Contacts of the helix formed by residues 82 - 111 (chain J) 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 J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.3 9.1 + - - -
80J TRP* 3.3 1.6 - - - +
81J GLU* 1.3 79.8 - - - +
83J PRO* 1.4 69.7 - - - +
84J LEU* 3.5 12.5 + - - +
85J LYS* 3.1 26.1 + - - +
86J ALA* 2.9 27.9 + - - +
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Residues in contact with PRO 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J TYR* 3.8 7.4 - - + +
31J PHE* 3.7 30.1 - - + -
34J LEU* 4.3 9.2 - - + -
36J LEU* 4.2 17.0 - - + -
39J PHE* 5.0 1.1 - - + -
82J SER* 1.4 87.4 - - - +
84J LEU* 1.3 59.8 + - - +
86J ALA* 3.5 2.0 + - + +
87J PHE* 3.2 21.3 + - - -
141J LEU* 3.4 27.9 - - + +
151J LEU* 4.3 18.2 - - + -
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Residues in contact with LEU 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J SER* 3.5 9.8 + - - +
83J PRO* 1.3 79.7 - - - +
85J LYS* 1.3 61.5 + - + +
87J PHE* 3.3 4.0 + - - +
88J GLU* 3.0 48.0 + - - +
138J LEU* 3.9 9.8 - - + +
141J LEU* 3.8 26.8 - - + +
142J LYS* 3.7 44.0 - - + +
145J LYS* 5.2 13.2 - - + -
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Residues in contact with LYS 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80J TRP* 3.7 6.7 - - + -
81J GLU* 4.1 33.0 - - + +
82J SER* 3.1 26.2 + - - +
84J LEU* 1.3 81.3 - - + +
86J ALA* 1.3 60.0 + - - +
88J GLU* 3.4 29.0 + - - +
89J ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 86 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J MET* 3.6 15.0 - - + +
30J TYR* 4.0 10.1 - - + -
31J PHE* 3.9 22.2 - - + -
80J TRP* 3.8 27.5 - - + +
82J SER 2.9 13.8 + - - +
83J PRO 3.6 7.0 - - - +
84J LEU 3.2 0.2 - - - -
85J LYS* 1.3 78.7 - - - +
87J PHE* 1.3 56.4 + - - +
89J ALA* 3.6 0.7 + - - +
90J ALA* 3.1 24.8 + - - +
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Residues in contact with PHE 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J PHE* 3.7 13.0 - + - -
39J PHE* 3.6 30.1 - + - -
42J TRP* 4.4 12.3 - + - -
43J MET* 3.7 25.1 - - + -
83J PRO 3.2 22.4 + - - +
84J LEU 3.8 3.8 - - - +
86J ALA* 1.3 77.2 - - - +
88J GLU* 1.3 60.3 + - - +
89J ALA 3.3 0.2 - - - -
90J ALA* 3.6 4.4 - - + +
91J TYR* 2.8 31.0 + - - +
134J VAL* 3.8 32.3 - - + +
137J ILE* 3.7 39.7 - - + -
138J LEU* 3.4 12.9 - - + +
141J LEU* 3.6 16.2 - - + -
158J LEU* 4.8 1.6 - - + -
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Residues in contact with GLU 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J LEU* 3.0 40.0 + - - +
85J LYS* 3.4 38.5 + - + +
86J ALA 3.4 0.2 - - - -
87J PHE* 1.3 78.1 - - - +
89J ALA* 1.3 56.5 + - - +
91J TYR* 4.0 2.1 - - - +
92J GLU* 3.1 29.4 + - - +
138J LEU* 3.7 22.7 - - + -
142J LYS* 4.4 11.7 - - - -
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Residues in contact with ALA 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J LEU* 5.1 0.5 - - - +
27J MET* 4.3 5.4 - - + +
80J TRP* 3.3 31.9 - - + +
85J LYS 3.0 12.6 + - - +
86J ALA 3.8 2.2 - - - +
88J GLU* 1.3 75.4 - - - +
90J ALA* 1.3 61.0 + - - +
92J GLU* 3.9 10.6 - - - +
93J HIS* 3.1 27.7 + - - +
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Residues in contact with ALA 90 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J TYR* 3.7 17.2 + - + -
27J MET* 3.8 22.6 - - + +
43J MET* 4.7 5.6 - - + -
86J ALA 3.1 18.4 + - - +
87J PHE* 3.6 10.5 - - + +
88J GLU 3.3 0.2 - - - -
89J ALA* 1.3 77.6 - - - +
91J TYR* 1.3 57.8 + - - +
93J HIS* 3.3 6.4 + - - +
94J GLU* 2.9 31.2 + - - +
134J VAL* 4.1 11.0 - - + -
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Residues in contact with TYR 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 3.8 21.2 - - + +
65G ASN* 4.9 5.2 - - - +
87J PHE 2.8 17.7 + - - +
88J GLU* 4.1 2.7 - - - +
90J ALA* 1.3 74.3 - - - +
92J GLU* 1.3 63.8 + - - +
94J GLU* 3.4 3.6 + - + +
95J LYS* 3.2 47.7 + - + +
131J GLU* 3.8 40.4 + - + -
134J VAL* 3.8 11.8 - - + +
135J LYS* 3.6 46.2 - - + +
138J LEU* 3.7 21.3 - - + -
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Residues in contact with GLU 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J GLU 3.1 20.3 + - - +
89J ALA* 3.9 9.8 - - - +
91J TYR* 1.3 77.4 - - - +
93J HIS* 1.3 58.1 + - - +
95J LYS* 3.3 19.2 + - - +
96J PHE* 3.1 23.0 + - - +
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Residues in contact with HIS 93 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG 5.5 0.2 - - - -
19J TYR* 3.7 32.4 - + - -
20J SER* 3.5 22.5 + - - -
23J LEU* 3.6 25.8 - - + +
24J TYR* 4.7 9.4 - - - +
89J ALA 3.1 19.3 + - - +
90J ALA 3.6 4.7 - - - +
91J TYR 3.3 0.2 - - - -
92J GLU* 1.3 76.2 - - - +
94J GLU* 1.3 59.8 + - - +
96J PHE* 3.2 32.2 + + - +
97J ILE* 3.0 36.8 + - + +
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Residues in contact with GLU 94 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J SER* 5.8 0.3 - - - -
24J TYR* 2.6 33.3 + - - +
50J GLU* 4.0 3.8 - - - +
90J ALA 2.9 14.3 + - - +
91J TYR* 3.6 9.0 - - + +
92J GLU 3.3 0.4 - - - -
93J HIS* 1.3 77.2 - - - +
95J LYS* 1.3 57.6 + - - +
97J ILE* 3.4 7.1 + - - +
98J SER* 3.1 31.2 + - - -
127J GLN* 2.9 29.8 + - - +
130J GLU* 3.1 38.6 - - - +
131J GLU* 3.7 16.1 + - + +
134J VAL* 4.0 18.4 - - + -
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Residues in contact with LYS 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 3.5 32.9 - - + +
91J TYR* 3.2 38.0 + - + +
92J GLU* 3.6 18.3 - - - +
93J HIS 3.2 0.2 - - - -
94J GLU* 1.3 75.0 - - - +
96J PHE* 1.3 58.9 + - - +
98J SER* 3.7 1.6 + - - -
99J LYS* 3.1 28.2 + - - +
102J TYR* 5.8 0.2 - - - -
131J GLU* 3.9 26.0 - - - +
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Residues in contact with PHE 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG* 4.1 34.1 - - + -
19J TYR* 6.2 0.4 - + - -
92J GLU 3.1 12.6 + - - +
93J HIS* 3.2 38.5 + + - +
95J LYS* 1.3 74.2 - - - +
97J ILE* 1.3 67.9 + - + +
99J LYS* 3.4 9.8 - - + +
100J SER* 3.2 22.6 + - - -
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Residues in contact with ILE 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLN* 4.0 15.3 - - - +
16J ARG* 4.1 25.4 - - + +
17J GLU* 4.1 10.5 - - - +
20J SER* 3.4 26.0 - - - +
50J GLU* 5.7 1.3 - - - +
93J HIS* 3.0 32.7 + - + +
94J GLU* 3.8 13.2 - - - +
95J LYS 3.4 0.4 - - - -
96J PHE* 1.3 83.5 - - + +
98J SER* 1.3 63.3 + - - +
100J SER* 2.7 18.5 + - - +
101J ILE* 3.0 18.6 + - + +
127J GLN* 3.5 27.8 - - - +
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Residues in contact with SER 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94J GLU 3.1 12.2 + - - -
95J LYS* 3.9 4.5 - - - -
96J PHE 3.4 0.2 - - - -
97J ILE* 1.3 75.1 - - - +
99J LYS* 1.3 53.0 + - - +
101J ILE* 3.2 10.2 + - - +
102J TYR* 2.8 59.4 + - - -
127J GLN* 3.2 25.0 + - - +
131J GLU* 2.7 28.1 + - - -
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Residues in contact with LYS 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J LYS 3.1 20.2 + - - +
96J PHE* 3.4 12.8 - - + +
97J ILE 3.2 0.2 - - - -
98J SER* 1.3 76.5 - - - +
100J SER* 1.3 56.5 + - - +
102J TYR* 3.2 18.0 + - + +
103J GLU* 2.9 51.7 + - - +
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Residues in contact with SER 100 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLN* 2.9 22.9 + - - -
16J ARG* 3.7 29.2 + - - -
96J PHE* 3.2 13.7 + - - -
97J ILE* 2.7 24.9 + - - -
99J LYS* 1.3 75.4 - - - +
101J ILE* 1.3 59.0 + - - +
103J GLU* 3.9 13.0 - - - +
104J LEU* 3.3 30.3 + - - +
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Residues in contact with ILE 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLN* 3.7 33.2 - - + +
17J GLU* 4.5 4.3 - - - +
57J PHE* 4.1 13.9 - - + -
97J ILE* 3.0 26.9 + - + +
98J SER* 3.5 10.5 - - - +
100J SER* 1.3 76.9 - - - +
102J TYR* 1.3 61.2 + - + +
103J GLU 3.3 0.2 - - - -
104J LEU* 3.2 5.5 + - + +
105J ALA* 2.9 27.0 + - - +
120J LEU* 4.4 12.8 - - + +
123J PHE* 4.1 25.4 - - + -
124J ILE* 3.8 30.1 - - + +
127J GLN* 4.8 5.4 - - + -
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Residues in contact with TYR 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G ARG* 3.2 19.5 + - - -
112G LYS 5.5 2.9 - - - +
113G ASP* 5.3 1.1 + - - -
114G TYR* 3.5 54.8 - + + -
115G SER* 2.7 27.9 + - - -
95J LYS 5.8 0.2 - - - -
98J SER* 2.8 43.6 + - - -
99J LYS* 3.2 17.7 + - + +
101J ILE* 1.3 78.5 - - + +
103J GLU* 1.3 57.6 + - + +
105J ALA* 3.3 2.4 + - - -
106J ALA* 3.0 24.6 + - - +
124J ILE* 4.6 11.7 - - + -
131J GLU* 5.0 0.5 + - - -
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Residues in contact with GLU 103 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG* 5.6 3.5 + - - -
99J LYS* 2.9 41.5 + - + +
100J SER* 4.1 9.7 - - - +
102J TYR* 1.3 74.8 - - + +
104J LEU* 1.3 61.1 + - - +
106J ALA* 3.5 7.6 + - - +
107J LEU* 3.0 27.5 + - - +
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Residues in contact with LEU 104 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J MET* 4.2 11.6 - - - +
9J ALA* 3.7 36.1 - - + +
10J LEU* 4.1 15.9 - - + -
13J GLN* 3.6 35.7 - - + -
16J ARG* 5.2 1.3 - - - +
57J PHE* 4.4 4.3 - - + -
100J SER 3.3 17.5 + - - +
101J ILE* 3.2 10.0 + - + +
103J GLU* 1.3 76.7 - - - +
105J ALA* 1.3 58.2 + - - +
107J LEU* 3.4 6.5 + - + +
108J ALA* 3.0 27.9 + - - +
120J LEU* 3.7 28.1 - - + +
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Residues in contact with ALA 105 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G TYR* 3.8 27.6 - - + -
101J ILE 2.9 13.8 + - - +
102J TYR* 3.3 10.1 + - - +
104J LEU* 1.3 77.1 - - - +
106J ALA* 1.3 56.2 + - - +
108J ALA* 3.4 2.6 + - - +
109J GLU* 3.1 32.6 + - - +
117J ARG* 3.8 16.9 - - - +
120J LEU* 3.8 10.7 - - + +
124J ILE* 4.5 9.2 - - + -
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Residues in contact with ALA 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G LYS* 5.6 10.8 - - + +
114G TYR* 3.3 18.1 + - + +
102J TYR 3.0 14.9 + - - +
103J GLU* 3.8 8.5 - - - +
104J LEU 3.3 0.2 - - - -
105J ALA* 1.3 73.6 - - - +
107J LEU* 1.3 60.1 + - - +
109J GLU* 4.1 4.6 - - - +
110J GLU* 3.2 29.7 + - - +
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Residues in contact with LEU 107 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ARG* 4.5 23.3 - - + +
6J MET* 3.8 19.6 - - + +
9J ALA* 3.7 30.1 - - + -
103J GLU 3.0 17.9 + - - +
104J LEU* 3.7 8.1 - - + +
105J ALA 3.3 0.2 - - - -
106J ALA* 1.3 75.8 - - - +
108J ALA* 1.3 58.9 + - - +
110J GLU* 4.0 16.2 - - - +
111J GLU* 3.2 43.9 + - + +
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J MET* 3.7 15.9 - - + +
104J LEU 3.0 15.8 + - - +
105J ALA* 3.7 6.3 - - - +
106J ALA 3.3 0.2 - - - -
107J LEU* 1.3 76.9 - - - +
109J GLU* 1.3 58.9 + - - +
111J GLU 3.6 0.3 + - - -
112J LYS 3.1 6.9 + - - -
113J ASP* 2.8 48.0 + - - +
116J THR* 4.3 6.3 - - + -
117J ARG* 3.8 22.2 - - + +
120J LEU* 4.7 0.2 - - + -
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Residues in contact with GLU 109 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G GLU* 6.0 1.6 - - - +
114G TYR* 2.9 32.3 + - - -
105J ALA 3.1 17.3 + - - +
106J ALA* 4.1 4.5 - - - +
107J LEU 3.4 0.2 - - - -
108J ALA* 1.3 75.4 - - - +
110J GLU* 1.3 61.9 + - - +
112J LYS* 3.5 15.4 + - - +
117J ARG* 3.3 34.3 + - + +
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Residues in contact with GLU 110 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J ALA 3.2 19.2 + - - +
107J LEU* 4.0 19.9 - - - +
109J GLU* 1.3 78.2 - - - +
111J GLU* 1.3 59.5 + - + +
112J LYS* 3.2 10.5 + - - +
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Residues in contact with GLU 111 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J SER* 2.7 35.4 + - - -
5J ARG* 4.0 21.4 - - - +
6J MET* 4.0 15.1 - - - +
107J LEU* 3.2 28.5 + - + +
108J ALA 4.3 1.8 - - - +
109J GLU 3.4 0.2 - - - -
110J GLU* 1.3 78.6 - - + +
112J LYS* 1.3 69.2 + - - +
113J ASP* 3.1 9.8 + - + +
----------------------------------------------------------
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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