Contacts of the helix formed by residues 123 - 148 (chain B) in PDB entry 2IB0
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 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASP* 4.6 1.2 + - - +
121B ALA* 4.6 0.6 - - - +
122B GLU* 1.3 81.8 - - + +
124B ALA* 1.3 59.0 + - - +
125B ASP* 3.7 7.8 + - - +
126B ASP* 3.2 33.3 + - - +
127B ARG* 2.9 33.8 + - - +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 3.6 27.6 - - + +
123B THR* 1.3 73.2 - - - +
125B ASP* 1.3 58.3 + - - +
127B ARG* 3.4 27.5 - - - +
128B VAL* 2.9 37.0 + - - +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 5.8 0.7 - - - +
123B THR* 3.3 8.5 + - - +
124B ALA* 1.3 78.7 - - - +
126B ASP* 1.3 62.3 + - - +
128B VAL* 3.4 5.5 + - - +
129B PHE* 3.0 26.9 + - - +
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASP* 4.9 0.2 - - - +
72B MET* 3.4 27.8 - - + +
76B ARG* 2.8 33.8 + - - +
117B VAL* 4.5 3.8 - - + +
121B ALA* 4.1 11.2 - - + +
123B THR* 3.2 23.8 + - - +
125B ASP* 1.3 79.0 - - - +
127B ARG* 1.3 61.5 + - - +
129B PHE* 3.7 7.9 - - - +
130B ALA* 3.0 28.4 + - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 3.6 16.4 + - + +
119A GLU 2.8 29.7 + - - -
120A HIS* 5.0 0.4 - - - +
121A ALA 4.2 7.7 + - - -
127A ARG* 2.9 45.7 - - - +
118B VAL* 3.6 11.8 - - - +
121B ALA* 3.3 27.5 + - + -
122B GLU 2.7 29.9 + - - -
123B THR 2.9 20.4 + - - +
124B ALA* 3.3 20.8 + - - +
126B ASP* 1.3 76.1 - - - +
128B VAL* 1.3 59.9 + - - +
130B ALA* 3.4 4.7 + - - +
131B SER* 2.9 28.4 + - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.1 31.6 - - + +
118A VAL* 4.6 2.5 - - + -
119A GLU* 3.7 41.5 - - + +
124B ALA 2.9 21.2 + - - +
125B ASP* 3.9 5.6 - - - +
127B ARG* 1.3 74.1 - - - +
129B PHE* 1.3 66.5 + - - +
131B SER* 3.0 20.4 + - - -
132B THR* 3.0 14.1 + - - +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 4.1 20.4 - - + -
68B ASP* 3.9 37.5 - - + -
69B VAL* 3.8 20.4 - - + -
72B MET* 3.8 27.4 - - + -
114B TRP* 3.9 17.3 - + - -
125B ASP 3.0 17.2 + - - +
126B ASP* 3.7 8.7 - - - +
127B ARG 3.3 0.2 - - - -
128B VAL* 1.3 77.8 - - - +
130B ALA* 1.3 64.0 + - - +
132B THR* 3.3 9.2 + - + -
133B ALA* 3.1 20.7 + - + +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 3.7 17.9 - - + +
117B VAL* 3.5 34.3 - - + -
118B VAL* 3.8 16.2 - - + +
126B ASP 3.0 17.6 + - - +
127B ARG 3.7 3.8 - - - +
129B PHE* 1.3 79.1 - - - +
131B SER* 1.3 51.4 + - - +
133B ALA* 3.2 2.9 + - - +
134B LEU* 2.8 35.3 + - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.6 4.2 + - - +
118A VAL* 4.0 18.2 - - - +
131A SER* 4.5 3.8 - - - -
134A LEU* 3.5 26.0 - - - +
118B VAL* 3.6 11.5 - - - +
127B ARG 2.9 15.7 + - - -
128B VAL* 3.0 19.2 + - - +
130B ALA* 1.3 72.4 - - - +
132B THR* 1.3 60.3 + - - +
134B LEU* 3.4 4.9 + - - +
135B THR* 2.9 34.4 + - - -
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG* 4.7 9.5 + - - -
134A LEU* 5.9 0.7 - - - -
128B VAL* 3.0 19.7 + - - +
129B PHE* 3.3 12.0 + - - -
131B SER* 1.3 77.8 + - - +
133B ALA* 1.3 57.3 + - - +
135B THR* 3.4 4.7 + - - -
136B GLU* 2.9 57.8 + - + +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 3.5 35.2 + - + +
114B TRP* 3.5 32.5 - - + -
129B PHE* 3.1 14.4 + - + +
130B ALA 3.6 3.6 - - - +
132B THR* 1.3 74.5 - - - +
134B LEU* 1.3 63.1 + - - +
136B GLU* 4.4 1.8 - - - -
137B SER* 2.8 30.2 + - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 3.4 33.2 - - - +
132A THR* 6.0 0.7 - - - -
135A THR* 3.8 16.8 - - + +
111B ALA* 3.5 32.8 - - + +
114B TRP* 3.7 14.5 - - + +
115B ARG* 3.7 39.3 - - + +
118B VAL* 4.3 5.6 - - + -
130B ALA 2.8 19.5 + - - +
131B SER* 3.7 4.0 - - - +
132B THR 3.3 0.2 - - - -
133B ALA* 1.3 72.2 - - - +
135B THR* 1.3 64.7 + - - +
137B SER* 3.2 5.2 + - - -
138B ALA* 3.0 21.3 + - + +
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER 4.5 0.2 + - - -
134A LEU* 3.9 16.7 - - + +
135A THR* 2.7 34.3 + - - -
138A ALA* 3.3 34.3 - - + -
131B SER 2.9 19.2 + - - -
132B THR* 3.8 4.7 - - - -
134B LEU* 1.3 78.3 - - - +
136B GLU* 1.3 58.1 + - + +
138B ALA* 3.3 2.3 + - - +
139B VAL* 2.9 31.1 + - + +
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Residues in contact with GLU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B GLN* 3.4 36.3 + - - +
65B ARG* 3.1 30.8 + - - +
132B THR* 2.9 42.7 + - + +
133B ALA* 4.4 1.0 - - - -
135B THR* 1.3 72.6 - - + +
137B SER* 1.3 57.6 + - - +
139B VAL* 3.5 6.3 + - - +
140B MET* 2.8 31.5 + - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 5.0 0.3 - - - -
65B ARG* 3.6 15.5 + - - +
107B GLU* 3.4 44.2 + - - +
110B GLY* 3.9 7.3 - - - -
111B ALA* 3.6 16.1 + - - -
114B TRP* 4.0 1.4 - - - -
133B ALA 2.8 22.9 + - - -
134B LEU 3.5 5.2 - - - -
136B GLU* 1.3 74.1 - - - +
138B ALA* 1.3 58.6 + - - +
140B MET* 3.2 1.7 + - - +
141B ALA* 2.9 25.6 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 3.3 34.5 - - + -
139A VAL* 4.2 6.5 - - + -
108B ASN* 5.7 1.1 - - - -
111B ALA* 4.7 9.3 - - + +
134B LEU* 3.0 13.0 + - + +
135B THR 3.7 1.3 - - - +
137B SER* 1.3 74.0 - - - +
139B VAL* 1.3 64.9 + - - +
141B ALA* 3.4 7.1 + - - +
142B THR* 3.1 27.5 + - - +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA* 4.0 19.3 - - + +
139A VAL* 4.0 13.0 - - + -
142A THR* 3.8 33.9 - - + -
135B THR* 2.9 21.9 + - + +
136B GLU* 3.9 6.7 - - - +
138B ALA* 1.3 75.7 - - - +
140B MET* 1.3 64.9 + - + +
142B THR* 2.7 23.0 + - - +
143B ARG* 3.1 27.1 + - + +
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 3.8 6.3 - - - +
54B LEU* 3.6 26.7 - - - -
57B ASP* 4.2 5.2 - - + +
58B ALA* 4.0 30.1 - - + +
61B GLN* 3.8 26.7 - - - +
107B GLU* 3.1 36.1 - - - +
136B GLU 2.8 19.2 + - - +
137B SER 3.2 0.9 + - - +
139B VAL* 1.3 79.1 - - + +
141B ALA* 1.3 60.9 + - - +
143B ARG* 3.1 26.0 + - - +
144B TRP* 3.1 31.1 + - + -
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.8 18.1 - - + +
107B GLU* 3.7 16.2 - - + +
108B ASN* 3.4 26.2 - - - +
137B SER 2.9 16.5 + - - +
138B ALA* 3.7 7.2 - - - +
139B VAL 3.4 0.2 - - - -
140B MET* 1.3 75.3 - - - +
142B THR* 1.3 58.4 + - + +
144B TRP* 3.3 1.5 + - - +
145B ASN* 2.8 31.4 + - - +
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Residues in contact with THR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A VAL* 4.0 27.5 - - + +
142A THR* 4.4 10.4 + - - -
143A ARG* 6.2 2.0 - - - -
146A ARG* 4.9 7.4 + - - -
138B ALA 3.1 15.0 + - - +
139B VAL* 2.7 24.1 + - - -
141B ALA* 1.3 76.2 - - + +
143B ARG* 1.3 63.6 + - - +
145B ASN* 3.1 8.0 + - - +
146B ARG* 3.0 30.0 + - - +
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Residues in contact with ARG 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A THR* 5.7 1.3 - - - +
146A ARG* 3.3 28.5 - - - +
53B PHE 5.5 0.4 - - - -
54B LEU* 3.2 45.6 - - + +
57B ASP* 3.3 25.5 + - - -
139B VAL* 3.1 29.5 + - + +
140B MET* 3.1 24.6 + - - +
142B THR* 1.3 77.4 + - - +
144B TRP* 1.3 60.4 + - - +
146B ARG* 3.4 6.4 + - - +
147B VAL* 3.4 21.7 + - - +
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Residues in contact with TRP 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 3.0 31.1 + + - -
43B VAL* 3.4 32.1 - - + -
47B SER* 3.9 11.9 - - - -
51B VAL* 4.2 10.3 - - + -
54B LEU* 3.6 27.6 - - + +
55B VAL* 3.6 25.8 - - + -
58B ALA* 4.6 0.6 - - - +
100B ALA* 3.7 29.8 - - + +
103B ALA* 3.6 12.8 - - + -
104B VAL* 3.7 17.5 - - + +
107B GLU* 4.8 1.8 - - + -
140B MET* 3.1 35.5 + - + +
141B ALA 3.9 0.2 - - - +
143B ARG* 1.3 75.6 - - - +
145B ASN* 1.3 60.6 + - - +
147B VAL* 3.1 32.5 + - + +
148B LEU* 2.8 22.8 + - - +
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Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.6 23.7 - - + +
141B ALA 2.8 18.4 + - - +
142B THR* 3.1 9.8 + - - +
144B TRP* 1.3 79.7 - - - +
146B ARG* 1.3 60.7 + - + +
148B LEU* 3.4 33.8 - - - +
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Residues in contact with ARG 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ARG* 3.6 45.2 + - - +
146A ARG* 3.1 51.6 - - - +
142B THR* 3.0 15.1 + - - +
143B ARG* 3.8 9.2 - - - +
144B TRP 3.2 0.4 - - - -
145B ASN* 1.3 76.6 - - + +
147B VAL* 1.3 62.9 + - - +
148B LEU 3.6 5.9 - - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 6.1 3.6 - - + -
51B VAL* 3.9 26.2 - - + -
54B LEU* 3.8 21.5 - - + -
96B ALA 5.5 2.5 - - - +
97B ALA* 6.5 0.2 - - - -
100B ALA* 3.9 16.2 - - + -
143B ARG 3.4 14.7 + - - +
144B TRP* 3.1 21.1 + - + +
146B ARG* 1.3 78.5 - - - +
148B LEU* 1.3 59.8 + - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 4.9 8.3 - - + +
100B ALA* 3.6 18.8 - - + -
101B ARG* 3.2 43.3 - - + +
104B VAL* 3.9 9.2 - - + -
144B TRP 2.8 31.2 - - - +
145B ASN* 3.4 37.8 - - - +
146B ARG* 3.6 6.6 - - - +
147B VAL* 1.3 81.4 - - - +
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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