Contacts of the helix formed by residues 115 - 141 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO 5.8 3.4 - - - -
26A PHE* 4.5 9.9 - - - +
28A ASP* 4.8 11.0 - - - -
31A GLU* 2.7 35.2 + - - -
109A PHE* 5.4 0.2 - - - -
113A LYS 4.3 0.6 - - - -
114A VAL* 1.3 76.6 - - - +
116A LEU* 1.3 66.2 + - - +
117A LEU* 3.1 3.9 + - - -
118A ARG* 3.2 9.4 + - - +
119A ALA* 2.9 21.1 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.2 59.6 + - + +
27A PHE* 5.6 8.3 - - + -
109A PHE* 4.3 27.4 - - + -
114A VAL 3.8 0.4 + - - -
115A SER* 1.3 73.4 - - - +
117A LEU* 1.3 63.5 + - + +
119A ALA* 3.6 4.3 + - + +
120A LEU* 3.3 42.0 + - + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE 4.3 2.0 + - - +
27A PHE 3.9 24.0 - - - +
28A ASP* 4.0 4.7 - - + +
29A LEU* 5.3 2.5 - - + -
31A GLU* 3.5 33.4 - - + +
32A LEU* 3.3 35.2 - - + +
37A PHE* 4.6 7.0 - - + -
115A SER* 3.1 4.1 + - - +
116A LEU* 1.3 80.9 - - + +
118A ARG* 1.3 59.0 + - - +
120A LEU* 3.2 11.8 + - + +
121A VAL* 3.0 37.0 + - + +
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.4 26.2 + - - +
36A SER* 5.8 0.8 - - - -
37A PHE* 3.6 33.4 - - + +
40A ALA* 3.9 11.5 - - - +
95A ILE 5.7 0.2 + - - -
96A SER 4.6 0.8 + - - -
114A VAL* 3.6 22.0 - - + +
115A SER* 3.2 15.7 + - - +
117A LEU* 1.3 75.7 - - - +
119A ALA* 1.3 60.4 + - - +
122A TYR* 2.8 85.8 + - + +
192A SER* 3.0 35.6 + - - -
194A VAL* 3.9 22.0 - - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A THR* 3.7 13.2 - - + -
109A PHE* 4.1 21.1 - - + -
114A VAL* 3.5 10.0 - - + +
115A SER 2.9 16.5 + - - +
116A LEU* 3.9 7.4 - - + +
118A ARG* 1.3 78.0 - - - +
120A LEU* 1.3 58.9 + - + +
122A TYR* 3.5 1.0 + - - +
123A MET* 3.0 53.0 + - + +
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Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.3 34.0 + - + +
117A LEU* 3.2 13.6 + - + +
119A ALA* 1.3 78.0 - - + +
121A VAL* 1.3 64.6 + - + +
123A MET* 3.6 11.3 + - + +
124A ILE* 3.1 34.9 + - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 6.3 0.9 - - + -
37A PHE* 3.2 32.5 - - + -
38A TRP* 3.9 17.7 - - + -
41A ALA* 3.7 27.1 - - + -
117A LEU* 3.0 23.3 + - + +
118A ARG 4.0 1.8 - - - +
120A LEU* 1.3 73.1 - - + +
122A TYR* 1.3 67.9 + - + +
124A ILE* 3.4 10.5 + - - +
125A ALA* 3.0 22.6 + - + +
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PHE* 5.3 3.4 - + - -
40A ALA* 3.3 21.1 - - + +
41A ALA* 4.4 9.4 - - + -
44A GLU* 3.7 27.8 - - + +
96A SER 2.5 30.7 + - - -
99A HIS* 3.8 31.2 - + - -
105A THR* 4.0 11.7 - - + -
114A VAL* 5.6 0.2 - - + -
118A ARG* 2.8 70.7 + - + +
119A ALA 3.6 4.3 - - - +
121A VAL* 1.3 80.3 - - + +
123A MET* 1.3 57.4 + - - +
125A ALA* 3.2 7.8 + - - +
126A GLN* 2.8 37.5 + - - +
194A VAL* 6.1 0.2 - - + -
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Residues in contact with MET 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 4.0 23.4 - - + +
105A THR* 3.6 20.0 - - + -
106A PHE* 4.0 23.1 - - + +
109A PHE* 5.3 2.0 - - + -
119A ALA* 3.0 38.0 + - + +
120A LEU* 4.0 11.7 - - + +
122A TYR* 1.3 72.9 - - - +
124A ILE* 1.3 60.4 + - + +
126A GLN* 3.2 8.7 + - - +
127A CYS* 2.8 35.0 + - - +
246A TRP* 6.3 0.9 - - - -
250A PHE* 4.3 24.9 - - + -
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Residues in contact with ILE 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.1 25.0 + - + +
121A VAL* 3.7 9.4 - - - +
123A MET* 1.3 75.0 - - + +
125A ALA* 1.3 55.8 + - - +
127A CYS* 3.0 6.4 + - - +
128A LEU* 2.7 61.4 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 3.3 33.0 - - + +
44A GLU* 4.4 4.0 - - + -
45A PHE* 3.5 19.9 - - + +
121A VAL* 3.0 17.6 + - + +
122A TYR* 3.4 7.0 - - - +
124A ILE* 1.3 78.6 - - - +
126A GLN* 1.3 51.9 + - - +
128A LEU* 4.5 5.6 - - - -
129A GLY* 2.8 30.3 + - - -
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Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 2.7 32.5 + - + +
48A THR* 2.9 42.6 - - - +
99A HIS* 3.6 1.8 - - - +
101A ASN 3.1 16.9 - - - +
102A PRO* 2.8 30.4 - - + +
105A THR* 3.0 23.6 + - - -
122A TYR* 2.8 24.0 + - - +
123A MET* 3.6 8.0 - - - +
125A ALA* 1.3 76.1 - - - +
127A CYS* 1.3 59.7 + - - +
129A GLY 3.8 0.2 - - - -
130A ALA* 3.1 11.1 + - - +
224A ALA* 3.4 14.5 - - + +
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Residues in contact with CYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 5.3 2.9 - - - -
123A MET* 2.8 19.7 + - - +
124A ILE* 3.6 6.1 - - - +
126A GLN* 1.3 76.5 - - - +
128A LEU* 1.3 66.8 + - + +
130A ALA* 3.2 14.2 + - - +
131A ILE* 3.2 22.9 + - - +
224A ALA* 4.4 12.1 - - - -
227A PHE* 3.4 35.7 - - + -
246A TRP* 4.1 21.1 - - - -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.1 21.4 - - + -
124A ILE* 2.7 44.6 + - + +
125A ALA* 4.1 4.9 - - - +
127A CYS* 1.3 73.3 - - + +
129A GLY* 1.3 63.8 + - - +
131A ILE* 4.7 11.9 - - + +
132A CYS* 3.6 19.2 + - - +
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Residues in contact with GLY 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 3.3 34.3 - - - -
48A THR* 4.3 1.1 - - - -
49A LEU* 2.9 29.2 - - - +
125A ALA 2.8 14.5 + - - -
126A GLN 4.1 0.9 - - - -
127A CYS 3.2 0.4 - - - -
128A LEU* 1.3 77.2 - - - +
130A ALA* 1.3 62.0 + - - +
132A CYS* 3.7 1.4 - - - +
133A GLY 3.2 9.7 + - - -
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 3.6 9.6 - - + +
52A LEU* 3.8 14.1 - - + +
126A GLN 3.1 15.3 + - - +
127A CYS* 3.2 10.9 + - - +
129A GLY* 1.3 74.7 - - - +
131A ILE* 1.3 68.0 + - - +
133A GLY* 2.9 5.0 + - - -
134A VAL* 2.9 26.8 + - - +
224A ALA 3.2 30.1 - - - +
228A GLY* 4.1 4.9 - - - -
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Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A CYS 3.2 17.2 + - - +
128A LEU* 4.7 12.3 - - + +
130A ALA* 1.3 77.4 - - - +
132A CYS* 1.3 53.2 + - - +
134A VAL 3.3 0.2 + - - -
135A GLY* 2.7 32.1 + - - -
227A PHE* 4.1 14.4 - - + -
228A GLY* 3.6 25.5 - - - +
231A VAL* 3.6 32.1 - - + -
232A ILE* 3.2 29.3 - - + +
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Residues in contact with CYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 4.0 15.9 - - - -
49A LEU* 3.8 17.7 - - + -
128A LEU 3.6 15.9 + - - +
129A GLY 3.7 8.9 + - - +
130A ALA 3.2 0.6 - - - -
131A ILE* 1.3 76.6 - - - +
133A GLY* 1.3 54.3 + - - +
135A GLY* 3.3 1.2 + - - -
136A LEU* 2.7 37.2 + - - +
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.5 31.1 - - - +
52A LEU* 4.2 0.4 - - - -
53A TYR* 3.7 12.5 - - - -
129A GLY 3.2 4.4 + - - -
130A ALA 2.9 8.0 + - - -
132A CYS* 1.3 79.9 - - - +
134A VAL* 1.3 60.8 + - - +
136A LEU* 3.3 8.6 + - - +
137A VAL* 3.2 23.7 + - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 26.7 - - + -
56A VAL* 4.3 7.2 - - + -
130A ALA 2.9 17.8 + - - +
131A ILE 3.7 1.1 - - - +
133A GLY* 1.3 72.5 - - - +
135A GLY* 1.3 68.1 + - - +
137A VAL* 2.9 25.8 + - - +
138A LYS* 3.1 5.7 + - - +
145A TYR* 3.2 32.4 - - + +
150A GLY 4.6 1.8 - - - +
228A GLY 3.6 21.1 - - - +
229A ALA* 3.8 10.8 - - + +
232A ILE* 3.4 21.3 - - + -
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE 2.7 21.7 + - - -
132A CYS* 3.7 1.8 - - - -
134A VAL* 1.3 73.0 - - - +
136A LEU* 1.3 62.0 + - - +
138A LYS* 3.1 4.9 + - - +
139A ALA* 2.9 24.2 + - - +
232A ILE* 3.5 23.2 - - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.7 11.2 - - + -
53A TYR* 3.8 26.9 - - + -
132A CYS 2.7 21.7 + - - +
133A GLY* 3.4 7.6 - - - +
134A VAL 3.1 0.2 - - - -
135A GLY* 1.3 71.4 - - - +
137A VAL* 1.3 59.9 + - - +
139A ALA* 3.9 6.2 + - + -
140A PHE* 3.0 60.7 + - + -
170D ILE* 4.2 20.9 - - + -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.8 31.4 - - + +
56A VAL* 3.8 33.9 - - + -
57A ALA* 4.0 15.7 - - + -
60A ILE* 4.3 2.9 - - + -
133A GLY 3.2 17.3 - - - +
134A VAL* 2.9 9.0 + - - +
136A LEU* 1.3 75.1 - - - +
138A LYS* 1.3 57.9 + - - +
140A PHE* 2.7 28.3 + - - +
141A MET* 2.9 27.3 + - + +
145A TYR* 4.0 10.5 - - + -
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL 3.1 6.7 + - - +
135A GLY* 3.1 8.9 + - - +
137A VAL* 1.3 79.1 - - - +
139A ALA* 1.3 59.9 + - - +
141A MET 3.1 0.3 + - - -
142A LYS* 2.5 59.7 + - + +
145A TYR* 3.9 27.9 - - + -
146A ASN* 3.6 30.7 + - - +
232A ILE* 3.7 38.4 + - + +
233A PHE 5.5 0.8 + - - -
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Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLY 2.9 15.2 + - - +
136A LEU* 3.9 11.4 - - + +
138A LYS* 1.3 76.4 - - - +
140A PHE* 1.3 70.4 + - + +
142A LYS* 4.7 3.4 + - - +
163D THR* 4.3 4.0 + - - -
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 3.6 34.1 - + - -
136A LEU* 3.0 41.1 - - + -
137A VAL* 2.7 14.7 + - - +
139A ALA* 1.3 80.6 - - + +
141A MET* 1.3 69.5 + - + +
142A LYS 3.9 0.2 - - - -
158D GLY 5.5 0.5 - - - +
159D TYR* 4.2 6.8 - - - -
160D ASN* 4.8 1.2 - - - +
163D THR* 3.2 48.7 + - + +
166D GLY* 3.6 21.8 - - - -
167D ALA* 3.4 24.5 - - + -
170D ILE* 4.5 2.0 - - + -
216D ILE* 4.8 2.0 - - + -
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Residues in contact with MET 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TYR* 5.5 0.9 - - + +
57A ALA* 4.3 17.9 - - + +
60A ILE* 3.9 28.7 - - + -
61A GLY* 4.9 1.6 - - - -
64A LYS* 4.9 1.3 - - - -
137A VAL* 2.9 30.9 + - + +
138A LYS 3.1 2.2 - - - -
140A PHE* 1.3 96.1 - - + +
142A LYS* 1.3 61.1 + - - +
143A GLY 3.2 3.5 + - - +
144A PRO* 3.6 18.1 - - + +
145A TYR* 2.8 26.8 + - + +
159D TYR* 3.9 24.5 - - + -
212D ALA 5.6 0.4 - - - +
216D ILE* 4.0 29.8 - - + -
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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