Contacts of the helix formed by residues 80 - 103 (chain K) in PDB entry 5DSV
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 LEU 80 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J PHE* 4.6 5.6 - - + -
18J GLY 6.0 0.2 - - - +
20J VAL* 4.5 17.9 - - + +
154J SER* 5.0 12.1 - - - +
156J VAL* 5.7 1.3 - - + -
29K ALA* 4.6 6.9 + - + +
79K GLY* 1.3 69.1 - - - -
81K LEU* 1.3 67.2 + - - +
82K ALA* 4.3 14.1 - - + +
83K ASP* 3.3 24.9 + - - +
84K ALA 3.3 9.0 + - - -
129K ARG* 4.1 17.7 - - - +
132K GLY* 2.9 28.4 + - - +
133K CYS* 3.8 5.2 - - - +
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Residues in contact with LEU 81 (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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156J VAL* 4.6 8.0 - - + +
158J TYR* 3.8 24.2 - - + +
63K ASN 4.2 12.6 - - - +
64K LYS 4.5 1.1 - - - +
65K ARG* 4.4 14.4 - - + -
67K PHE* 4.4 16.4 - - + -
77K VAL* 4.1 24.9 - - + -
79K GLY 3.2 9.2 + - - +
80K LEU* 1.3 75.6 - - - +
82K ALA* 1.3 66.0 + - - +
84K ALA* 3.3 5.3 + - + -
85K ARG* 3.0 52.2 + - - +
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Residues in contact with ALA 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120J HIS* 3.7 19.9 + - + +
154J SER* 2.9 30.7 - - - +
155J GLY 4.1 10.6 - - - +
156J VAL* 3.7 22.0 - - + +
80K LEU* 4.6 6.3 - - + -
81K LEU* 1.3 79.5 - - - +
83K ASP* 1.3 63.1 + - - +
85K ARG* 3.5 8.2 + - - +
86K SER* 3.3 16.5 + - - -
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Residues in contact with ASP 83 (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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120J HIS* 2.7 35.6 + - - -
123J THR* 4.5 0.3 + - - -
124J LEU* 4.9 0.2 - - - -
80K LEU* 3.3 19.6 + - - +
82K ALA* 1.3 74.1 - - - +
84K ALA* 1.3 66.9 + - - +
86K SER* 2.9 17.1 + - - -
87K LEU* 2.9 13.9 + - - +
129K ARG* 2.4 34.4 + - - -
131K PHE* 3.6 17.3 - - + -
132K GLY* 2.9 21.1 + - - +
133K CYS* 4.0 9.9 - - - -
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Residues in contact with ALA 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K PHE* 5.1 1.6 - - + -
75K MET* 3.9 4.9 - - + +
77K VAL* 3.8 37.2 - - + -
78K ALA 5.6 0.4 - - - +
80K LEU 3.3 7.3 + - - +
81K LEU* 3.3 12.0 + - + +
83K ASP* 1.3 78.3 - - - +
85K ARG* 1.3 57.3 + - - +
87K LEU* 2.9 7.2 + - - +
88K ALA* 2.8 29.4 + - - +
133K CYS* 3.5 22.2 - - + -
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Residues in contact with ARG 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J ASP* 4.3 18.3 + - - -
117J MET* 5.3 1.1 - - - -
155J GLY 5.4 0.6 + - - -
156J VAL* 4.2 8.5 - - - +
157J SER* 3.5 39.7 + - - +
158J TYR* 4.6 1.4 - - - -
62K SER 5.3 0.2 - - - -
63K ASN* 4.2 22.4 - - - +
64K LYS 4.2 5.1 + - - +
67K PHE* 3.7 29.9 - - + -
81K LEU* 3.0 48.5 + - + +
82K ALA* 3.8 8.0 - - - +
83K ASP 3.2 0.2 - - - -
84K ALA* 1.3 74.1 - - - +
86K SER* 1.3 62.3 + - - +
88K ALA* 3.3 10.0 + - + +
89K ASP* 3.2 24.1 + - - +
92K ARG* 4.6 1.6 + - - -
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Residues in contact with SER 86 (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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117J MET* 3.8 30.4 - - - +
120J HIS* 3.6 29.4 - - - -
82K ALA 3.3 3.7 + - - -
83K ASP 2.9 10.7 + - - -
85K ARG* 1.3 76.9 - - - +
87K LEU* 1.3 65.9 + - - +
89K ASP* 3.2 7.0 + - - +
90K ILE* 3.2 28.0 + - - +
131K PHE* 3.8 12.8 - - - -
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Residues in contact with LEU 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75K MET* 4.4 9.0 - - + +
83K ASP 2.9 7.1 + - - +
84K ALA* 3.4 7.0 - - - +
86K SER* 1.3 78.2 + - - +
88K ALA* 1.3 65.3 + - - +
90K ILE* 3.2 16.7 + - + +
91K ALA* 3.0 22.5 + - - +
115K VAL* 4.6 10.8 - - + +
118K TYR* 4.4 4.7 - - + -
119K VAL* 3.6 27.1 - - + -
131K PHE* 3.8 35.9 - - + -
133K CYS* 3.3 34.5 - - - +
135K PHE* 4.0 20.9 - - + -
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Residues in contact with ALA 88 (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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67K PHE* 4.7 9.6 - - + -
69K VAL* 4.5 3.3 - - + +
75K MET* 3.8 25.9 - - + +
84K ALA 2.8 12.0 + - - +
85K ARG* 3.3 14.8 - - - +
87K LEU* 1.3 74.7 - - - +
89K ASP* 1.3 54.0 + - - +
91K ALA* 3.1 5.3 + - - +
92K ARG* 2.7 59.7 + - - +
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Residues in contact with ASP 89 (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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100B SER 4.5 7.2 - - - +
101B ASN* 5.5 1.9 - - - +
117J MET* 3.3 31.8 - - - +
85K ARG 3.2 10.6 + - - +
86K SER* 3.3 11.4 - - - +
88K ALA* 1.3 78.6 - - - +
90K ILE* 1.3 62.5 + - + +
92K ARG* 2.9 31.6 + - - +
93K GLU* 3.0 24.4 + - - +
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Residues in contact with ILE 90 (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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86K SER* 3.2 23.6 + - - +
87K LEU* 3.4 17.3 - - + +
88K ALA 3.1 0.6 - - - -
89K ASP* 1.3 79.1 - - + +
91K ALA* 1.3 64.2 + - - +
93K GLU* 3.3 5.6 + - - +
94K GLU* 3.0 28.3 + - - +
115K VAL* 4.4 15.7 - - + -
118K TYR* 3.4 66.6 - - + +
131K PHE* 5.0 0.9 - - + -
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Residues in contact with ALA 91 (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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69K VAL* 3.7 24.7 - - + -
75K MET* 4.9 4.0 - - - -
87K LEU 3.0 12.4 + - - +
88K ALA* 3.4 8.3 - - - +
90K ILE* 1.3 77.9 - - - +
92K ARG* 1.3 61.8 + - - +
94K GLU* 3.2 1.7 + - - +
95K ALA* 2.9 27.5 + - - +
111K LEU* 3.7 8.7 - - + +
115K VAL* 3.6 27.6 - - + +
135K PHE* 6.1 0.2 - - + -
137K LEU* 5.3 4.3 - - + -
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Residues in contact with ARG 92 (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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99B ARG* 4.4 12.1 - - + +
100B SER* 3.9 25.1 - - - +
101B ASN 5.9 0.4 - - - -
103B GLY* 5.3 10.8 + - - -
67K PHE* 3.8 25.5 - - - +
68K ASN 3.3 25.2 + - - -
69K VAL* 3.2 27.4 - - - +
85K ARG 4.6 1.8 + - - -
88K ALA* 2.7 29.0 + - - +
89K ASP* 2.9 42.5 + - - +
91K ALA* 1.3 72.6 - - - +
93K GLU* 1.3 63.0 + - - +
95K ALA* 3.4 1.9 + - - +
96K SER* 3.0 25.2 + - - -
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Residues in contact with GLU 93 (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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97B ASN* 3.8 7.6 - - - +
100B SER* 3.5 32.4 + - - +
101B ASN* 5.6 1.4 - - - +
89K ASP 3.0 15.3 + - - +
90K ILE* 3.8 6.5 - - - +
92K ARG* 1.3 75.2 - - - +
94K GLU* 1.3 59.0 + - - +
96K SER* 3.1 1.6 + - - -
97K ASN* 2.7 61.8 + - - +
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Residues in contact with GLU 94 (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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90K ILE* 3.0 23.2 + - + +
91K ALA* 3.6 5.6 - - - +
93K GLU* 1.3 81.5 - - - +
95K ALA* 1.3 56.8 + - - +
97K ASN* 4.0 4.4 - - - +
98K PHE* 3.2 23.7 + - - +
106K ILE* 4.1 7.8 - - + +
110K HIS* 5.4 1.3 - - + -
111K LEU* 4.1 11.4 - - + -
114K ARG* 2.7 64.0 + - + +
115K VAL* 4.8 2.9 - - + -
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Residues in contact with ALA 95 (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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69K VAL* 4.7 6.1 - - + -
70K ASP* 3.9 19.1 - - + +
91K ALA 2.9 16.6 + - - +
92K ARG* 3.9 2.7 - - - +
94K GLU* 1.3 73.8 - - - +
96K SER* 1.3 61.5 + - - +
98K PHE* 3.5 13.2 - - - +
99K ARG* 3.7 16.0 + - - +
106K ILE* 3.5 34.5 - - + +
111K LEU* 4.0 10.7 - - + +
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Residues in contact with SER 96 (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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96B SER* 2.3 54.0 + - - -
99B ARG* 4.5 9.3 + - - +
100B SER* 3.6 17.8 + - - -
70K ASP* 6.0 0.2 - - - -
92K ARG 3.0 17.5 + - - -
93K GLU 3.4 4.0 - - - -
95K ALA* 1.3 75.8 - - - +
97K ASN* 1.3 56.1 + - - +
98K PHE 3.0 4.0 - - - -
99K ARG* 2.7 29.7 + - - +
100K SER* 3.0 4.5 + - - -
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Residues in contact with ASN 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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93B GLU* 3.9 10.9 - - - +
97B ASN* 3.1 22.3 - - - +
100B SER* 4.8 1.0 + - - -
93K GLU* 2.7 46.7 + - - +
94K GLU* 4.0 4.7 - - - +
96K SER* 1.3 68.2 - - - +
98K PHE* 1.3 64.6 + - - +
100K SER* 3.9 8.5 + - - -
101K ASN* 3.1 23.1 + - - +
102K PHE* 4.9 1.2 - - - -
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Residues in contact with PHE 98 (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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102A PHE* 2.7 44.4 - + - -
94K GLU 3.2 14.0 + - - +
95K ALA 3.5 13.5 - - - +
96K SER 3.0 0.2 - - - -
97K ASN* 1.3 76.0 - - - +
99K ARG* 1.3 61.1 + - + +
101K ASN* 2.6 31.7 + - - +
102K PHE* 3.0 37.0 + + + -
104K TYR* 3.9 26.9 - + - -
105K ASN 3.2 24.7 - - - -
106K ILE* 3.8 28.0 - - + -
107K PRO* 3.9 12.3 - - + -
110K HIS* 5.2 0.4 - + - -
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Residues in contact with ARG 99 (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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69B VAL 5.4 4.9 - - - +
70B ASP* 3.9 24.0 - - - +
71B ARG 5.2 2.9 - - - +
92B ARG* 4.3 8.0 - - + +
96B SER* 4.7 4.4 + - - +
99B ARG* 4.3 15.9 - - - +
70K ASP* 2.8 36.5 + - - -
71K ARG* 3.1 25.8 - - - +
95K ALA 3.7 12.2 + - - +
96K SER* 2.7 16.3 + - - +
98K PHE* 1.3 83.5 - - - +
100K SER* 1.3 65.8 + - - +
101K ASN 3.1 0.6 + - - -
103K GLY* 3.4 25.5 + - - +
104K TYR 3.3 15.2 + - - +
105K ASN* 2.7 28.5 + - - +
106K ILE 4.8 0.2 - - - +
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Residues in contact with SER 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASP* 4.5 6.6 - - - +
92B ARG* 3.6 33.9 - - - +
93B GLU* 3.7 30.2 + - - -
96B SER* 3.4 25.4 + - - -
96K SER 3.0 8.7 + - - -
97K ASN* 3.9 13.0 + - - -
98K PHE 2.8 5.0 + - - -
99K ARG* 1.3 75.1 - - - +
101K ASN* 1.3 68.6 + - - +
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Residues in contact with ASN 101 (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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110A HIS* 3.8 13.0 + - - +
114A ARG* 3.4 28.6 + - - +
89B ASP* 5.5 2.4 - - - +
92B ARG* 5.7 0.9 + - - -
93B GLU* 5.7 0.7 - - - +
97K ASN* 3.1 22.4 + - - +
98K PHE 2.6 8.7 + - - +
100K SER* 1.3 83.7 - - - +
102K PHE* 1.3 86.4 + - + +
103K GLY* 3.2 3.4 + - - -
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Residues in contact with PHE 102 (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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98A PHE* 3.6 35.2 - + - -
102A PHE* 4.3 19.3 - + - -
107A PRO* 6.0 1.6 - - + -
110A HIS* 3.1 44.9 - + - +
114A ARG* 5.6 2.0 - - - -
97K ASN 5.1 0.9 - - - -
98K PHE* 3.0 47.3 + + + -
101K ASN* 1.3 99.7 - - + +
103K GLY* 1.3 57.6 + - - +
104K TYR* 2.9 36.0 - - + -
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Residues in contact with GLY 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 5.4 10.3 + - - -
99K ARG* 3.4 24.4 + - - +
100K SER 5.2 0.4 - - - -
101K ASN 3.2 5.2 - - - -
102K PHE* 1.3 78.5 - - - +
104K TYR* 1.3 61.8 + - - +
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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