Contacts of the helix formed by residues 101 - 126 (chain J) in PDB entry 2YW7
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 THR 101 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J VAL* 3.8 3.5 - - - +
43J VAL 3.9 17.0 - - - +
44J GLY* 5.5 0.4 - - - -
45J PRO* 4.4 14.4 - - + -
100J ASP* 1.3 98.3 + - - +
102J VAL* 1.3 68.3 + - - +
103J GLN* 4.3 7.1 + - - +
104J ALA* 3.4 12.4 + - - +
105J HIS* 3.3 26.3 + - - -
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Residues in contact with VAL 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J VAL* 4.6 13.5 - - + -
43J VAL 5.0 3.3 + - - +
45J PRO* 4.2 22.2 - - + +
46J ASN* 3.4 22.0 - - + +
47J PHE* 5.1 1.1 - - - +
50J VAL* 3.2 35.2 - - + -
101J THR* 1.3 75.6 - - - +
103J GLN* 1.3 79.1 + - + +
104J ALA 2.9 9.5 + - - -
105J HIS 3.3 0.6 + - - +
106J LEU* 3.1 44.9 + - + +
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Residues in contact with GLN 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO* 6.0 3.6 - - - +
45J PRO* 6.1 2.7 - - + -
101J THR* 4.3 5.7 + - - +
102J VAL* 1.3 86.4 - - + +
104J ALA* 1.3 55.3 + - - +
106J LEU* 4.9 6.2 - - - +
107J ALA* 3.4 21.7 + - - +
156J LEU* 3.5 41.9 - - + +
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Residues in contact with ALA 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J VAL* 4.8 6.0 - - + +
100J ASP* 3.2 39.0 - - + +
101J THR* 3.4 10.2 + - - +
102J VAL 2.9 0.6 - - - -
103J GLN* 1.3 79.3 - - - +
105J HIS* 1.3 66.3 + - - +
107J ALA* 3.4 6.1 - - - +
108J ALA* 3.3 17.3 + - - +
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Residues in contact with HIS 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J HIS* 5.3 0.7 - + - -
38J VAL* 3.6 25.6 - - + +
41J ASN* 2.5 32.5 + - + +
42J VAL* 3.3 17.5 - - + -
95J TYR* 2.7 29.8 + + - +
97J VAL* 3.3 36.3 - - + +
98J GLU 2.9 16.8 + - - -
100J ASP* 4.3 4.6 + - + -
101J THR 3.3 13.1 + - - +
102J VAL 4.1 1.6 - - - +
104J ALA* 1.3 74.5 - - - +
106J LEU* 1.3 53.6 + - + +
107J ALA 3.0 3.6 - - - -
108J ALA* 2.8 8.6 + - - +
109J LEU* 2.6 38.1 + - - +
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J VAL* 5.4 0.4 - - + -
50J VAL* 3.7 27.6 - - + -
53J MET* 4.3 12.3 - - + -
54J ILE* 5.2 1.8 - - + -
102J VAL* 3.1 30.4 + - + +
103J GLN* 4.9 4.9 - - - +
105J HIS* 1.3 82.6 - - + +
107J ALA* 1.3 55.3 + - - +
109J LEU* 3.8 15.7 - - + -
110J ASP* 3.1 22.9 + - - +
152J VAL* 3.2 30.8 - - + +
155J HIS* 3.6 35.9 - - + +
156J LEU* 5.5 4.5 - - + +
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Residues in contact with ALA 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J GLN 3.4 16.7 + - - +
104J ALA* 3.4 12.6 + - - +
105J HIS 3.0 0.4 - - - -
106J LEU* 1.3 78.8 - - - +
108J ALA* 1.3 61.7 + - - +
110J ASP* 3.3 18.7 - - - +
111J LEU* 3.8 12.6 + - - +
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95J TYR* 4.0 12.6 - - + +
96J SER* 5.7 0.2 - - - +
97J VAL* 3.6 31.2 - - + -
104J ALA 3.3 4.7 + - - +
105J HIS 2.8 9.1 + - - +
107J ALA* 1.3 73.0 - - - +
109J LEU* 1.3 65.9 + - - +
110J ASP 3.2 0.4 - - - -
111J LEU* 3.2 21.2 + - - +
112J VAL* 3.3 14.2 + - - +
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Residues in contact with LEU 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 5.1 0.7 - - + -
34J THR* 4.6 9.0 - - + -
35J LEU* 3.8 33.9 - - + -
38J VAL* 3.8 36.1 - - + -
54J ILE* 4.7 7.0 - - + -
95J TYR* 4.1 4.1 + - - +
105J HIS 2.6 20.4 + - - +
106J LEU* 3.8 16.6 - - + +
108J ALA* 1.3 72.7 - - - +
110J ASP* 1.3 62.4 + - - +
112J VAL* 3.3 27.5 + - + +
113J TYR* 3.3 31.1 + - + -
148J PHE* 5.1 7.4 - - + -
152J VAL* 4.9 8.3 - - + -
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Residues in contact with ASP 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J LEU 3.1 14.8 + - - +
107J ALA* 3.3 15.3 - - - +
108J ALA 3.2 0.2 - - - -
109J LEU* 1.3 78.2 - - - +
111J LEU* 1.3 60.0 + - - +
113J TYR* 3.5 5.8 + - - +
114J ASN* 3.1 26.8 + - - +
149J GLN* 2.7 33.9 + - - +
152J VAL* 4.4 10.9 - - + +
153J ARG* 3.6 24.6 + - - +
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Residues in contact with LEU 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107J ALA 3.8 15.4 + - - +
108J ALA* 3.2 12.7 + - - +
110J ASP* 1.3 81.3 - - + +
112J VAL* 1.3 68.2 + - - +
114J ASN* 3.4 16.7 + - + +
115J GLY* 3.2 15.1 + - - -
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Residues in contact with VAL 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J ASP* 5.5 5.4 - - - +
31J LEU* 4.6 13.0 - - + -
34J THR* 4.8 7.2 - - + -
92J TRP* 6.0 6.5 - - + +
95J TYR* 4.1 22.4 - - + -
108J ALA 3.3 14.1 + - - +
109J LEU* 3.3 19.9 + - + +
111J LEU* 1.3 77.2 - - - +
113J TYR* 1.3 63.6 + - + +
115J GLY* 2.9 19.4 + - - -
116J VAL* 3.0 25.1 + - + +
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Residues in contact with TYR 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 3.7 32.9 - - + +
35J LEU* 3.4 10.8 - - + +
57J GLN* 2.8 44.4 + - - +
61J VAL* 4.4 0.2 - - - +
109J LEU* 3.3 29.1 + - + +
110J ASP* 3.7 9.6 - - - +
112J VAL* 1.3 79.0 - - + +
114J ASN* 1.3 61.2 + - - +
115J GLY 3.0 1.6 - - - -
116J VAL* 2.7 8.9 + - + -
117J ILE* 2.6 55.9 + - + +
145J LEU* 4.1 15.3 - - + -
148J PHE* 3.2 27.3 - + + -
149J GLN* 3.9 12.8 - - + -
152J VAL* 6.2 1.1 - - + -
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Residues in contact with ASN 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J ASP* 3.1 12.1 + - - +
111J LEU* 3.5 22.9 - - + +
113J TYR* 1.3 76.1 - - - +
115J GLY* 1.3 56.3 + - - +
117J ILE* 4.0 5.0 - - - +
118J GLU* 2.9 49.6 + - - +
149J GLN* 2.9 36.1 + - - +
153J ARG* 3.1 15.7 + - - +
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Residues in contact with GLY 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J LEU 3.2 5.5 + - - -
112J VAL 2.9 10.8 + - - -
113J TYR 2.9 0.4 + - - -
114J ASN* 1.3 75.2 - - - +
116J VAL* 1.3 63.3 + - - -
118J GLU* 3.3 12.9 + - - +
119J ASP* 3.0 30.5 + - - +
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Residues in contact with VAL 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 5.1 0.4 - - - +
27J THR* 4.0 30.7 - - + +
28J TYR* 4.8 7.6 - - + -
31J LEU* 3.8 30.7 - - + -
92J TRP* 6.3 0.7 - - + -
112J VAL* 3.0 21.9 + - + +
113J TYR* 2.7 16.3 + - + +
115J GLY* 1.3 68.0 - - - +
117J ILE* 1.3 64.9 + - + +
119J ASP* 3.2 2.6 + - - +
120J THR* 2.7 40.0 + - - +
145J LEU* 3.8 18.6 - - + -
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Residues in contact with ILE 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J TYR* 2.6 60.1 + - + +
114J ASN* 4.0 5.4 - - - +
116J VAL* 1.3 74.0 - - + +
118J GLU* 1.3 58.0 + - + +
120J THR* 4.2 5.4 - - - -
121J ARG* 2.6 67.0 + - + +
142J ALA* 6.2 0.9 - - - +
145J LEU* 4.1 15.5 - - + -
146J GLU* 3.7 28.7 - - + +
149J GLN* 3.7 22.2 - - + +
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Residues in contact with GLU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J ASN* 2.9 46.6 + - - +
115J GLY* 3.3 9.8 + - - +
117J ILE* 1.3 77.5 - - + +
119J ASP* 1.3 53.3 - - - +
121J ARG* 3.3 8.9 - - - +
122J LYS* 2.7 63.3 + - - +
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Residues in contact with ASP 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 4.6 4.7 - - - +
27J THR* 5.5 8.2 + - + +
91J THR* 4.5 11.8 + - - -
92J TRP* 5.0 9.4 - - - -
115J GLY* 3.0 17.8 + - - +
116J VAL* 3.8 3.6 - - - +
118J GLU* 1.3 74.7 - - - +
120J THR* 1.3 57.7 + - - +
122J LYS* 3.2 28.2 + - - +
123J SER* 2.5 38.1 + - - -
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Residues in contact with THR 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 3.3 33.2 + - - +
28J TYR* 4.0 9.6 - - - +
116J VAL* 2.7 40.3 + - - +
117J ILE* 3.5 6.5 - - - -
119J ASP* 1.3 70.5 - - - +
121J ARG* 1.3 65.8 + - - +
123J SER* 2.9 3.6 + - - -
124J ILE* 2.8 26.9 + - + +
138J LEU* 4.4 13.9 - - + +
142J ALA* 4.4 27.8 - - + +
145J LEU* 3.9 5.5 - - + +
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Residues in contact with ARG 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ARG* 3.9 2.4 - - - +
75C LEU* 3.7 20.0 - - - +
131C ASP* 4.0 15.7 + - - +
133C VAL* 5.6 7.9 - - + +
117J ILE* 2.6 39.3 + - + +
118J GLU* 3.3 7.4 - - - +
120J THR* 1.3 72.6 - - - +
122J LYS* 1.3 61.2 + - + +
124J ILE* 3.3 13.8 + - - +
125J GLU* 3.2 30.6 + - - +
142J ALA* 5.5 2.4 - - + +
146J GLU* 2.7 42.9 + - - +
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Residues in contact with LYS 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118J GLU* 2.7 45.3 + - - +
119J ASP* 3.2 31.6 + - - +
120J THR 3.0 0.2 - - - -
121J ARG* 1.3 71.0 - - + +
123J SER* 1.3 65.4 + - - +
125J GLU* 3.0 23.5 + - - +
126J LYS* 3.2 19.6 + - + +
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Residues in contact with SER 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 3.5 31.4 + - - +
24J GLN* 3.9 18.2 + - - -
119J ASP 2.5 19.5 + - - -
120J THR 3.5 3.4 - - - -
122J LYS* 1.3 72.3 - - - +
124J ILE* 1.3 62.1 - - - +
126J LYS* 3.3 24.9 + - - +
127J LEU* 3.5 13.5 + - - +
138J LEU* 3.5 15.6 - - - +
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Residues in contact with ILE 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU* 4.1 13.2 - - + -
133C VAL* 4.3 5.8 - - + -
120J THR* 2.8 18.9 + - + +
121J ARG* 3.3 14.4 - - - +
123J SER* 1.3 72.1 - - - +
125J GLU* 1.3 67.2 + - + +
126J LYS 3.0 1.6 - - - -
127J LEU* 3.0 13.9 + - - +
135J GLN* 3.1 36.0 + - + +
138J LEU* 3.7 23.1 - - + -
139J ILE* 3.5 48.5 - - + +
142J ALA* 3.7 19.7 - - + -
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Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LEU 5.6 2.1 - - - +
132C LEU* 5.1 15.5 - - + -
121J ARG* 3.2 16.4 + - - +
122J LYS* 3.0 13.4 + - - +
124J ILE* 1.3 80.8 - - + +
126J LYS* 1.3 59.9 + - + +
127J LEU 3.5 0.3 + - - -
128J GLU* 4.1 13.1 + - - +
129J ASP* 5.1 3.1 - - - +
135J GLN* 5.1 0.4 - - - +
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Residues in contact with LYS 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J LEU* 3.4 38.7 - - + +
23J LYS* 5.5 5.9 - - - +
122J LYS* 3.4 18.4 - - + +
123J SER* 3.5 11.9 - - - +
124J ILE 3.0 0.8 - - - -
125J GLU* 1.3 80.2 - - + +
127J LEU* 1.3 59.1 + - - +
128J GLU 3.7 0.4 - - - -
129J ASP* 4.7 4.2 + - - +
130J LEU* 4.2 18.4 - - - +
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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