Contacts of the helix formed by residues 108 - 133 (chain B) in PDB entry 2ITB
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 108 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 1.3 89.3 - - + +
109B VAL* 1.3 67.2 + - + +
110B LYS 3.2 3.4 - - - -
111B LEU* 3.0 8.2 + - + +
112B VAL* 2.9 26.5 + - - +
165B TYR* 4.0 35.9 - - + +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 3.5 48.9 - - + +
106B HIS* 3.0 26.6 + - + +
107B GLU 5.0 0.9 - - - -
108B PRO* 1.3 83.0 - - + +
110B LYS* 1.3 65.7 + - - +
112B VAL* 3.4 10.8 - - + +
113B ASP* 2.9 30.1 + - - -
165B TYR 5.9 0.4 - - - +
170B ASP* 6.1 1.1 - - - +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS* 4.9 14.5 - - - +
52B TYR* 4.0 7.9 - - - +
103B VAL* 3.6 14.2 - - + +
104B ARG 3.3 27.1 + - - +
105B ALA* 4.0 14.1 + - - +
106B HIS 2.8 20.6 + - - +
107B GLU* 3.4 25.8 + - + +
109B VAL* 1.3 74.5 - - - +
111B LEU* 1.3 58.0 + - - +
113B ASP* 3.3 2.9 + - - +
114B THR* 2.8 34.3 + - - +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 5.3 1.6 - - + -
52B TYR* 3.5 38.8 - - + +
55B HIS* 4.0 14.8 - - + +
58B LEU* 4.1 10.1 - - + -
107B GLU* 3.3 15.8 + - - +
108B PRO* 3.0 7.8 + - + +
110B LYS* 1.3 77.1 - - - +
112B VAL* 1.3 66.7 + - - +
114B THR* 4.1 7.9 - - + -
115B LEU* 3.0 45.3 + - + +
165B TYR* 3.5 43.1 - - + +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 4.4 8.1 - - - +
108B PRO 2.9 17.6 + - - +
109B VAL* 3.4 17.7 - - + +
111B LEU* 1.3 77.3 - - - +
113B ASP* 1.3 57.1 + - - +
115B LEU* 3.3 7.4 + - - +
116B VAL* 3.0 35.0 + - + +
162B ALA* 4.5 3.0 - - - +
165B TYR* 3.7 36.1 - - + +
166B GLY* 4.2 4.5 - - - +
170B ASP* 5.3 2.9 - - + +
171B ILE* 3.7 24.9 - - + -
174B CYS* 4.1 20.4 - - + -
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Residues in contact with ASP 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 3.7 6.5 - - + +
103B VAL* 3.9 17.3 - - + -
104B ARG* 2.8 57.1 + - - +
109B VAL 2.9 14.7 + - - +
110B LYS 3.6 4.3 - - - +
112B VAL* 1.3 73.3 - - - +
114B THR* 1.3 67.8 + - - +
116B VAL* 3.9 0.9 - - - +
117B VAL* 3.0 29.3 + - + +
174B CYS* 3.4 11.9 - - - -
178B VAL* 5.2 0.3 - - - +
508B EDO 2.8 25.6 + - - -
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR* 6.4 0.7 - - + -
48B LEU* 3.9 36.1 - - + -
52B TYR* 4.8 3.0 + - + -
103B VAL* 3.6 19.9 - - - +
110B LYS* 2.8 25.3 + - - +
111B LEU* 3.5 14.7 - - + +
112B VAL 3.2 0.2 - - - -
113B ASP* 1.3 79.0 - - - +
115B LEU* 1.3 57.3 + - - +
117B VAL* 3.4 5.7 + - - +
118B GLY* 3.0 22.7 + - - -
158B TYR* 5.1 1.2 - - - -
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.8 4.5 - - + -
58B LEU* 4.9 1.3 - - + -
62B MSE 3.8 29.6 - - + -
111B LEU* 3.0 46.0 + - + +
112B VAL 3.8 3.4 - - - +
114B THR* 1.3 73.9 - - - +
116B VAL* 1.3 62.1 + - - +
118B GLY* 3.2 2.4 + - - -
119B ALA* 2.9 23.4 + - - +
158B TYR* 3.5 32.8 - - + +
161B LEU* 3.9 17.3 - - + +
162B ALA* 3.8 30.5 - - + +
165B TYR* 4.0 9.6 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 5.0 1.6 - - + -
112B VAL* 3.0 22.9 + - + +
113B ASP 4.0 2.0 - - - +
115B LEU* 1.3 73.2 - - - +
117B VAL* 1.3 63.8 + - - +
119B ALA* 3.1 8.2 + - - +
120B PHE* 3.1 34.4 + - + -
159B LEU* 4.7 3.6 - - + -
162B ALA* 4.3 15.5 - - + -
171B ILE* 4.3 13.2 - - + -
174B CYS* 3.5 26.0 - - + -
175B VAL* 3.9 18.6 - - + -
178B VAL* 3.7 24.5 - - + -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.9 39.3 - - + +
100B ARG* 4.7 14.8 - - + +
102B LEU* 4.9 2.7 - - + -
103B VAL* 4.4 8.3 - - + -
113B ASP* 3.0 23.1 + - + +
114B THR* 3.6 6.3 - - - +
116B VAL* 1.3 76.2 - - - +
118B GLY* 1.3 63.0 + - - +
120B PHE* 3.2 4.2 + - - +
121B ILE* 3.0 40.2 + - + +
178B VAL* 4.3 25.8 - - + -
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR 3.0 14.6 + - - -
115B LEU 3.2 4.6 + - - -
117B VAL* 1.3 77.3 - - - +
119B ALA* 1.3 62.5 + - - +
121B ILE* 3.4 5.0 + - - +
122B GLU* 3.1 28.6 + - - +
158B TYR* 3.6 25.6 - - - -
510B EDO 4.1 8.9 - - - -
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.9 19.7 - - + -
115B LEU 2.9 10.1 + - - +
116B VAL 3.1 9.8 + - - +
118B GLY* 1.3 76.0 - - - +
120B PHE* 1.3 55.8 + - - +
122B GLU* 3.5 1.6 + - - +
123B ALA* 2.9 31.2 + - - +
155B TYR* 3.6 28.7 - - + +
158B TYR* 3.6 14.9 - - + +
159B LEU* 4.2 11.7 - - + +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.3 51.4 - + - -
11B LEU* 3.8 21.8 - - + +
12B GLY 5.2 0.2 - - - -
95B TYR* 3.7 2.5 + - - -
99B LEU* 4.9 2.5 - - + -
116B VAL* 3.1 25.1 + - + +
117B VAL* 3.2 7.6 + - - +
119B ALA* 1.3 74.5 - - - +
121B ILE* 1.3 65.6 + - - +
123B ALA* 3.8 1.4 - - - +
124B ARG* 2.9 26.7 + - - +
175B VAL* 3.7 20.9 - - + -
178B VAL* 3.6 23.1 - - + -
179B ARG* 3.4 38.8 - - + -
182B GLU* 4.0 20.9 - - + -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TYR* 3.8 22.4 - - + -
96B ALA* 4.7 11.7 - - + -
99B LEU* 4.1 7.9 - - + -
100B ARG* 3.9 22.4 - - - +
117B VAL* 3.0 34.7 + - + +
118B GLY* 3.4 6.9 + - - +
120B PHE* 1.3 75.1 - - - +
122B GLU* 1.3 59.7 + - - +
124B ARG* 3.7 2.1 - - - +
125B SER* 2.9 35.4 + - - +
196B HIS* 4.1 16.0 + - + +
503B UNL 4.6 2.9 - - - +
504B EDO 4.3 15.5 - - - +
510B EDO 3.9 25.4 - - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 4.5 0.3 - - - +
69B GLU* 3.1 2.3 - - - +
118B GLY 3.1 17.8 + - - +
119B ALA 3.7 3.8 - - - +
121B ILE* 1.3 81.0 - - - +
123B ALA* 1.3 57.3 + - - +
125B SER* 3.3 5.8 + - - -
126B CYS* 2.9 28.4 + - - +
151B GLU* 3.1 24.0 - - - +
154B HIS* 3.3 23.3 + - + +
155B TYR* 3.7 16.4 - - - +
158B TYR* 3.8 11.0 - - + -
502B FE 2.4 31.0 - - - -
503B UNL 2.6 8.0 + - - -
510B EDO 2.5 26.2 + - - -
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.6 22.7 - - + +
10B PHE* 3.8 23.8 - - + -
11B LEU* 3.5 19.3 - - + +
119B ALA 2.9 19.1 + - - +
120B PHE 3.8 3.8 - - - +
122B GLU* 1.3 75.0 - - - +
124B ARG* 1.3 58.2 + - - +
126B CYS* 3.4 3.1 + - - +
127B GLU* 2.9 23.4 + - - +
155B TYR* 3.9 10.0 - - + +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.9 22.6 - - + +
12B GLY 4.7 0.2 - - - +
13B CYS* 2.9 45.6 + - - +
14B PRO 3.6 10.1 + - - -
15B THR* 3.7 7.3 + - - +
95B TYR* 3.3 13.9 - - + +
120B PHE 2.9 18.6 + - - +
121B ILE 3.7 2.5 - - - +
123B ALA* 1.3 75.2 - - - +
125B SER* 1.4 56.1 + - - +
127B GLU* 3.0 24.8 + - - +
128B ARG* 2.8 41.7 + - + +
182B GLU* 2.8 37.7 + - - +
186B ILE* 3.6 24.0 - - + +
196B HIS* 4.1 12.6 - - + -
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 2.9 14.4 + - - +
122B GLU* 3.5 6.5 - - - -
124B ARG* 1.4 72.2 - - - +
126B CYS* 1.3 60.4 + - - +
128B ARG* 3.9 0.3 - - - +
129B PHE* 2.8 44.9 + - - -
151B GLU* 3.6 20.2 - - - -
195B PHE* 4.0 13.0 - - - -
196B HIS* 2.9 27.4 + - - -
503B UNL 3.9 11.8 + - - -
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Residues in contact with CYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.4 29.8 - - + -
122B GLU 2.9 14.5 + - - +
123B ALA 3.4 9.2 - - - +
125B SER* 1.3 75.9 - - - +
127B GLU* 1.3 62.6 + - - +
129B PHE* 4.3 0.2 - - - -
130B ALA* 3.1 6.9 + - - +
148B LEU* 2.9 59.4 - - - +
151B GLU* 3.7 14.7 - - + +
152B ALA* 4.4 3.8 - - - -
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.5 6.7 - - + +
11B LEU* 3.5 30.3 - - + -
14B PRO* 3.3 15.1 - - + +
15B THR* 2.5 51.4 + - - +
123B ALA 2.9 7.5 + - - +
124B ARG* 3.0 15.3 + - - +
126B CYS* 1.3 77.1 - - - +
128B ARG* 1.3 57.4 + - - +
130B ALA* 3.3 7.7 + - + +
131B ALA* 2.9 30.1 + - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 2.7 44.6 + - + +
16B PRO* 3.6 15.0 - - - +
19B TRP* 3.5 35.3 - - + +
124B ARG* 2.8 27.2 + - + +
125B SER 3.9 2.9 - - - +
127B GLU* 1.3 76.6 + - - +
129B PHE* 1.3 66.2 + - - +
131B ALA* 3.3 3.1 + - - +
132B LEU* 3.1 23.6 + - + +
186B ILE* 3.7 24.4 + - - +
195B PHE* 3.1 44.7 + - + -
196B HIS* 3.7 8.6 - - - +
197B SER 3.1 24.7 + - - -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B HIS* 3.4 36.8 - + - -
38B GLU* 4.3 1.1 - - - -
125B SER* 2.8 32.5 + - - -
126B CYS* 4.3 1.8 - - - -
128B ARG* 1.3 71.7 - - - +
130B ALA* 1.3 63.0 + - - +
132B LEU* 3.2 4.0 + - - +
133B VAL* 3.0 27.6 + - - +
144B TYR* 3.6 35.2 - + + +
147B LEU* 3.7 20.6 - - + -
148B LEU* 3.3 17.3 - - + -
151B GLU* 3.6 33.9 - - + -
195B PHE* 3.2 32.3 - + - -
503B UNL 5.1 1.8 - - - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B CYS* 3.1 12.2 + - - +
127B GLU* 3.4 12.8 - - + +
128B ARG 3.2 0.2 - - - -
129B PHE* 1.3 81.7 - - - +
131B ALA* 1.3 61.9 + - - +
132B LEU 3.3 0.3 + - - -
133B VAL* 3.4 12.7 + - - +
134B PRO* 3.4 11.6 - - - +
148B LEU* 3.5 23.1 - - + +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR* 4.3 11.2 - - + +
20B ILE* 4.0 25.9 - - + +
127B GLU* 2.9 29.1 + - - +
128B ARG* 3.3 5.3 + - - +
130B ALA* 1.3 75.6 - - - +
132B LEU* 1.3 61.2 + - + +
134B PRO* 3.5 4.4 - - - +
135B HIS* 3.4 19.8 + - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 3.9 37.0 - - + -
20B ILE* 4.4 11.2 - - + -
23B ALA* 4.2 9.6 - - + -
24B LEU* 4.2 24.5 - - + -
30B LEU* 4.2 10.1 - - + -
128B ARG 3.1 19.4 + - - +
129B PHE 3.7 5.2 - - - +
130B ALA 3.2 0.4 - - - -
131B ALA* 1.3 79.3 - - - +
133B VAL* 1.3 66.1 + - - +
134B PRO 3.3 0.4 - - - -
135B HIS* 2.9 18.2 + - - +
136B LEU* 3.4 23.8 + - + +
144B TYR* 4.2 22.9 - - + -
195B PHE* 4.5 8.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE 3.0 22.8 + - - +
130B ALA* 3.8 8.3 - - - +
132B LEU* 1.3 75.9 - - - +
134B PRO* 1.3 73.6 - - + +
135B HIS 2.9 1.7 + - - -
136B LEU* 3.3 18.0 + - - +
141B GLY* 3.5 34.5 - - - +
144B TYR* 4.0 6.1 - - + -
145B HIS* 3.7 32.5 - - + +
148B LEU* 5.3 0.2 - - + -
----------------------------------------------------------
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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
------------------------------------------------------------
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