Contacts of the helix formed by residues 115 - 141 (chain B) in PDB entry 4IA4
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.0 14.1 - - - -
28B ASP* 4.1 15.9 - - - -
31B GLU* 2.4 34.9 + - - -
114B VAL* 1.3 81.0 - - - +
116B LEU* 1.3 59.5 + - - +
117B LEU 4.0 3.1 - - - -
118B ARG* 2.9 22.0 + - - +
119B ALA* 3.0 24.4 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.3 21.7 - - + -
27B PHE* 4.2 33.1 - - + +
109B PHE* 3.8 34.8 - - + -
114B VAL 3.7 0.6 + - - -
115B SER* 1.3 70.9 - - - +
117B LEU* 1.3 66.6 + - - +
119B ALA* 3.6 3.1 + - + +
120B LEU* 3.3 42.5 + - + +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 5.0 17.1 - - + +
28B ASP* 3.1 27.8 - - - +
29B LEU* 3.9 15.7 - - + -
31B GLU* 3.7 24.9 - - + +
32B LEU* 3.1 39.0 - - + +
37B PHE* 4.7 4.9 - - + -
115B SER* 4.0 2.0 - - - +
116B LEU* 1.3 82.7 - - - +
118B ARG* 1.3 64.8 + - - +
120B LEU* 3.4 12.5 + - + +
121B VAL* 3.0 22.5 + - + +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 3.4 21.2 + - - +
34B LEU* 6.3 1.0 - - - +
36B SER 5.9 0.4 - - - -
37B PHE* 3.5 40.6 - - + +
40B ALA* 3.9 10.1 - - - +
114B VAL* 3.5 21.5 - - + -
115B SER* 2.9 25.4 + - - +
117B LEU* 1.3 76.2 - - - +
119B ALA* 1.3 64.3 + - - +
121B VAL* 2.9 15.6 + - - +
122B TYR* 3.0 54.4 + - + +
190B ARG 5.2 2.6 + - - -
191B ASP* 5.1 3.2 + - - +
192B SER* 3.2 26.8 + - - -
194B VAL* 3.5 26.3 - - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 3.9 25.7 - - + +
109B PHE* 4.5 16.4 - - + -
114B VAL* 3.8 5.6 - - + +
115B SER 3.0 14.8 + - - +
116B LEU* 3.7 9.6 - - + +
117B LEU 3.3 0.2 - - - -
118B ARG* 1.3 80.8 - - - +
120B LEU* 1.3 62.3 + - + +
122B TYR* 3.5 1.5 + - - +
123B MET* 3.0 40.3 + - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 6.5 1.1 - - + -
116B LEU* 3.3 39.5 + - + +
117B LEU* 3.9 9.0 - - + +
118B ARG 3.3 0.6 - - - -
119B ALA* 1.3 77.2 - - + +
121B VAL* 1.3 61.0 + - + +
123B MET* 3.9 12.9 + - + +
124B ILE* 3.0 39.2 + - + +
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Residues in contact with VAL 121 (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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32B LEU* 6.0 1.1 - - + -
37B PHE* 3.2 26.2 - - + -
38B TRP* 3.6 31.0 - - + -
41B ALA* 4.0 18.2 - - + -
117B LEU* 3.0 24.0 - - + +
118B ARG 2.9 4.7 + - - +
120B LEU* 1.3 75.4 - - + +
122B TYR* 1.3 70.3 + - + +
124B ILE* 2.8 20.2 + - - +
125B ALA* 3.0 11.5 + - + +
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 5.4 2.5 - + - -
40B ALA* 3.2 36.4 - - + +
41B ALA* 4.3 8.3 - - + -
44B GLU* 4.1 15.3 - - + -
96B SER* 2.5 30.2 + - - -
99B HIS* 3.7 31.6 - + - -
105B THR* 4.0 12.1 - - + +
114B VAL* 5.4 0.2 - - + -
118B ARG* 3.0 54.0 + - + +
119B ALA 3.6 8.3 - - - +
121B VAL* 1.3 79.0 - - + +
123B MET* 1.3 52.3 + - - +
125B ALA* 2.8 13.6 + - - +
126B GLN* 2.8 46.6 + - - +
194B VAL* 5.2 0.9 - - + +
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 3.7 36.0 - - + +
105B THR* 4.3 9.2 - - + -
106B PHE* 3.8 30.5 - - + +
109B PHE* 5.9 0.9 - - + -
119B ALA* 3.0 27.8 + - + +
120B LEU* 4.0 15.7 - - + +
122B TYR* 1.3 78.6 - - - +
124B ILE* 1.3 61.0 + - + +
126B GLN* 3.9 9.4 - - - +
127B CYS* 3.2 28.1 + - - +
246B TRP* 6.2 1.3 - - - -
250B PHE* 4.3 20.0 - - + -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 3.0 25.5 + - + +
121B VAL* 2.8 14.0 + - + +
123B MET* 1.3 75.0 - - + +
125B ALA* 1.3 55.3 + - - +
127B CYS* 4.1 3.6 - - - +
128B LEU* 2.7 61.0 + - + +
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Residues in contact with ALA 125 (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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41B ALA* 3.5 30.3 - - + +
44B GLU* 4.7 1.3 - - + -
45B PHE* 3.3 22.0 - - + +
121B VAL* 3.0 10.3 + - + +
122B TYR* 2.8 11.1 + - - +
124B ILE* 1.3 80.4 - - - +
126B GLN* 1.3 52.0 + - - +
128B LEU* 3.8 9.2 - - - -
129B GLY* 2.5 30.5 + - - -
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Residues in contact with GLN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 2.7 35.3 + - + +
48B THR* 3.1 25.7 - - - +
99B HIS* 3.8 0.2 - - - +
100B ILE 3.6 1.0 - - - +
101B ASN 3.1 16.3 - - - +
102B PRO* 2.7 34.8 - - - +
105B THR* 3.4 20.4 + - - -
122B TYR* 2.8 26.6 + - - +
123B MET* 3.9 5.0 - - - +
125B ALA* 1.3 74.9 - - - +
127B CYS* 1.3 61.7 + - - +
128B LEU 3.1 1.1 - - - -
129B GLY 4.1 0.2 - - - +
130B ALA* 2.9 26.2 + - - +
224B ALA* 3.7 12.6 - - + +
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Residues in contact with CYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PRO* 5.2 2.2 - - - -
123B MET 3.2 17.6 + - - +
124B ILE* 4.1 4.3 - - - +
126B GLN* 1.3 77.9 - - - +
128B LEU* 1.3 62.6 + - + +
130B ALA* 3.4 3.6 + - - +
131B ILE* 3.2 32.9 + - + +
224B ALA* 3.9 20.6 - - - +
227B PHE* 3.2 33.7 - - + -
246B TRP* 3.9 22.4 - - - -
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Residues in contact with LEU 128 (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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45B PHE* 3.2 22.3 - - + -
124B ILE* 2.7 47.0 + - + +
125B ALA* 3.6 9.2 - - - +
127B CYS* 1.3 81.2 - - + +
129B GLY* 1.3 61.0 + - - +
131B ILE* 4.1 12.4 + - + +
132B CYS* 3.8 14.0 + - - +
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Residues in contact with GLY 129 (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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45B PHE* 3.3 28.0 - - - -
48B THR* 4.3 1.3 - - - -
49B LEU* 3.2 18.1 - - - +
125B ALA 2.5 20.1 + - - -
126B GLN 3.1 2.8 + - - -
128B LEU* 1.3 74.5 - - - +
130B ALA* 1.3 62.6 + - - +
132B CYS* 3.3 2.6 + - - +
133B GLY 3.0 18.7 + - - -
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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
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48B THR* 3.4 7.4 - - + +
52B LEU* 3.7 21.5 - - + +
126B GLN 2.9 14.2 + - - +
127B CYS 3.4 4.7 + - - +
129B GLY* 1.3 75.4 - - - +
131B ILE* 1.3 55.9 + - - +
133B GLY* 3.0 2.8 + - - -
134B VAL* 2.7 36.4 + - - +
224B ALA 2.8 32.5 - - - +
228B GLY* 3.8 8.1 - - - -
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Residues in contact with ILE 131 (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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127B CYS 3.2 20.5 + - - +
128B LEU* 4.5 14.4 - - + +
129B GLY 3.5 0.2 - - - -
130B ALA* 1.3 75.0 - - - +
132B CYS* 1.3 57.4 + - - +
135B GLY* 2.9 23.9 + - - -
227B PHE* 3.9 15.7 - - + -
228B GLY* 3.6 25.1 - - - +
231B VAL* 3.7 30.3 - - + -
232B ILE* 3.5 22.6 - - + +
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Residues in contact with CYS 132 (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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45B PHE* 4.6 10.5 - - + -
49B LEU* 3.7 23.8 - - + -
128B LEU 3.8 10.5 + - - +
129B GLY 3.3 5.1 + - - +
130B ALA 3.1 0.8 - - - -
131B ILE* 1.3 74.6 - - - +
133B GLY* 1.3 68.5 + - - +
135B GLY* 3.0 2.1 + - - -
136B LEU* 2.8 26.5 + - - +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 3.3 36.0 - - - +
52B LEU* 4.2 0.9 - - - -
53B TYR* 3.6 12.1 - - - -
129B GLY 3.0 11.6 + - - -
130B ALA 3.4 3.1 - - - -
132B CYS* 1.3 78.1 - - - +
134B VAL* 1.3 60.3 + - - +
136B LEU* 3.4 13.4 + - - +
137B VAL* 3.5 13.3 - - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.4 32.5 - - + -
56B VAL* 4.2 9.2 - - + -
130B ALA 2.7 22.3 + - - +
133B GLY* 1.3 72.1 - - - -
135B GLY* 1.3 62.5 + - - +
137B VAL* 3.2 20.0 + - - +
138B LYS* 3.4 9.7 + - - +
145B TYR* 3.5 28.5 - - + +
150B GLY 4.6 1.1 - - - +
228B GLY 3.8 1.6 - - - +
229B ALA* 3.8 27.1 - - + +
232B ILE* 3.6 18.2 - - + -
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Residues in contact with GLY 135 (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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131B ILE 2.9 18.8 + - - -
132B CYS* 3.0 4.4 + - - -
134B VAL* 1.3 77.0 - - - +
136B LEU* 1.3 56.5 + - - +
137B VAL 3.2 0.2 - - - -
138B LYS* 3.4 4.3 + - - +
139B ALA* 3.1 24.4 + - - +
232B ILE* 3.8 21.1 - - - +
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Residues in contact with LEU 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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49B LEU* 4.5 20.9 - - + -
53B TYR* 4.4 11.9 - - + -
132B CYS 2.8 14.7 + - - +
133B GLY 3.5 6.1 - - - +
134B VAL 3.1 0.4 - - - -
135B GLY* 1.3 74.3 - - - +
137B VAL* 1.3 64.6 + - - +
139B ALA* 3.4 8.8 + - + +
140B PHE* 3.1 51.6 + - + -
170C ILE* 4.3 24.2 - - + -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.5 36.8 - - + +
56B VAL* 3.8 26.2 - - + -
57B ALA* 3.9 18.8 - - + +
60B ILE* 4.2 4.9 - - + -
133B GLY 3.5 15.5 - - - +
134B VAL 3.2 7.8 + - - +
136B LEU* 1.3 75.4 - - - +
138B LYS* 1.3 66.4 + - - +
140B PHE* 3.1 7.5 + - - +
141B MET* 3.1 33.9 + - + +
145B TYR* 4.2 10.8 - - + -
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Residues in contact with LYS 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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134B VAL 3.4 6.3 + - - +
135B GLY 3.4 10.4 + - - +
136B LEU 3.2 0.2 - - - -
137B VAL* 1.3 80.6 - - - +
139B ALA* 1.3 58.8 + - - +
142B LYS* 2.7 72.9 + - + +
145B TYR* 3.3 33.6 - - + -
146B ASN* 3.7 18.6 + - - -
232B ILE* 3.8 29.9 + - + -
233B PHE 5.7 0.2 + - - -
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLY 3.1 14.0 + - - +
136B LEU* 3.6 17.9 - - + +
137B VAL 3.2 0.2 - - - -
138B LYS* 1.3 76.9 - - - +
140B PHE* 1.3 66.7 + - + +
142B LYS* 4.7 1.6 + - - +
163C THR* 4.7 3.5 + - - -
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Residues in contact with PHE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 2.9 44.0 - + - -
136B LEU* 3.1 36.4 + - + -
137B VAL 3.4 9.2 - - - +
138B LYS 3.1 0.4 - - - -
139B ALA* 1.3 82.5 - - + +
141B MET* 1.3 73.0 + - + +
159C TYR* 4.6 4.0 - - - -
160C ASN* 4.6 2.1 - - - +
163C THR* 3.3 46.0 + - + +
166C GLY* 3.7 14.4 - - - -
167C ALA* 3.6 29.2 - - + -
170C ILE* 4.3 6.7 - - + -
216C ILE* 4.6 5.8 - - + -
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Residues in contact with MET 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ALA* 4.6 18.8 - - + +
60B ILE* 4.0 23.1 - - + -
61B GLY* 5.0 2.7 - - - -
64B LYS* 4.6 4.3 - - - -
137B VAL* 3.1 28.2 + - + +
138B LYS 3.3 2.2 - - - -
140B PHE* 1.3 98.3 - - + +
142B LYS* 1.3 66.9 + - - +
143B GLY 3.2 3.5 + - - +
144B PRO* 3.8 17.4 - - + -
145B TYR* 3.0 17.8 + - + +
158C GLY 5.7 1.8 - - - +
159C TYR* 4.0 32.8 - - + -
212C ALA 5.9 0.9 - - - +
216C ILE* 5.1 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