Contacts of the helix formed by residues 82 - 111 (chain L) in PDB entry 2X17
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 SER 82 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.2 9.8 + - - -
80L TRP* 3.4 1.4 - - - +
81L GLU* 1.3 79.6 - - - +
83L PRO* 1.4 71.8 - - - +
84L LEU* 3.7 12.6 + - - +
85L LYS* 3.1 27.7 + - - +
86L ALA* 2.9 26.9 + - - +
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Residues in contact with PRO 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.6 6.0 - - - +
31L PHE* 3.6 30.3 - - + -
34L LEU* 4.2 9.2 - - + -
36L LEU* 4.1 16.8 - - + -
39L PHE* 5.0 0.7 - - + -
82L SER* 1.4 87.6 - - - +
84L LEU* 1.3 60.1 - - - +
86L ALA* 3.4 3.6 + - + +
87L PHE* 3.1 21.3 + - - -
141L LEU* 3.4 29.2 - - + +
151L LEU* 4.3 17.5 - - + -
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Residues in contact with LEU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82L SER* 3.1 11.6 + - - +
83L PRO* 1.3 80.4 - - - +
85L LYS* 1.3 62.0 + - + +
87L PHE* 3.4 3.8 + - - +
88L GLU* 3.1 46.5 + - - +
138L LEU* 3.8 7.6 - - + +
141L LEU* 3.7 27.4 - - + +
142L LYS* 3.5 45.5 - - + +
145L LYS* 5.1 15.0 - - + -
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Residues in contact with LYS 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L TRP* 3.9 7.5 - - + -
81L GLU* 4.4 26.9 - - + +
82L SER* 3.1 29.8 + - - +
84L LEU* 1.3 81.6 - - + +
86L ALA* 1.3 60.2 + - - +
87L PHE 3.3 0.2 - - - -
88L GLU* 3.3 28.1 + - + +
89L ALA* 3.1 26.3 + - - +
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Residues in contact with ALA 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L MET* 3.4 20.3 - - - +
30L TYR* 3.8 25.1 - - + -
31L PHE* 3.9 14.1 - - + -
80L TRP* 3.8 21.0 - - + +
82L SER 2.9 16.3 + - - +
83L PRO 3.6 6.3 - - - +
84L LEU 3.3 0.2 - - - -
85L LYS* 1.3 77.7 - - - +
87L PHE* 1.3 57.6 + - - +
89L ALA* 3.6 1.4 + - - +
90L ALA 3.3 17.0 + - - -
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Residues in contact with PHE 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L PHE* 3.9 8.3 - + - -
39L PHE* 3.7 28.7 - + - -
42L TRP* 4.2 14.8 - + + -
43L MET* 3.7 29.2 - - + -
83L PRO 3.1 15.4 + - - +
84L LEU 3.9 2.9 - - - +
85L LYS 3.3 0.2 - - - -
86L ALA* 1.3 73.0 - - - +
88L GLU* 1.3 59.9 + - - +
89L ALA 3.3 0.7 - - - -
90L ALA* 3.7 4.2 - - + +
91L TYR* 3.0 23.7 + - - +
134L VAL* 3.8 35.4 - - + +
137L ILE* 3.7 39.5 - - + -
138L LEU* 3.4 19.4 - - - +
141L LEU* 3.7 24.7 - - + -
158L LEU* 4.9 1.1 - - + -
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Residues in contact with GLU 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84L LEU* 3.1 37.7 + - - +
85L LYS* 3.3 43.5 + - + +
87L PHE* 1.3 78.4 - - - +
89L ALA* 1.3 55.9 + - - +
91L TYR* 3.8 2.4 + - - +
92L GLU* 3.2 27.5 + - - +
138L LEU* 3.7 22.9 - - + -
142L LYS* 4.2 14.0 - - - -
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Residues in contact with ALA 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L LEU* 5.2 0.7 - - - +
27L MET* 4.2 6.8 - - + +
80L TRP* 3.4 30.7 - - + +
85L LYS 3.1 11.9 + - - +
86L ALA 3.9 2.9 - - - +
87L PHE 3.3 0.2 - - - -
88L GLU* 1.3 74.4 - - - +
90L ALA* 1.3 59.4 + - - +
92L GLU* 3.5 13.7 - - - +
93L HIS* 3.1 27.0 + - - +
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Residues in contact with ALA 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L TYR* 3.7 21.4 + - + -
27L MET* 3.8 18.4 - - + +
43L MET* 4.7 5.6 - - + -
86L ALA 3.3 14.9 + - - +
87L PHE* 3.7 9.6 - - - +
88L GLU 3.3 0.4 - - - -
89L ALA* 1.3 77.4 - - - +
91L TYR* 1.3 58.9 + - - +
93L HIS* 3.2 7.0 + - - +
94L GLU* 2.9 30.7 + - - +
134L VAL* 4.1 12.8 - - + -
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Residues in contact with TYR 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87L PHE 3.0 18.6 + - - +
88L GLU 4.2 2.7 - - - +
90L ALA* 1.3 72.9 - - - +
92L GLU* 1.3 65.1 + - - +
94L GLU* 3.5 4.1 + - + +
95L LYS* 3.3 51.8 + - + +
131L GLU* 3.7 39.5 + - + -
134L VAL* 3.7 12.0 - - + +
135L LYS* 3.6 46.6 - - + +
138L LEU* 3.6 21.8 - - + -
1N MET 5.8 1.6 + - - -
65N ASN* 4.9 9.9 + - - +
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Residues in contact with GLU 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88L GLU 3.2 20.1 + - - +
89L ALA* 3.5 13.6 - - - +
91L TYR* 1.3 78.7 - - - +
93L HIS* 1.3 56.0 + - - +
95L LYS* 3.4 17.0 + - - +
96L PHE* 3.1 23.0 + - - +
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Residues in contact with HIS 93 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ARG 4.7 0.2 + - - -
19L TYR* 3.8 33.7 - + - -
20L SER* 3.2 29.1 + - - -
23L LEU* 3.6 24.8 - - + +
24L TYR* 4.6 9.2 - - - +
89L ALA 3.1 17.9 + - - +
90L ALA* 3.2 6.0 + - - +
92L GLU* 1.3 73.4 - - - +
94L GLU* 1.3 60.6 + - - +
96L PHE* 3.1 32.1 + + - +
97L ILE* 2.9 36.1 + - + +
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Residues in contact with GLU 94 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L SER* 5.5 0.5 + - - -
24L TYR* 2.6 32.2 + - - +
50L GLU* 4.0 3.3 - - - +
90L ALA 2.9 14.1 + - - +
91L TYR* 3.7 9.2 - - - +
92L GLU 3.3 0.4 - - - -
93L HIS* 1.3 78.2 - - - +
95L LYS* 1.3 54.5 + - - +
97L ILE* 4.6 8.0 - - - +
98L SER* 2.8 36.1 + - - -
127L GLN* 3.0 27.6 + - - +
130L GLU* 3.0 38.4 - - - +
131L GLU* 4.0 16.9 + - + -
134L VAL* 4.1 19.7 - - + -
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Residues in contact with LYS 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L TYR* 3.3 44.7 + - + +
92L GLU* 3.6 16.6 - - - +
93L HIS 3.2 0.4 - - - -
94L GLU* 1.3 75.5 - - - +
96L PHE* 1.3 59.1 + - - +
98L SER* 3.9 5.8 - - - -
99L LYS* 3.1 27.4 + - - +
131L GLU* 3.6 21.8 - - - +
1N MET 6.3 0.9 - - - +
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Residues in contact with PHE 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ARG* 4.0 34.3 - - + -
19L TYR* 6.2 0.2 - + - -
92L GLU 3.1 13.5 + - - +
93L HIS* 3.1 40.0 + + - +
95L LYS* 1.3 75.2 - - - +
97L ILE* 1.3 70.8 + - + +
99L LYS* 3.3 28.5 + - + +
100L SER* 3.1 24.9 + - - -
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Residues in contact with ILE 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLN* 3.8 7.2 - - - +
16L ARG* 4.1 24.9 - - + +
17L GLU* 3.7 19.5 - - - +
20L SER* 3.4 26.2 - - - +
50L GLU* 5.6 1.6 - - - +
93L HIS* 2.9 34.0 + - + +
94L GLU* 4.0 11.4 - - - +
96L PHE* 1.3 82.2 - - + +
98L SER* 1.3 63.5 + - - +
100L SER* 2.8 17.6 + - - +
101L ILE* 3.0 19.7 + - + +
127L GLN* 3.5 27.8 - - - +
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Residues in contact with SER 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94L GLU 2.8 17.8 + - - -
95L LYS* 3.9 5.2 - - - -
97L ILE* 1.3 76.2 - - - +
99L LYS* 1.3 56.4 - - - +
101L ILE* 3.3 5.4 + - - +
102L TYR* 3.0 50.5 + - - -
127L GLN* 3.1 30.9 + - - +
131L GLU* 2.7 28.3 + - - -
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Residues in contact with LYS 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L LYS 3.1 18.8 + - - +
96L PHE* 3.3 31.2 - - + +
97L ILE 3.2 0.4 - - - -
98L SER* 1.3 77.0 - - - +
100L SER* 1.3 60.0 + - - +
102L TYR* 3.1 17.5 + - - +
103L GLU* 3.0 50.0 + - + +
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Residues in contact with SER 100 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLN* 3.0 22.1 + - - -
16L ARG* 3.8 27.3 + - - -
96L PHE* 3.1 17.7 + - - -
97L ILE* 2.8 19.9 + - - -
99L LYS* 1.3 75.0 - - - +
101L ILE* 1.3 62.7 + - - +
103L GLU* 3.7 17.6 - - - +
104L LEU* 3.3 27.5 + - - +
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Residues in contact with ILE 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L GLN* 3.8 33.7 - - + +
17L GLU* 4.5 2.7 - - - +
57L PHE* 4.0 15.0 - - + -
97L ILE* 3.0 26.6 + - + +
98L SER* 3.5 11.9 - - - +
100L SER* 1.3 76.5 - - - +
102L TYR* 1.3 60.6 + - + +
104L LEU* 3.4 7.8 + - + +
105L ALA* 3.0 25.5 + - - +
120L LEU* 4.4 8.8 - - + +
123L PHE* 4.1 26.0 - - + -
124L ILE* 3.8 30.3 - - + +
127L GLN* 4.5 6.1 - - + -
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Residues in contact with TYR 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L SER* 3.0 41.1 + - - -
99L LYS* 3.1 13.0 + - - +
101L ILE* 1.3 76.4 - - + +
103L GLU* 1.3 58.0 + - + +
105L ALA* 3.2 6.8 + - - +
106L ALA* 2.8 30.2 + - - +
124L ILE* 4.5 13.5 - - + -
127L GLN* 6.0 0.8 - - + +
131L GLU* 4.8 0.5 + - - -
64N ARG* 3.5 15.8 + - - -
112N LYS 5.8 1.8 - - - -
113N ASP* 5.3 0.8 + - - -
114N TYR* 3.6 50.0 - + + -
115N SER* 2.6 28.1 + - - -
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Residues in contact with GLU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L ARG* 5.0 7.1 + - - -
99L LYS* 3.0 44.2 + - + +
100L SER* 3.7 18.1 - - - +
101L ILE 3.3 0.2 - - - -
102L TYR* 1.3 76.8 - - + +
104L LEU* 1.3 56.2 + - + +
106L ALA* 3.4 6.9 + - - +
107L LEU* 2.9 32.0 + - - +
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Residues in contact with LEU 104 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L MET* 4.6 9.1 - - - +
9L ALA* 3.7 40.2 - - + +
10L LEU* 4.0 17.3 - - + +
13L GLN* 3.7 35.0 - - + +
16L ARG* 5.2 2.2 - - - +
57L PHE* 4.4 2.9 - - + -
100L SER 3.3 17.8 + - - +
101L ILE* 3.6 10.1 - - + +
102L TYR 3.3 0.2 - - - -
103L GLU* 1.3 78.1 - - - +
105L ALA* 1.3 58.5 + - - +
107L LEU* 3.2 7.3 + - + +
108L ALA* 2.9 30.0 + - - +
120L LEU* 3.6 26.5 - - + +
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L ILE 3.0 14.6 + - - +
102L TYR* 3.5 10.3 - - - +
104L LEU* 1.3 74.9 - - - +
106L ALA* 1.3 61.8 + - - +
108L ALA* 3.6 0.6 + - - -
109L GLU* 3.3 29.5 + - - +
117L ARG* 3.6 20.6 - - - +
120L LEU* 3.7 11.6 - - + +
124L ILE* 4.5 8.1 - - + -
114N TYR* 3.9 24.7 - - + -
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Residues in contact with ALA 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L TYR 2.8 15.0 + - - +
103L GLU* 3.7 7.9 - - - +
105L ALA* 1.3 75.2 - - - +
107L LEU* 1.3 62.0 + - - +
109L GLU* 3.7 6.2 + - - +
110L GLU* 3.3 22.9 + - - +
114N TYR* 3.4 20.6 + - + +
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Residues in contact with LEU 107 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L ARG* 4.6 11.9 - - + +
6L MET* 3.6 24.4 - - + +
9L ALA* 3.8 28.7 - - + -
103L GLU 2.9 18.5 + - - +
104L LEU* 3.2 8.7 + - - +
106L ALA* 1.3 76.9 - - - +
108L ALA* 1.3 64.6 + - - +
110L GLU* 3.3 19.4 + - - +
111L GLU* 3.3 23.8 + - - +
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Residues in contact with ALA 108 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L MET* 3.6 10.5 - - + +
104L LEU 2.9 16.3 + - - +
105L ALA* 3.9 4.0 - - - +
106L ALA 3.4 0.2 - - - -
107L LEU* 1.3 77.9 - - - +
109L GLU* 1.3 56.1 + - - +
111L GLU 3.5 0.9 + - - -
112L LYS* 3.1 5.7 + - - -
113L ASP* 2.8 49.9 + - - +
116L THR* 4.1 12.3 - - + -
117L ARG* 3.7 24.2 - - + +
120L LEU* 4.6 0.2 - - + -
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Residues in contact with GLU 109 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L ALA 3.3 16.2 + - - +
106L ALA* 4.0 5.1 - - - +
107L LEU 3.3 0.2 - - - -
108L ALA* 1.3 74.9 - - - +
110L GLU* 1.3 65.0 + - - +
112L LYS* 3.4 16.6 + - - +
117L ARG* 3.0 35.8 + - + +
114N TYR* 3.3 28.5 + - - -
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Residues in contact with GLU 110 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106L ALA 3.3 15.2 + - - +
107L LEU* 3.6 20.9 - - - +
108L ALA 3.3 0.4 - - - -
109L GLU* 1.3 80.5 - - - +
111L GLU* 1.3 61.0 + - + +
112L LYS* 3.2 5.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L SER* 2.7 35.7 + - - -
5L ARG* 3.4 24.7 - - - +
6L MET* 3.4 26.2 + - - +
107L LEU* 3.3 14.5 + - - +
108L ALA 3.5 3.6 + - - +
110L GLU* 1.3 78.9 - - + +
112L LYS* 1.3 69.0 + - - +
113L ASP* 3.4 11.7 + - + +
----------------------------------------------------------
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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