Contacts of the helix formed by residues 124 - 149 (chain A) in PDB entry 4PQ6
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 GLY 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 5.5 0.7 - - - -
120A PRO 3.8 6.1 + - - -
121A GLY 5.3 0.4 - - - -
122A ASP 3.9 1.0 - - - -
123A PHE* 1.3 78.6 - - - +
125A ALA* 1.3 59.7 + - - -
126A ASP 3.3 2.5 - - - -
127A ALA* 3.2 6.4 + - - +
128A GLN* 2.9 32.4 + - - +
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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
----------------------------------------------------------
124A GLY* 1.3 71.6 - - - +
126A ASP* 1.3 63.8 + - - +
128A GLN* 3.4 9.5 + - - +
129A GLY* 2.9 25.8 + - - -
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.9 15.8 - - + +
124A GLY 3.3 0.6 - - - -
125A ALA* 1.3 82.4 - - - +
127A ALA* 1.3 57.1 + - - +
129A GLY* 3.3 2.6 + - - +
130A ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.0 34.0 - - + +
10A VAL* 5.3 0.5 - - - +
13A VAL* 5.8 0.2 - - - +
122A ASP 4.1 7.2 - - - +
123A PHE* 3.7 29.7 - - + +
124A GLY 3.2 10.1 + - - +
126A ASP* 1.3 77.3 - - - +
128A GLN* 1.3 60.2 + - - +
130A ALA* 3.2 3.5 + - - +
131A MET* 2.9 28.6 + - - +
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Residues in contact with GLN 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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112A ILE* 4.0 19.0 - - + +
116A HIS* 3.1 26.1 + - - +
123A PHE* 2.9 50.6 + - + +
124A GLY* 2.9 22.5 + - - +
125A ALA* 3.7 7.5 - - - +
127A ALA* 1.3 74.8 - - - +
129A GLY* 1.3 58.5 + - - +
131A MET* 3.3 1.4 + - - +
132A ASN* 2.8 32.7 + - - +
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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
----------------------------------------------------------
6A GLU* 6.0 0.2 - - - -
125A ALA 2.9 15.2 + - - -
126A ASP* 3.3 4.7 + - - -
128A GLN* 1.3 75.6 - - - +
130A ALA* 1.3 57.2 + - - +
132A ASN* 3.4 7.7 + - - +
133A LYS* 3.0 36.6 + - - +
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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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2A LEU* 3.7 2.3 - - - +
6A GLU* 3.5 46.7 - - + +
9A LEU* 4.1 10.3 - - + -
10A VAL* 3.5 10.3 - - + +
126A ASP 2.9 13.6 + - - +
127A ALA 3.6 7.4 - - - +
129A GLY* 1.3 73.9 - - - +
131A MET* 1.3 59.9 + - - +
133A LYS* 3.2 8.2 + - - +
134A ALA* 2.9 24.3 + - - +
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Residues in contact with MET 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 3.8 32.6 - - + +
13A VAL* 3.6 27.8 - - + -
14A TRP* 4.3 13.2 - - + -
76A LEU* 4.4 9.6 - - - -
111A ILE* 5.0 3.1 - - + -
112A ILE* 3.5 19.1 - - + -
115A LEU* 3.9 16.8 - - + -
123A PHE* 3.8 15.3 - - + -
127A ALA 2.9 16.5 + - - +
128A GLN 3.8 2.2 - - - +
130A ALA* 1.3 76.9 - - - +
132A ASN* 1.3 62.8 + - - +
134A ALA* 3.2 4.3 + - - +
135A LEU* 2.9 43.2 + - + +
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Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 5.9 2.6 - - - -
112A ILE* 3.7 26.8 - - - +
128A GLN 2.8 17.8 + - - +
129A GLY* 3.6 7.4 - - - +
130A ALA 3.2 0.2 - - - -
131A MET* 1.3 77.2 - - - +
133A LYS* 1.3 57.5 + - - +
135A LEU* 3.4 5.4 + - - +
136A GLU* 2.8 35.9 + - - +
139A ARG* 4.9 10.5 + - - +
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A VAL 5.0 7.2 + - - +
2A LEU* 3.9 17.6 - - + +
6A GLU* 2.9 40.1 + - - +
129A GLY 3.0 19.5 + - - +
130A ALA 3.2 8.0 + - - +
132A ASN* 1.3 76.4 - - + +
134A ALA* 1.3 57.0 + - - +
136A GLU* 3.2 14.7 + - - +
137A LEU* 2.9 30.3 + - - +
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Residues in contact with ALA 134 (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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2A LEU* 3.8 11.6 - - + +
7A TRP* 3.9 19.9 - - + -
10A VAL* 4.0 8.7 - - + -
76A LEU* 3.8 26.6 - - + +
82A HIS* 6.0 0.3 - - - -
130A ALA 2.9 13.5 + - - +
131A MET* 3.6 9.0 - - - +
133A LYS* 1.3 77.7 - - - +
135A LEU* 1.3 58.0 + - - +
137A LEU* 3.4 5.5 + - - +
138A PHE* 3.0 26.3 + - - +
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Residues in contact with LEU 135 (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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72A LEU* 4.2 33.2 - - + -
76A LEU* 4.8 5.2 - - + -
108A SER* 3.9 35.2 - - - +
111A ILE* 4.2 15.7 - - + -
112A ILE* 4.3 6.7 - - + -
131A MET* 2.9 42.3 + - + +
132A ASN* 4.0 4.9 - - - +
134A ALA* 1.3 75.0 - - - +
136A GLU* 1.3 59.5 + - - +
138A PHE* 3.3 10.8 + - + +
139A ARG* 2.9 48.5 + - - +
201A HEM 5.8 1.1 - - + -
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Residues in contact with GLU 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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132A ASN* 2.8 22.8 + - - +
133A LYS* 3.5 15.0 - - - +
135A LEU* 1.3 76.6 - - - +
137A LEU* 1.3 56.7 + - - +
139A ARG* 3.3 26.0 + - + +
140A LYS* 2.9 31.4 + - + +
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Residues in contact with LEU 137 (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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1A VAL* 5.6 10.5 - - + +
2A LEU* 4.3 11.4 - - + +
7A TRP* 4.0 20.0 - - + -
80A GLY* 4.0 27.1 - - - +
82A HIS* 4.1 7.0 - - + -
133A LYS 2.9 16.7 + - - +
134A ALA* 3.6 4.7 - - - +
136A GLU* 1.3 75.6 - - - +
138A PHE* 1.3 59.2 + - - +
140A LYS* 3.3 14.9 + - + +
141A ASP* 2.9 52.8 + - - +
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Residues in contact with PHE 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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72A LEU* 4.7 9.6 - - + -
75A ILE* 4.0 24.7 - - + -
76A LEU* 6.1 1.6 - - + -
82A HIS* 4.7 10.2 - - + -
86A LEU* 3.5 30.6 - - + +
89A LEU* 3.8 20.0 - - + -
104A LEU* 4.4 18.6 - - + -
108A SER* 5.3 3.1 - - - -
134A ALA 3.0 14.7 + - - +
135A LEU* 3.4 22.2 - - + +
137A LEU* 1.3 75.7 - - - +
139A ARG* 1.3 65.9 + - + +
141A ASP* 3.8 2.3 - - - +
142A ILE* 2.9 40.4 + - + +
201A HEM 3.8 37.5 - - + -
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Residues in contact with ARG 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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101A ILE* 4.0 15.1 - - + +
104A LEU* 3.7 15.0 - - + -
105A GLU* 3.5 49.1 + - - +
108A SER* 3.0 28.9 + - - +
132A ASN* 4.9 10.1 + - - +
135A LEU* 2.9 33.1 + - - +
136A GLU* 3.7 31.0 - - + +
138A PHE* 1.3 87.6 - - + +
140A LYS* 1.3 57.5 + - - +
142A ILE* 3.4 9.8 - - - +
143A ALA* 3.0 30.5 + - - +
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Residues in contact with LYS 140 (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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136A GLU* 2.9 19.1 + - + +
137A LEU* 3.6 14.8 - - + +
139A ARG* 1.3 76.1 - - - +
141A ASP* 1.3 73.5 + - - +
143A ALA* 3.3 7.9 + - - +
144A ALA* 3.2 21.0 + - - +
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Residues in contact with ASP 141 (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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80A GLY 4.7 2.1 - - - +
82A HIS* 2.8 26.3 + - + +
86A LEU* 3.5 21.1 - - + -
137A LEU* 2.9 36.0 + - - +
138A PHE 4.0 0.4 - - - +
140A LYS* 1.3 88.4 + - - +
142A ILE* 1.3 62.8 + - - +
144A ALA* 3.3 4.8 + - - +
145A LYS* 3.1 40.6 + - - +
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Residues in contact with ILE 142 (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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86A LEU* 3.8 23.7 - - + +
89A LEU* 4.3 9.9 - - + +
90A ALA* 3.7 35.9 - - + +
93A HIS* 5.1 2.9 - - + -
101A ILE* 3.8 4.9 - - + -
104A LEU* 3.4 31.4 - - + -
138A PHE* 2.9 32.1 + - + +
139A ARG* 3.4 12.1 - - - +
141A ASP* 1.3 76.7 - - - +
143A ALA* 1.3 55.2 + - - +
145A LYS* 3.1 3.4 + - - +
146A TYR* 2.7 48.2 + - + +
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Residues in contact with ALA 143 (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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101A ILE* 3.8 26.0 - - + -
139A ARG 3.0 19.2 + - - +
140A LYS* 3.6 7.0 - - - +
141A ASP 3.3 0.2 - - - -
142A ILE* 1.3 76.5 - - - +
144A ALA* 1.3 59.9 + - - +
146A TYR* 3.3 7.5 - - - +
147A LYS* 3.1 36.0 + - - +
153A GLY* 5.6 2.6 - - - -
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Residues in contact with ALA 144 (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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140A LYS* 3.2 15.5 + - - +
141A ASP* 3.6 10.8 - - - +
142A ILE 3.3 0.4 - - - -
143A ALA* 1.3 75.3 - - - +
145A LYS* 1.3 72.4 + - + +
147A LYS* 3.4 10.9 + - - +
148A GLU* 3.1 26.6 + - - +
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Residues in contact with LYS 145 (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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83A GLU* 5.0 17.0 - - - +
86A LEU* 4.7 11.5 - - + +
87A LYS* 4.5 24.0 - - + -
90A ALA* 3.6 23.8 - - + -
141A ASP* 3.1 37.1 + - - +
142A ILE* 3.6 4.7 - - - +
144A ALA* 1.3 84.3 - - - +
146A TYR* 1.3 65.5 + - - +
148A GLU* 3.2 35.4 + - - +
149A LEU* 3.2 21.9 + - + +
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Residues in contact with TYR 146 (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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90A ALA* 3.7 12.8 - - + -
93A HIS* 3.5 17.6 - - + +
94A ALA* 3.4 33.0 - - + -
99A ILE* 2.8 32.5 + - - +
101A ILE* 3.6 30.7 - - + -
104A LEU* 4.1 10.7 - - - +
142A ILE* 2.7 33.4 + - + +
143A ALA* 3.3 9.4 - - - +
145A LYS* 1.3 72.5 - - - +
147A LYS* 1.3 62.1 - - - +
149A LEU* 3.0 12.2 + - - +
150A GLY 3.1 0.2 + - - -
151A TYR* 2.9 51.5 + + + +
153A GLY* 4.0 9.6 - - - +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ALA* 3.1 22.9 + - - +
144A ALA* 3.7 9.9 - - - +
145A LYS 3.2 0.2 - - - -
146A TYR* 1.3 79.2 - - - +
148A GLU* 1.3 59.0 + - - +
150A GLY* 2.8 20.3 + - - +
151A TYR 3.6 10.3 - - - +
152A GLN* 2.8 49.3 + - - +
153A GLY* 4.8 3.4 - - - +
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Residues in contact with GLU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 6.0 1.7 - - - +
144A ALA* 3.1 18.1 + - - +
145A LYS* 3.2 30.9 + - - +
147A LYS* 1.3 76.2 - - - +
149A LEU* 1.3 60.7 + - + +
150A GLY 3.3 0.2 - - - -
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS 5.3 0.7 - - - +
90A ALA* 3.7 12.3 - - + +
91A GLN* 3.4 59.2 - - + +
94A ALA* 4.0 11.0 - - + -
95A THR* 4.5 13.6 - - + +
145A LYS* 3.4 16.8 - - + +
146A TYR* 3.0 8.3 + - - +
148A GLU* 1.3 78.1 - - + +
150A GLY* 1.3 59.5 + - - +
151A TYR* 3.5 1.9 + - + +
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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