Contacts of the helix formed by residues 115 - 141 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ASP* 3.5 24.5 - - - -
31D GLU* 2.5 31.7 + - - -
109D PHE* 4.6 0.9 - - - -
114D VAL* 1.3 76.8 - - - +
116D LEU* 1.3 65.5 + - - +
117D LEU* 4.2 2.5 - - - -
118D ARG* 3.0 14.8 + - - +
119D ALA* 2.9 21.8 + - - +
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.4 47.3 - - + +
109D PHE* 3.9 36.3 - - + -
114D VAL 3.9 1.6 + - - -
115D SER* 1.3 71.6 - - - +
117D LEU* 1.3 63.8 + - - +
119D ALA* 3.9 3.0 - - + +
120D LEU* 3.3 46.0 + - + +
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D PHE* 5.0 12.0 - - + +
28D ASP* 3.4 27.6 - - - +
29D LEU* 3.7 21.5 - - + +
31D GLU* 4.0 17.0 - - + +
32D LEU* 3.0 38.4 - - + +
37D PHE* 4.7 4.5 - - + -
115D SER* 3.1 7.4 - - - +
116D LEU* 1.3 77.9 - - - +
118D ARG* 1.3 60.2 + - - +
120D LEU* 3.5 6.1 + - + +
121D VAL* 2.8 37.6 + - + +
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Residues in contact with ARG 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLU* 3.6 24.5 + - - +
34D LEU* 6.2 2.4 - - - +
36D SER* 6.3 0.2 - - - -
37D PHE* 3.6 39.8 - - + +
40D ALA* 3.9 12.9 - - - +
96D SER 5.0 1.4 + - - -
114D VAL* 3.4 22.9 - - + -
115D SER* 3.0 22.1 + - - +
117D LEU* 1.3 79.1 - - - +
119D ALA* 1.3 63.1 + - - +
121D VAL* 3.1 6.1 + - - +
122D TYR* 2.9 58.8 + - + +
191D ASP 4.6 3.6 + - - -
192D SER* 4.1 22.6 + - - -
194D VAL* 4.0 21.0 - - - +
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Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D THR* 3.9 24.2 - - + -
109D PHE* 4.4 18.8 - - + -
114D VAL* 3.8 6.5 - - + +
115D SER 2.9 15.2 + - - +
116D LEU* 3.9 7.0 - - + +
118D ARG* 1.3 75.3 - - - +
120D LEU* 1.3 59.9 + - + +
122D TYR* 2.8 6.1 + - - +
123D MET* 2.8 44.8 + - + +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D LEU* 3.3 44.9 + - + +
117D LEU* 4.0 5.6 - - + +
119D ALA* 1.3 78.6 - - + +
121D VAL* 1.3 60.1 + - + +
123D MET* 4.0 15.6 + - + +
124D ILE* 2.8 37.6 + - + +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 5.7 1.1 - - + -
37D PHE* 3.4 30.3 - - + -
38D TRP* 4.0 19.7 - - + -
41D ALA* 4.1 17.3 - - + -
117D LEU* 2.8 31.4 - - + +
118D ARG 3.1 6.0 + - - +
120D LEU* 1.3 75.4 - - + +
122D TYR* 1.3 68.2 - - + +
124D ILE* 3.2 11.3 + - + +
125D ALA* 3.0 21.0 + - - +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 5.4 3.4 - + - -
40D ALA* 3.2 28.4 - - + +
41D ALA* 4.2 7.9 - - + -
44D GLU* 3.8 15.0 - - + -
96D SER* 2.8 45.3 + - - -
99D HIS* 3.9 30.7 - + - -
105D THR* 3.9 12.3 - - + -
114D VAL* 5.7 0.4 - - + -
118D ARG* 2.9 44.1 + - + +
119D ALA 2.8 8.6 + - - +
121D VAL* 1.3 76.2 - - + +
123D MET* 1.3 68.1 + - - +
124D ILE 3.0 1.3 - - - -
125D ALA* 2.9 17.2 + - - +
126D GLN* 2.9 32.1 + - - +
194D VAL* 6.0 1.1 - - + -
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Residues in contact with MET 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO* 3.9 24.9 - - + +
105D THR* 4.3 7.6 - - - -
106D PHE* 3.7 44.2 - - + +
109D PHE* 5.5 2.2 - - + -
119D ALA* 2.8 34.2 + - + +
120D LEU* 4.4 15.5 - - + +
122D TYR* 1.3 73.4 - - - +
124D ILE* 1.3 57.6 + - + +
126D GLN* 4.0 9.1 - - - +
127D CYS* 3.1 29.5 + - - +
246D TRP* 6.0 3.8 - - + -
250D PHE* 4.1 23.3 - - + -
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Residues in contact with ILE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 2.8 27.8 - - + +
121D VAL* 3.2 11.0 + - - +
122D TYR 3.0 0.8 - - - -
123D MET* 1.3 78.1 - - + +
125D ALA* 1.3 59.5 + - - +
127D CYS* 3.2 6.1 + - + +
128D LEU* 2.8 54.9 + - + +
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA* 3.6 33.2 - - + +
44D GLU* 4.4 4.5 - - + -
45D PHE* 3.4 21.9 - - + +
121D VAL 3.0 12.0 + - - +
122D TYR* 2.9 7.9 + - - +
124D ILE* 1.3 74.8 - - - +
126D GLN* 1.3 56.8 + - - +
128D LEU* 4.5 7.2 - - - -
129D GLY* 2.6 31.0 + - - -
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Residues in contact with GLN 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 3.0 32.0 + - + +
48D THR* 3.1 27.8 - - - +
99D HIS* 3.9 4.2 - - - +
100D ILE 4.9 0.4 - - - -
101D ASN 2.9 10.2 - - - +
102D PRO* 2.6 37.7 - - + +
105D THR* 3.2 19.0 + - - -
122D TYR* 2.9 32.3 + - - +
123D MET* 4.0 3.2 - - - +
125D ALA* 1.3 73.9 - - - +
127D CYS* 1.3 57.9 + - - +
130D ALA* 2.8 32.1 + - - +
224D ALA* 3.8 12.7 - - + +
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Residues in contact with CYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D PRO* 6.2 0.2 - - - -
123D MET 3.1 19.9 + - - +
124D ILE* 3.3 9.2 - - - +
126D GLN* 1.3 78.4 - - - +
128D LEU* 1.3 64.2 + - + +
130D ALA* 3.5 2.9 + - - +
131D ILE* 3.3 30.8 + - - +
224D ALA* 4.1 9.6 - - - +
227D PHE* 3.1 41.8 - - + -
246D TRP* 4.2 18.8 - - - -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PHE* 3.2 25.8 - - + -
124D ILE* 2.8 39.0 + - + +
125D ALA* 3.9 5.2 - - - +
127D CYS* 1.3 76.0 - - + +
129D GLY* 1.3 66.2 + - - +
131D ILE* 4.3 10.5 - - + +
132D CYS* 3.5 15.8 + - - +
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PHE* 3.4 27.6 - - - -
48D THR* 3.8 1.6 - - - -
49D LEU* 3.1 17.7 - - - +
125D ALA 2.6 22.7 + - - -
126D GLN 3.1 2.9 + - - -
128D LEU* 1.3 77.6 - - - +
130D ALA* 1.3 61.6 + - - +
132D CYS* 3.3 0.7 + - - +
133D GLY 3.0 17.2 + - - -
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D THR* 3.3 6.1 - - + +
52D LEU* 3.7 21.5 - - + +
126D GLN 2.8 17.9 + - - +
127D CYS 3.8 3.6 - - - +
128D LEU 3.4 0.2 - - - -
129D GLY* 1.3 70.4 - - - +
131D ILE* 1.3 53.8 + - - +
133D GLY* 2.7 21.3 + - - -
134D VAL* 2.8 20.4 + - - +
224D ALA 2.8 32.1 - - - +
228D GLY* 3.7 9.9 - - - -
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D CYS 3.3 17.6 + - - +
128D LEU* 4.3 12.3 - - + +
129D GLY 3.5 0.2 - - - -
130D ALA* 1.3 73.5 - - - +
132D CYS* 1.3 56.3 + - - +
135D GLY* 2.9 24.5 + - - -
227D PHE* 3.6 28.3 - - + -
228D GLY* 3.5 25.1 - - - +
231D VAL* 3.8 20.6 - - + -
232D ILE* 3.6 23.0 - - + +
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Residues in contact with CYS 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PHE* 4.5 10.1 - - + -
49D LEU* 3.9 22.9 - - + +
128D LEU 3.5 14.4 + - - +
129D GLY 3.3 3.9 + - - +
130D ALA 3.1 1.0 - - - -
131D ILE* 1.3 76.9 - - - +
133D GLY* 1.3 62.9 + - - +
135D GLY* 4.7 1.3 - - - -
136D LEU* 2.9 31.2 + - - +
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.2 34.7 - - - +
52D LEU* 3.9 1.8 - - - -
53D TYR* 3.5 20.6 - - - -
129D GLY 3.0 8.4 + - - -
130D ALA 2.7 8.6 + - - -
132D CYS* 1.3 80.6 - - - +
134D VAL* 1.3 58.8 + - - -
136D LEU* 3.4 13.2 + - - +
137D VAL* 3.6 3.8 - - - +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.2 35.4 - - + -
56D VAL* 4.3 10.1 - - + -
130D ALA 2.8 17.9 + - - +
133D GLY* 1.3 69.2 - - - -
135D GLY* 1.3 65.3 + - - +
137D VAL* 3.2 17.8 + - - +
138D LYS* 3.3 12.1 + - - +
145D TYR* 3.5 29.7 - - + +
150D GLY 4.4 4.3 - - - +
228D GLY 3.7 31.2 - - - +
229D ALA* 4.0 10.3 - - + +
232D ILE* 4.0 4.3 - - + -
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Residues in contact with GLY 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ILE 2.9 22.5 + - - -
132D CYS* 3.8 1.6 - - - -
134D VAL* 1.3 77.5 - - - +
136D LEU* 1.3 61.8 + - - +
138D LYS* 3.5 4.2 + - - +
139D ALA* 3.3 19.6 + - - +
232D ILE* 3.6 21.4 - - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 4.1 21.5 - - + -
49D LEU* 4.4 15.7 - - + -
53D TYR* 4.0 22.4 - - + -
132D CYS 2.9 17.5 + - - +
133D GLY 3.5 5.6 - - - +
134D VAL 3.2 0.2 - - - -
135D GLY* 1.3 77.2 - - - +
137D VAL* 1.3 64.3 + - - +
139D ALA* 3.0 23.1 + - + +
140D PHE* 3.3 37.0 + - + -
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D TYR* 3.6 35.9 - - + +
56D VAL* 4.3 17.7 - - + +
57D ALA* 3.8 24.5 - - + +
60D ILE* 4.9 2.2 - - + -
133D GLY 3.6 15.7 - - - +
134D VAL* 3.2 7.3 + - - +
136D LEU* 1.3 72.0 - - - +
138D LYS* 1.3 55.3 + - - +
139D ALA 2.8 5.1 + - - -
140D PHE* 2.5 31.0 + - - +
141D MET* 3.0 33.2 + - + +
145D TYR* 4.7 7.6 - - + -
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Residues in contact with LYS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D VAL 3.3 3.6 + - - +
135D GLY 3.8 9.0 - - - +
136D LEU 3.4 0.2 - - - -
137D VAL* 1.3 78.8 - - - +
139D ALA* 1.3 57.1 + - - +
142D LYS* 2.9 66.6 + - + +
145D TYR* 3.3 39.8 - - + -
146D ASN* 3.8 15.3 + - - +
232D ILE* 3.6 34.4 + - + +
233D PHE 5.8 0.6 + - - -
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Residues in contact with ALA 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B THR* 4.4 4.5 + - - -
135D GLY 3.3 9.4 + - - +
136D LEU* 3.0 18.8 + - + +
137D VAL 2.8 0.8 + - - -
138D LYS* 1.3 80.1 - - - +
140D PHE* 1.3 68.2 + - + +
142D LYS* 4.8 1.2 + - - +
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B GLY 5.3 0.9 - - - +
159B TYR* 4.0 8.7 - - - -
160B ASN* 4.9 0.7 - - - +
163B THR* 3.6 42.8 + - + +
166B GLY* 3.5 21.5 - - - -
167B ALA* 3.3 29.8 - - + -
170B ILE* 4.5 2.0 - - + -
216B ILE* 5.2 2.5 - - + -
53D TYR* 3.7 27.8 - + - -
136D LEU* 3.4 36.6 - - + -
137D VAL* 2.5 15.4 + - - +
139D ALA* 1.3 82.8 - - + +
141D MET* 1.3 72.4 + - + +
142D LYS 4.0 0.4 - - - -
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Residues in contact with MET 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLY 5.9 1.1 - - - +
159B TYR* 4.2 23.1 - - + -
212B ALA 5.5 0.7 - - - +
216B ILE* 4.0 29.2 - - + -
53D TYR* 5.9 0.9 - - + -
57D ALA* 4.3 17.0 - - + +
60D ILE* 3.6 31.0 - - + -
61D GLY* 5.0 2.5 - - - -
64D LYS* 5.2 0.9 - - - -
137D VAL* 3.0 29.9 + - + +
138D LYS 3.7 2.0 - - - -
140D PHE* 1.3 92.0 - - + +
142D LYS* 1.3 60.2 + - - +
143D GLY 3.1 4.0 + - - +
144D PRO* 3.6 15.0 - - + +
145D TYR* 2.9 30.2 + - + +
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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