Contacts of the helix formed by residues 85 - 114 (chain K) in PDB entry 5GSE
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 GLN 85 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I A 6.2 0.2 - - - +
206I G 4.8 9.4 + - - -
50J G 3.2 35.7 + - - +
83K ARG 4.3 0.6 - - - -
84K PHE* 1.3 74.0 - - - +
86K SER* 1.3 66.6 + - - +
87K SER* 4.4 10.8 + - - +
88K ALA* 2.9 21.4 + - - +
89K VAL* 3.5 4.2 + - - +
80L THR* 4.8 8.7 + - - +
81L VAL 3.5 15.3 + - - +
82L THR* 2.9 34.7 + - - -
83L ALA* 3.2 16.9 - - - +
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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
----------------------------------------------------------
50J G 3.8 13.6 + - - -
68K GLN* 4.9 9.6 - - - +
84K PHE 3.7 2.7 + - - -
85K GLN* 1.3 73.2 - - - +
87K SER* 1.3 69.3 + - - +
88K ALA 3.1 0.5 + - - -
89K VAL* 3.1 9.8 + - - +
90K MET* 3.0 30.3 + - - +
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Residues in contact with SER 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85K GLN* 3.2 13.6 + - - +
86K SER* 1.3 82.4 + - - +
88K ALA* 1.3 58.0 - - - +
90K MET* 3.4 5.9 + - - +
91K ALA* 2.9 28.9 + - - +
83L ALA* 3.9 17.1 - - - +
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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
----------------------------------------------------------
84K PHE* 4.9 4.3 - - + -
85K GLN* 2.9 13.0 + - + +
87K SER* 1.3 75.9 - - - +
89K VAL* 1.3 65.2 + - - +
91K ALA* 3.0 5.2 + - - +
92K LEU* 2.9 29.7 + - + +
81L VAL* 3.5 25.1 - - + +
83L ALA* 3.8 23.6 - - - +
86L VAL* 3.9 15.3 - - + +
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Residues in contact with VAL 89 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K PHE* 4.0 9.4 - - + -
68K GLN* 3.5 48.9 - - + +
71K VAL* 3.8 22.7 - - + -
72K ARG* 5.4 0.7 - - - +
84K PHE* 3.7 36.3 - - + +
85K GLN 4.0 5.2 - - - +
86K SER* 3.1 5.7 + - - +
88K ALA* 1.3 74.5 - - - +
90K MET* 1.3 62.5 + - + +
92K LEU* 3.4 8.4 - - + +
93K GLN* 2.9 26.9 + - - +
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Residues in contact with MET 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K LEU* 4.0 23.3 - - - -
64K LYS* 3.7 23.8 - - + +
68K GLN* 4.7 9.2 - - - +
86K SER* 3.0 22.1 + - - +
87K SER* 3.9 6.1 - - - +
89K VAL* 1.3 86.5 - - + +
91K ALA* 1.3 60.7 + - - +
93K GLN* 3.3 27.2 - - - +
94K GLU* 3.0 41.9 + - - +
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Residues in contact with ALA 91 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87K SER 2.9 14.5 + - - +
88K ALA* 3.0 8.3 + - - +
90K MET* 1.3 76.3 - - - +
92K LEU* 1.3 57.9 + - - +
94K GLU* 3.3 13.1 + - - +
95K ALA* 2.9 26.7 + - - +
83L ALA* 4.9 4.5 - - + -
86L VAL* 3.5 22.9 - - + -
87L VAL* 5.1 7.0 - - + -
90L LEU* 4.7 5.2 - - + +
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Residues in contact with LEU 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K PHE* 4.2 7.6 - - + -
71K VAL* 3.6 20.0 - - + -
84K PHE* 5.2 5.2 - - + -
88K ALA* 2.9 36.1 + - + +
89K VAL* 3.4 17.7 - - + +
91K ALA* 1.3 69.6 - - - +
93K GLN* 1.3 63.4 + - - +
95K ALA* 3.7 8.6 - - + +
96K CYS* 2.9 31.9 + - - -
61L PHE* 5.1 0.4 - - + -
62L LEU* 3.5 28.7 - - + +
65L VAL* 4.9 11.2 - - + -
66L ILE* 3.6 22.2 - - + -
86L VAL* 4.5 20.1 - - + +
90L LEU* 5.3 1.8 - - + -
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Residues in contact with GLN 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K LEU* 3.7 24.5 - - + +
62K ILE* 2.9 44.5 - - + +
64K LYS* 3.8 15.0 + - - +
67K PHE* 3.4 37.0 - - + +
89K VAL* 2.9 16.2 + - - +
90K MET* 3.3 30.9 - - - +
91K ALA 3.2 0.2 - - - -
92K LEU* 1.3 74.8 - - - +
94K GLU* 1.3 60.2 + - - +
96K CYS* 3.2 2.3 + - - +
97K GLU* 2.9 33.0 + - - +
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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
----------------------------------------------------------
60K LEU* 4.5 16.6 - - + +
90K MET* 3.0 27.0 + - - +
91K ALA* 3.6 10.1 - - - +
93K GLN* 1.3 76.0 - - - +
95K ALA* 1.3 62.6 + - - +
97K GLU* 3.2 8.2 + - - +
98K ALA* 3.0 23.9 + - - +
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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
----------------------------------------------------------
91K ALA 2.9 16.5 + - - +
92K LEU* 3.7 8.3 - - + +
94K GLU* 1.3 75.7 - - - +
96K CYS* 1.3 62.5 + - - +
98K ALA* 3.2 6.5 + - - +
99K TYR* 2.9 25.3 + - - +
61L PHE* 4.3 9.7 - - + -
65L VAL* 6.4 0.2 - - + -
90L LEU* 3.6 37.5 - - + -
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Residues in contact with CYS 96 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ILE* 4.9 6.1 - - + -
67K PHE* 3.6 15.5 - - + -
92K LEU 2.9 20.9 + - - +
93K GLN 3.4 9.4 - - - +
95K ALA* 1.3 76.3 - - - +
97K GLU* 1.3 57.7 + - - +
99K TYR* 3.4 1.6 + - - +
100K LEU* 2.9 37.4 + - + +
58L LEU* 3.5 26.2 - - + -
61L PHE* 4.0 14.5 - - - -
62L LEU* 3.4 31.2 - - - -
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Residues in contact with GLU 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K LEU* 3.3 19.4 - - + +
61K LEU* 2.7 42.6 + - + +
62K ILE* 3.0 31.3 + - + +
93K GLN 2.9 20.1 + - - +
94K GLU* 3.2 7.2 + - - +
96K CYS* 1.3 74.2 - - - +
98K ALA* 1.3 64.1 + - - +
100K LEU* 3.3 3.2 + - - +
101K VAL* 2.9 31.2 + - + +
37L LEU* 3.0 30.5 - - + +
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Residues in contact with ALA 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94K GLU 3.0 17.1 + - - +
95K ALA* 3.6 6.1 - - - +
97K GLU* 1.3 75.7 - - - +
99K TYR* 1.3 64.3 + - - +
101K VAL* 3.1 13.5 - - - +
102K GLY* 3.0 20.1 + - - -
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Residues in contact with TYR 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K ALA 2.9 16.6 + - - +
96K CYS* 3.7 2.7 - - - +
98K ALA* 1.3 76.2 - - - +
100K LEU* 1.3 72.7 + - + +
102K GLY* 3.4 1.1 + - - -
103K LEU* 3.0 33.8 + - + +
128K ARG* 3.9 1.7 + - - -
131K ARG* 3.5 27.3 + - - +
133K GLU* 2.6 29.1 + - - -
57L VAL* 3.4 34.7 + - + +
58L LEU* 5.2 1.3 - - + -
60L VAL* 5.4 2.4 - - - +
61L PHE* 3.8 53.2 - + + +
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Residues in contact with LEU 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62K ILE* 5.7 3.1 - - + -
96K CYS* 2.9 24.8 + - + +
97K GLU* 3.8 3.1 - - - +
99K TYR* 1.3 95.3 - - + +
101K VAL* 1.3 58.8 + - - +
103K LEU* 3.5 7.5 + - + +
104K PHE* 2.9 41.7 + - + -
29L ILE* 6.0 1.8 - - + -
34L ILE* 6.5 0.9 - - + -
37L LEU* 3.5 31.6 - - + -
54L THR* 3.7 25.8 - - - +
57L VAL* 4.6 10.3 - - + -
58L LEU* 4.3 33.0 - - + -
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Residues in contact with VAL 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K LEU* 5.5 0.2 - - + -
97K GLU* 2.9 16.9 + - + +
98K ALA* 3.1 23.1 - - - +
100K LEU* 1.3 75.9 - - - +
102K GLY* 1.3 59.3 + - - +
104K PHE* 3.1 8.4 + - - +
105K GLU* 2.9 41.0 + - - +
37L LEU* 3.7 19.7 - - + +
40L ARG* 3.5 35.2 - - + +
41L GLY* 4.1 7.3 - - - +
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Residues in contact with GLY 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98K ALA 3.0 13.6 + - - -
99K TYR* 3.8 2.2 - - - -
101K VAL* 1.3 75.3 - - - +
103K LEU* 1.3 64.8 + - - +
105K GLU* 3.1 16.7 + - - +
106K ASP* 3.0 25.7 + - - -
131K ARG* 3.6 11.2 - - - -
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Residues in contact with LEU 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K TYR* 3.0 25.4 + - + +
100K LEU* 3.8 11.0 - - + +
102K GLY* 1.3 73.7 - - - +
104K PHE* 1.3 54.1 + - + +
106K ASP* 3.4 1.7 + - + +
107K THR* 2.3 42.3 + - - +
124K ILE* 3.7 22.7 - - + -
127K ALA* 4.0 19.1 - - + -
128K ARG* 3.8 25.8 - - + -
131K ARG* 3.3 25.1 - - - +
57L VAL* 3.6 31.2 - - + -
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Residues in contact with PHE 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K LEU* 2.9 36.1 + - + +
101K VAL* 3.1 7.1 + - - +
103K LEU* 1.3 75.9 - - + +
105K GLU* 1.3 60.0 + - - +
107K THR* 3.3 12.4 + - + -
108K ASN* 2.9 28.6 + - - +
119K ILE* 4.8 9.2 - - + -
124K ILE* 5.8 5.2 - - + -
34L ILE* 4.1 17.7 - - + -
37L LEU* 3.9 15.5 - - + -
38L ALA* 3.8 49.1 - - + -
41L GLY* 4.2 9.0 - - - +
43L VAL* 4.1 10.4 - - + +
46L ILE* 5.9 0.2 - - + -
50L ILE* 4.3 15.3 - - + -
54L THR* 3.9 26.0 - - + -
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Residues in contact with GLU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K VAL* 2.9 26.6 + - - +
102K GLY* 3.6 13.8 - - - +
104K PHE* 1.3 76.2 - - - +
106K ASP* 1.3 66.8 + - - +
108K ASN* 3.1 4.6 + - - +
109K LEU* 3.0 33.3 + - + +
40L ARG 5.7 0.5 - - - +
41L GLY* 3.8 22.4 - - - +
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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
----------------------------------------------------------
102K GLY 3.0 11.9 + - - +
103K LEU 3.7 7.6 - - - +
105K GLU* 1.3 77.4 - - - +
107K THR* 1.3 63.1 + - - +
109K LEU* 3.0 16.5 + - - +
110K CYS* 3.0 24.8 + - - -
127K ALA* 3.9 12.3 - - + -
131K ARG* 2.9 30.6 + - - +
129O ARG 5.1 0.9 - - - +
130O ILE* 3.3 41.6 - - + +
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Residues in contact with THR 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K LEU* 2.3 38.4 + - - +
104K PHE* 3.5 13.2 - - + -
105K GLU 3.2 0.2 - - - -
106K ASP* 1.3 75.7 - - - +
108K ASN* 1.3 57.9 + - - +
110K CYS 3.2 1.9 + - - -
111K ALA 3.0 23.2 + - - -
119K ILE* 3.6 28.2 - - + +
123K ASP* 3.4 26.2 - - + +
124K ILE* 3.2 38.4 - - + +
127K ALA* 4.3 1.0 - - - +
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Residues in contact with ASN 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K PHE 2.9 16.7 + - - +
105K GLU* 3.1 6.9 + - - +
107K THR* 1.3 76.7 - - - +
109K LEU* 1.3 61.5 + - + +
111K ALA* 4.5 0.7 - - - +
112K ILE* 2.9 63.3 + - - +
117K VAL* 4.3 10.6 - - - +
119K ILE* 3.5 18.8 - - - +
41L GLY 4.8 0.2 - - - +
42L GLY 3.1 24.5 + - - +
43L VAL* 4.0 15.0 - - + +
44L LYS* 4.9 5.2 + - - +
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Residues in contact with LEU 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105K GLU* 3.0 31.0 + - + +
106K ASP* 3.3 16.6 - - - +
108K ASN* 1.3 82.2 - - + +
110K CYS* 1.3 56.6 + - - +
112K ILE* 3.5 9.9 + - + +
113K HIS* 2.9 29.8 + - - +
126O LEU* 3.9 20.2 - - + +
129O ARG* 3.8 44.0 - - + +
130O ILE* 4.6 7.2 - - + -
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Residues in contact with CYS 110 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K ASP 3.0 17.5 + - - -
107K THR 3.2 7.6 + - - +
109K LEU* 1.3 76.2 - - - +
111K ALA* 1.3 63.1 + - - +
113K HIS* 3.1 9.0 + - - +
114K ALA 2.9 18.0 + - - -
123K ASP* 3.6 30.7 - - + +
126K LEU* 3.5 25.1 - - + -
127K ALA* 4.1 3.8 - - - -
113O HIS* 3.3 16.2 + - - +
126O LEU* 4.5 5.6 - - - -
130O ILE* 3.6 22.7 - - - -
----------------------------------------------------------
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Residues in contact with ALA 111 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K THR 3.0 6.4 + - - +
108K ASN* 3.7 3.8 - - - +
110K CYS* 1.3 76.6 - - - +
112K ILE* 1.3 61.8 + - - +
114K ALA* 3.0 13.5 + - - +
116K ARG* 3.2 34.3 + - - +
117K VAL 4.9 1.3 - - - -
118K THR 4.0 8.3 - - - +
119K ILE* 3.4 26.7 - - + -
123K ASP* 3.3 25.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 112 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K ASN* 2.9 48.8 + - - +
109K LEU* 3.9 9.4 - - + +
111K ALA* 1.3 75.2 - - - +
113K HIS* 1.3 63.1 + - - +
115K LYS* 3.0 16.6 + - - +
116K ARG 3.6 12.3 - - - +
117K VAL* 5.6 4.9 - - + -
----------------------------------------------------------
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Residues in contact with HIS 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109K LEU 2.9 19.0 + - - +
110K CYS 3.1 5.3 + - - +
112K ILE* 1.3 78.6 - - - +
114K ALA* 1.3 56.5 + - - +
115K LYS* 3.2 6.3 + - - +
110O CYS* 3.7 12.6 + - + -
113O HIS* 4.7 3.6 - - - -
114O ALA* 3.6 31.3 + - + +
116O ARG* 4.0 2.0 - - - -
122O LYS* 3.7 48.8 + - + +
123O ASP* 3.0 30.4 + - - -
126O LEU* 3.5 29.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K CYS 2.9 5.8 + - - +
111K ALA 3.0 6.0 + - - +
113K HIS* 1.3 74.7 + - - +
115K LYS* 1.3 70.2 + - - +
116K ARG* 3.2 34.6 + - - +
113O HIS* 3.7 31.4 - - + +
114O ALA* 4.3 11.4 - - - +
----------------------------------------------------------
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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