Contacts of the helix formed by residues 81 - 104 (chain U) in PDB entry 3SDI
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 PRO 81 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15T PHE* 6.3 1.3 - - + -
19T GLY 5.8 0.2 - - - +
30U ALA* 3.6 18.8 - - + +
33U GLN* 4.0 28.5 - - - +
34U THR* 4.1 10.0 - - + -
80U GLY* 1.3 85.8 - - - +
82U ILE* 1.3 66.2 + - - +
83U PRO* 3.3 11.3 - - + -
84U ASP* 3.4 11.9 + - + +
85U ALA* 3.0 17.2 + - - +
133U GLY* 3.0 20.9 - - - +
134U VAL* 4.3 0.9 - - + -
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Residues in contact with ILE 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156T SER* 3.4 29.2 - - - +
158T TRP* 3.6 25.6 - - + -
65U SER 3.7 18.2 - - - +
66U TYR* 3.7 28.5 + - + +
68U PHE* 4.2 8.5 - - + -
80U GLY 3.6 1.2 + - - -
81U PRO* 1.3 70.4 - - - +
83U PRO* 1.4 80.2 - - + +
85U ALA* 3.0 9.6 + - + -
86U ARG* 2.8 62.1 + - - +
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Residues in contact with PRO 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118T GLN* 5.2 0.5 - - - +
121T GLN* 3.5 20.3 - - + +
124T THR* 5.8 0.2 - - - +
154T SER* 3.2 37.2 - - - +
155T GLY 4.1 9.2 - - - +
156T SER* 3.4 21.1 - - - +
81U PRO* 3.4 13.5 - - + -
82U ILE* 1.4 98.6 - - + +
84U ASP* 1.3 64.8 + - - +
86U ARG* 3.3 6.2 + - + +
87U ASN* 3.1 21.8 + - - +
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Residues in contact with ASP 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15T PHE* 4.6 0.7 - - - -
121T GLN* 2.9 15.3 - - - +
81U PRO* 3.4 16.7 + - + +
82U ILE 3.3 0.4 - - - -
83U PRO* 1.3 82.0 - - - +
85U ALA* 1.3 60.3 + - - +
87U ASN* 3.5 4.5 + - - +
88U ALA* 3.1 22.9 + - - +
130U ARG* 2.6 47.1 + - - -
132U LEU* 3.4 16.0 - - + +
133U GLY* 3.0 17.5 + - - +
134U VAL* 3.8 17.3 - - + +
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Residues in contact with ALA 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U TYR* 4.8 1.8 - - + -
68U PHE* 4.3 5.3 - - + -
76U MET* 4.0 5.5 - - - +
78U VAL* 3.5 38.9 - - + +
80U GLY 4.7 1.6 - - - +
81U PRO 3.0 13.3 + - - +
82U ILE* 3.0 24.1 + - + +
84U ASP* 1.3 77.0 - - - +
86U ARG* 1.3 57.6 + - - +
88U ALA* 3.3 6.0 + - - +
89U ALA* 2.9 25.8 + - - +
134U VAL* 3.9 1.5 - - - +
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Residues in contact with ARG 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114T ASP* 3.9 7.9 - - - +
118T GLN* 3.2 19.9 + - - +
155T GLY 4.9 1.7 + - - -
157T TYR* 2.8 76.4 + - - +
158T TRP* 3.5 27.5 - - - +
63U THR 4.1 7.7 + - - -
65U SER 5.2 1.4 + - - -
68U PHE* 4.1 20.2 - - + -
82U ILE* 2.8 39.6 + - - +
83U PRO* 3.8 6.3 - - + +
85U ALA* 1.3 73.4 - - - +
87U ASN* 1.3 58.1 + - - +
89U ALA* 3.0 6.9 + - - +
90U LEU* 2.8 31.4 + - - +
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Residues in contact with ASN 87 (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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118T GLN* 3.6 15.9 + - - +
121T GLN* 2.9 33.7 + - - +
125T LEU* 4.0 10.9 - - - +
83U PRO 3.1 16.0 + - - +
84U ASP* 3.5 6.5 - - - +
86U ARG* 1.3 75.5 - - - +
88U ALA* 1.3 65.8 + - - +
90U LEU* 4.1 1.4 - - - +
91U ARG* 3.3 23.8 + - - +
123U TYR* 5.7 1.8 + - - -
132U LEU* 3.7 22.9 - - - +
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Residues in contact with ALA 88 (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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76U MET* 3.8 2.9 - - + +
84U ASP 3.1 14.0 + - - +
85U ALA 3.3 7.6 + - - +
86U ARG 3.1 0.2 - - - -
87U ASN* 1.3 81.7 - - - +
89U ALA* 1.3 61.3 + - - +
92U ALA* 3.2 20.8 + - - +
116U MET* 3.3 18.6 - - + +
132U LEU* 4.6 11.0 - - + -
134U VAL* 4.7 1.8 - - + -
136U LEU* 3.8 36.1 - - + -
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Residues in contact with ALA 89 (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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68U PHE* 3.6 35.9 - - + -
70U ILE* 3.9 4.7 - - + +
76U MET* 3.4 15.7 - - + -
85U ALA 2.9 13.9 + - - +
86U ARG* 3.0 7.8 + - - +
88U ALA* 1.3 74.7 - - - +
90U LEU* 1.3 65.3 + - - +
92U ALA* 3.3 2.6 + - - +
93U LYS* 2.9 34.4 + - - +
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Residues in contact with LEU 90 (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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692 GLN* 3.3 38.8 - - + +
114T ASP* 4.7 8.7 - - - +
118T GLN* 3.6 34.1 - - + +
86U ARG 2.8 19.0 + - - +
87U ASN* 4.1 3.4 - - - +
89U ALA* 1.3 72.5 - - - +
91U ARG* 1.3 63.4 + - - +
93U LYS* 3.2 8.9 + - + +
94U ALA* 2.9 29.4 + - + +
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Residues in contact with ARG 91 (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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87U ASN* 3.3 19.0 + - - +
88U ALA* 4.0 4.3 - - - +
89U ALA 3.3 0.6 - - - -
90U LEU* 1.3 79.1 - - - +
92U ALA* 1.3 52.9 + - - +
94U ALA* 3.5 9.7 - - - +
95U GLU* 2.7 67.4 + - + +
115U ARG* 3.4 16.4 - - - +
116U MET* 4.2 9.4 - - + -
119U LEU* 3.5 33.7 - - + +
123U TYR* 4.9 6.7 + - - +
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Residues in contact with ALA 92 (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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70U ILE* 3.6 21.9 - - + +
76U MET* 5.0 0.2 - - - -
88U ALA 3.2 16.5 + - - +
89U ALA 3.8 3.4 - - - +
91U ARG* 1.3 76.2 - - - +
93U LYS* 1.3 60.2 + - - +
95U GLU* 3.8 1.5 - - - +
96U ALA* 2.9 31.2 + - - +
112U LEU* 4.0 22.8 - - + +
116U MET* 4.0 16.6 - - + -
138U PHE* 4.5 5.2 - - + -
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Residues in contact with LYS 93 (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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652 LEU* 4.3 4.5 - - + -
682 SER* 2.8 39.2 + - - +
692 GLN* 4.2 20.3 + - + +
68U PHE* 4.9 11.0 - - - -
69U CYS 3.1 23.8 + - - +
70U ILE* 3.4 32.1 - - - +
89U ALA* 2.9 28.1 + - - +
90U LEU* 3.4 10.8 - - + +
92U ALA* 1.3 75.9 - - - +
94U ALA* 1.3 62.4 - - - +
96U ALA* 3.0 4.5 + - - +
97U ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 94 (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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612 TYR* 4.9 2.6 + - - -
652 LEU* 3.6 20.9 - - + +
90U LEU* 2.9 21.2 + - + +
91U ARG* 3.5 12.1 - - - +
93U LYS* 1.3 76.3 - - - +
95U GLU* 1.3 62.3 + - + +
97U ALA* 3.5 2.6 + - - +
98U GLU* 3.1 23.2 + - - +
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Residues in contact with GLU 95 (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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91U ARG* 2.7 61.0 + - + +
92U ALA* 3.8 7.9 - - - +
93U LYS 3.3 0.2 - - - -
94U ALA* 1.3 73.1 - - + +
96U ALA* 1.3 57.6 + - - +
98U GLU* 3.4 16.3 + - - +
99U PHE* 3.1 23.9 + - - +
107U MET* 3.3 16.4 - - + +
112U LEU* 4.3 4.3 - - + -
115U ARG* 2.9 50.6 + - + +
116U MET* 4.8 3.6 - - - -
119U LEU* 4.7 0.4 - - - -
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Residues in contact with ALA 96 (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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642 GLU* 4.3 1.9 - - - +
70U ILE* 4.2 15.9 - - + +
71U SER* 4.3 17.4 - - - -
74U ILE* 5.6 1.6 - - + -
92U ALA 2.9 17.7 + - - +
93U LYS 3.0 3.6 + - - +
95U GLU* 1.3 74.3 - - - +
97U ALA* 1.3 63.3 + - - +
99U PHE* 3.8 2.4 + - - +
100U ARG* 3.3 21.1 + - - +
107U MET* 2.9 30.1 + - + +
112U LEU* 4.9 2.0 - - + -
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Residues in contact with ALA 97 (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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612 TYR* 3.4 30.1 - - + +
642 GLU* 3.9 15.6 - - + +
652 LEU* 3.7 30.3 - - + +
93U LYS 3.0 14.6 + - - +
94U ALA 3.8 0.2 - - - +
95U GLU 3.3 0.2 - - - -
96U ALA* 1.3 76.4 - - - +
98U GLU* 1.3 65.6 + - - +
100U ARG* 3.3 4.9 + - - +
101U TYR* 3.1 16.1 + - - +
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Residues in contact with GLU 98 (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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612 TYR* 3.7 17.4 - - + +
94U ALA 3.1 17.0 + - - +
95U GLU* 3.7 17.3 - - - +
96U ALA 3.4 0.2 - - - -
97U ALA* 1.3 73.4 - - - +
99U PHE* 1.3 67.3 + - - +
101U TYR* 2.9 17.9 + - + +
102U LYS* 2.9 47.5 + - + +
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Residues in contact with PHE 99 (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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95U GLU 3.1 14.7 + - - +
96U ALA 3.8 5.4 - - - +
98U GLU* 1.3 77.4 + - - +
100U ARG* 1.3 57.0 + - - +
103U TYR* 2.9 55.5 + + + +
105U TYR* 3.4 60.8 - + - -
107U MET* 3.4 41.5 - - + -
108U PRO* 3.9 8.1 - - + -
111U VAL* 4.1 19.5 - - + -
66V HIS* 3.5 21.5 - + - -
70V THR* 4.5 3.6 - - + -
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Residues in contact with ARG 100 (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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602 GLN* 4.3 23.7 + - + +
642 GLU* 3.4 34.6 + - - +
221M THR* 3.3 32.9 + - - +
222M GLN* 5.1 1.6 - - - +
96U ALA 3.3 7.6 + - - +
97U ALA 3.3 6.2 + - - +
98U GLU 3.2 0.8 - - - -
99U PHE* 1.3 80.6 - - - +
101U TYR* 1.3 58.7 + - - +
104U GLY* 3.0 36.2 + - - -
105U TYR* 3.5 29.2 - - - +
106U ASP* 3.8 16.3 + - - +
81V GLN* 4.8 5.7 - - - +
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Residues in contact with TYR 101 (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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542 ALA* 4.9 1.0 + - - +
572 ASP* 3.8 32.8 - - + -
582 ILE* 3.4 37.3 - - + +
612 TYR* 3.9 29.6 - + + -
97U ALA 3.1 11.2 + - - +
98U GLU* 2.9 11.0 + - + +
100U ARG* 1.3 77.8 - - - +
102U LYS* 1.3 71.7 + - + +
81V GLN* 3.2 29.1 + - - +
85V GLN* 3.2 42.7 + - - +
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Residues in contact with LYS 102 (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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98U GLU* 2.9 47.1 + - + +
101U TYR* 1.3 89.9 - - + +
103U TYR* 1.3 101.3 + - + +
81V GLN* 3.7 15.4 - - - +
82V MET* 4.0 12.4 + - + +
85V GLN* 4.2 14.4 - - - +
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Residues in contact with TYR 103 (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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99U PHE* 2.9 52.7 + + + +
102U LYS* 1.3 121.3 + - + +
104U GLY* 1.3 57.2 + - - +
105U TYR* 3.3 21.4 + - + -
66V HIS* 3.5 33.3 - + + +
77V VAL 3.9 1.2 - - - -
78V SER* 2.5 41.7 + - - +
81V GLN* 4.4 1.3 - - - -
82V MET* 4.2 30.7 - - + -
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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
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221M THR* 3.8 23.7 - - - +
100U ARG* 3.0 38.6 + - - -
102U LYS 3.9 0.6 - - - -
103U TYR* 1.3 77.2 - - - +
105U TYR* 1.3 59.0 + - - +
77V VAL* 3.7 18.0 - - - +
81V GLN* 4.4 5.2 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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