 - - - +
98K GLY 3.3 13.5 + - - +
99K LEU* 3.7 24.7 - - + +
101K ALA* 1.3 74.1 - - - +
103K SER* 1.3 65.1 + - - +
105K ILE* 3.3 1.0 + - - +
106K ASP* 2.9 23.4 + - - +
287K GLY* 3.9 3.4 - - - +
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Residues in contact with SER 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K GLU 4.6 0.7 - - - -
99K LEU 2.8 14.0 + - - -
100K PHE 3.1 9.4 + - - -
102K ILE* 1.3 74.6 - - - +
104K GLY* 1.3 57.2 + - - +
106K ASP* 3.6 1.2 - - - +
107K MET* 3.0 31.0 + - - +
283K TYR 3.4 21.5 - - - +
284K ASN 3.5 11.4 - - - -
285K ARG 3.1 7.6 - - - -
287K GLY 2.7 39.1 + - - -
288K GLY* 3.6 4.6 - - - +
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Residues in contact with GLY 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K VAL* 3.5 24.1 - - - +
41K GLY* 3.5 5.4 - - - -
42K GLU 3.4 29.1 + - - -
43K ALA* 4.0 1.8 - - - -
100K PHE 3.1 11.2 + - - -
101K ALA 3.4 2.4 + - - -
102K ILE 3.2 0.2 - - - -
103K SER* 1.3 75.3 - - - +
105K ILE* 1.3 61.9 + - - +
107K MET* 4.6 0.7 - - - -
108K ALA* 3.3 15.2 + - - +
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Residues in contact with ILE 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K VAL* 4.2 11.2 - - + -
12K PHE* 3.8 17.0 - - + -
29K VAL* 3.7 20.9 - - + -
31K VAL* 4.4 10.8 - - + -
66K ILE* 3.8 34.1 - - + +
67K LYS* 5.2 0.9 - - - +
70K VAL* 4.5 11.9 - - + -
85K MET* 3.8 22.7 - - - -
101K ALA 3.3 14.0 + - - +
102K ILE 3.3 2.5 + - - +
104K GLY* 1.3 73.5 - - - +
106K ASP* 1.3 62.0 + - - +
108K ALA* 3.0 4.0 + - - +
109K LEU* 2.8 44.4 + - + +
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Residues in contact with ASP 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K PHE* 4.7 4.3 - - - +
82K TYR* 4.3 8.8 + - + +
85K MET* 4.2 8.2 - - + +
102K ILE 2.9 17.8 + - - +
103K SER 3.6 4.0 - - - +
105K ILE* 1.3 76.5 - - - +
107K MET* 1.3 62.6 + - - +
109K LEU* 3.1 21.8 + - - +
110K TYR* 3.2 24.2 + - - -
287K GLY 3.8 11.4 - - - +
289K VAL* 2.8 30.8 + - - -
290K THR* 2.5 37.1 + - - -
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Residues in contact with MET 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K LEU 3.9 2.5 - - - +
41K GLY* 3.8 4.9 - - - -
42K GLU 3.7 33.0 - - - +
103K SER 3.0 14.6 + - - +
104K GLY 3.9 5.4 - - - +
106K ASP* 1.3 76.7 + - - +
108K ALA* 1.3 62.3 + - - +
110K TYR* 3.2 18.1 + - - +
111K ASP 3.3 8.5 + - - -
283K TYR* 3.9 32.5 - - + +
284K ASN* 4.4 0.7 - - + -
289K VAL* 4.8 11.2 - - + +
315K ILE* 3.9 17.0 - - - +
316K THR* 3.7 20.6 - - - +
319K ALA* 4.1 20.0 - - + -
369K LEU* 3.9 18.2 - - + +
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Residues in contact with ALA 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K VAL* 3.8 6.1 - - + +
31K VAL* 3.6 23.8 - - + -
39K GLY* 3.6 8.8 - - - +
40K LEU 3.5 13.5 - - - -
41K GLY* 3.4 18.3 - - - +
104K GLY 3.3 8.3 + - - +
105K ILE* 3.0 10.1 + - - +
107K MET* 1.3 79.0 - - - +
109K LEU* 1.3 58.5 + - - +
111K ASP* 3.1 5.5 + - - +
112K LEU* 2.8 26.2 + - - +
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Residues in contact with LEU 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 3.4 31.9 - - + -
31K VAL* 4.1 16.6 - - + -
70K VAL* 4.3 11.0 - - + -
75K PRO* 3.9 20.0 - - + +
78K PHE* 4.1 9.4 - - + -
81K ASN* 4.3 16.2 - - + +
85K MET* 4.2 15.3 - - + -
105K ILE* 2.8 38.3 + - + +
106K ASP* 3.4 11.4 - - - +
108K ALA* 1.3 70.9 - - - +
110K TYR* 1.3 59.7 + - - +
112K LEU* 3.9 3.5 - - + +
113K ALA* 2.8 34.5 + - - +
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Residues in contact with TYR 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K PHE* 3.5 45.6 - + - +
106K ASP* 3.2 29.0 + - - -
107K MET* 3.2 6.2 + - - +
109K LEU* 1.3 72.4 - - - +
111K ASP* 1.3 65.0 + - - +
114K GLY* 3.1 19.6 + - - -
121K ALA* 4.1 18.2 - - + +
124K LEU* 3.7 26.3 + - + +
125K MET* 3.9 29.4 - - + -
289K VAL* 3.6 27.8 - - + -
290K THR* 2.9 36.8 + - - +
293K LEU* 3.7 10.4 - - - +
368K GLY* 4.1 3.8 - - - -
369K LEU* 4.7 2.9 - - + -
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Residues in contact with ASP 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLY* 3.3 5.0 - - - -
40K LEU* 2.6 47.0 + - - +
107K MET 3.3 2.8 + - - -
108K ALA 3.1 10.0 + - - +
110K TYR* 1.3 79.1 - - - +
112K LEU* 1.3 62.4 + - - +
115K LYS* 3.1 37.5 + - - +
368K GLY* 3.4 8.5 - - - -
369K LEU* 2.8 44.7 + - + +
370K GLY 4.2 2.8 + - - -
371K ILE* 4.3 7.7 + - - +
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Residues in contact with LEU 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K ILE* 4.1 19.1 - - + -
31K VAL* 3.7 22.9 - - + +
33K ASP* 4.1 12.8 - - + +
37K VAL* 3.6 33.9 - - + +
38K TYR 3.8 12.8 - - - -
39K GLY* 3.6 10.3 - - - +
75K PRO* 4.1 23.1 - - + -
108K ALA 2.8 15.6 + - - +
109K LEU* 3.9 6.3 - - + +
111K ASP* 1.3 72.8 - - - +
113K ALA* 1.3 67.4 + - - +
115K LYS* 2.9 5.9 + - - +
116K GLN* 2.8 33.2 + - + +
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Residues in contact with ALA 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K PRO* 3.9 23.9 - - - +
76K LEU* 4.2 10.5 - - + +
78K PHE* 3.9 7.9 - - + -
109K LEU 2.8 21.9 + - - +
112K LEU* 1.3 72.5 - - - +
114K GLY* 1.3 56.8 + - - +
116K GLN* 3.5 13.3 + - - +
117K LEU* 3.0 34.0 + - - +
124K LEU* 3.8 16.8 - - + -
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Residues in contact with GLY 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K TYR 3.1 13.3 + - - -
112K LEU 3.1 1.0 - - - -
113K ALA* 1.3 76.5 - - - +
115K LYS* 1.3 57.9 + - - +
118K GLY* 2.8 26.0 + - - -
119K VAL* 2.9 33.2 + - - +
120K PRO 5.3 0.2 - - - -
124K LEU* 3.6 14.0 - - - +
367K PRO* 3.7 0.9 - - - +
368K GLY* 3.6 8.3 - - - -
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Residues in contact with LYS 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K VAL* 4.0 21.5 - - + -
38K TYR* 2.7 51.3 + - - +
111K ASP* 3.1 34.0 + - - +
112K LEU 2.9 7.6 + - - +
114K GLY* 1.3 73.4 - - - +
116K GLN* 1.3 66.6 + - - +
117K LEU 3.1 1.0 + - - -
118K GLY* 3.2 11.1 + - - -
367K PRO* 4.0 26.9 - - + +
371K ILE 5.9 1.2 + - - -
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Residues in contact with GLN 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K ALA 2.9 36.9 + - - +
33K ASP* 2.8 34.9 + - - +
37K VAL* 4.6 6.4 - - + +
74K ASP* 4.4 3.8 - - - +
75K PRO* 3.0 30.4 - - - +
76K LEU* 5.1 0.7 + - - +
112K LEU* 2.8 26.7 + - + +
113K ALA* 3.6 8.9 - - - +
115K LYS* 1.3 74.8 - - - +
117K LEU* 1.3 66.8 + - + +
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Residues in contact with LEU 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I LEU* 4.2 50.5 - - + +
119I VAL* 5.1 9.6 - - + -
76K LEU* 4.0 31.9 - - + -
113K ALA* 3.0 22.7 + - + +
114K GLY 4.4 0.9 - - - +
116K GLN* 1.3 84.0 - - + +
118K GLY* 1.3 61.4 + - - +
119K VAL* 4.3 13.8 - - + +
124K LEU* 4.3 13.9 - - + -
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Residues in contact with GLY 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K GLY 2.8 10.5 + - - -
115K LYS 3.2 9.1 + - - -
117K LEU* 1.3 79.1 - - - +
119K VAL* 1.3 59.8 + - - +
120K PRO* 4.6 1.4 - - - +
365K ASP 5.1 1.6 - - - +
367K PRO* 4.0 20.2 - - - +
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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