Contacts of the helix formed by residues 121 - 149 (chain A) in PDB entry 5C5B
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 ARG 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN* 2.9 53.0 + - + +
120A GLU* 1.3 80.6 - - - +
122A ASP* 1.3 86.9 + - - +
123A LEU 3.7 0.4 - - - -
124A LYS* 4.0 0.7 - - - +
125A GLU* 3.0 35.7 + - + +
191A LYS* 4.5 9.4 - - - +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLN 3.5 2.8 - - - +
118A PHE* 3.3 46.6 + - + +
121A ARG* 1.3 99.3 + - - +
123A LEU* 1.3 60.9 + - - +
125A GLU* 3.3 9.9 + - - +
126A ILE* 2.9 34.5 + - + +
188A LEU* 5.0 3.8 - - + -
191A LYS* 2.5 43.6 + - + +
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 4.8 4.9 - - + +
33A ILE* 4.6 5.6 - - + -
34A SER* 3.9 28.3 - - - +
37A MET* 4.6 3.6 - - + -
118A PHE* 3.1 45.3 + - + +
119A LYS* 3.5 47.3 - - + +
122A ASP* 1.3 78.2 - - - +
124A LYS* 1.3 59.6 - - - +
126A ILE* 3.2 10.7 + - + +
127A LEU* 2.9 28.9 + - - +
188A LEU* 4.5 15.7 - - + -
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 3.4 27.9 + - - +
120A GLU* 3.8 37.5 - - - +
121A ARG 3.8 1.1 + - - +
122A ASP 3.3 0.4 - - - -
123A LEU* 1.3 80.1 - - + +
125A GLU* 1.3 57.7 + - - +
127A LEU* 3.3 22.1 + - + +
128A THR* 2.8 33.6 + - - +
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 3.0 24.7 + - + +
122A ASP* 3.7 13.2 - - - +
124A LYS* 1.3 73.3 - - - +
126A ILE* 1.3 64.0 + - + +
128A THR* 3.2 6.9 + - - -
129A LEU* 2.9 54.8 + - + +
184A ALA* 5.2 7.0 - - + +
191A LYS* 4.9 5.9 + - - -
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA* 4.8 11.9 - - + -
122A ASP* 2.9 21.8 + - + +
123A LEU* 3.3 13.0 - - + +
125A GLU* 1.3 77.4 - - + +
127A LEU* 1.3 58.4 + - - +
129A LEU* 4.0 2.6 - - - -
130A LYS* 2.9 32.7 + - + +
181A TYR* 3.9 11.6 - - + +
184A ALA* 3.6 43.3 - - + +
185A LEU* 4.0 26.5 - - + +
188A LEU* 4.3 19.7 - - + -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU 2.9 12.7 + - - +
124A LYS* 3.7 28.3 - - + +
126A ILE* 1.3 77.5 - - - +
128A THR* 1.3 58.4 + - - +
130A LYS* 3.3 15.6 - - + +
131A GLU* 3.0 48.9 + - + +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LYS* 2.8 25.1 + - - +
125A GLU* 3.4 9.0 - - - -
127A LEU* 1.3 78.7 - - - +
129A LEU* 1.3 65.2 + - + +
131A GLU* 3.1 5.7 + - - +
132A VAL* 2.9 43.5 + - + +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 2.9 50.8 + - + +
126A ILE* 4.0 3.4 - - - +
128A THR* 1.3 82.6 - - + +
130A LYS* 1.3 57.4 + - - +
132A VAL* 3.7 8.6 - - + +
133A PHE* 2.9 31.0 + - - +
177A THR* 4.8 2.4 - - - +
180A HIS* 3.4 44.2 - - + +
181A TYR* 4.4 13.7 - - + +
184A ALA* 3.8 15.5 - - + -
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 3.2 22.8 + - + +
31A THR* 5.1 7.3 + - - -
126A ILE* 2.9 21.2 + - + +
127A LEU* 3.3 16.4 - - + +
129A LEU* 1.3 77.5 - - - +
131A GLU* 1.3 67.9 + - + +
133A PHE* 3.2 6.1 + - + +
134A GLN* 2.9 54.6 + - + +
181A TYR* 3.3 36.0 - - + +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.0 35.6 + - + +
128A THR* 3.1 4.0 + - - +
130A LYS* 1.3 82.4 - - + +
132A VAL* 1.3 61.5 + - + +
134A GLN* 3.5 28.8 + - - +
135A ILE* 2.9 37.1 + - + +
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 2.9 34.6 + - + +
129A LEU* 3.7 7.2 - - + +
131A GLU* 1.3 77.8 - - - +
133A PHE* 1.3 57.5 + - - +
135A ILE* 3.3 7.0 + - - +
136A ALA* 2.9 28.1 + - - +
173A LYS* 4.7 14.0 + - - +
177A THR* 3.6 23.8 - - + -
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Residues in contact with PHE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.8 35.2 - - - -
23A LEU* 3.6 24.9 - - + -
27A GLU* 5.2 2.0 - - - -
129A LEU 2.9 18.1 + - - +
130A LYS 3.4 5.2 - - - +
132A VAL* 1.3 77.3 - - - +
134A GLN* 1.3 65.4 + - + +
136A ALA* 3.4 1.0 + - - +
137A SER* 2.9 28.9 + - - -
174A GLN* 4.4 6.7 - - + -
177A THR* 3.8 21.0 - - - +
178A MET* 3.5 48.5 - - + -
181A TYR* 3.7 23.8 - + + -
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU* 5.0 1.4 + - - -
130A LYS* 2.9 50.1 + - + +
131A GLU* 3.5 29.3 + - - +
132A VAL 3.3 0.2 - - - -
133A PHE* 1.3 83.8 - - + +
135A ILE* 1.3 57.3 + - + +
137A SER* 3.2 7.7 + - - -
138A ASN* 3.0 38.8 + - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 2.9 23.3 + - + +
132A VAL* 3.3 6.7 + - - +
134A GLN* 1.3 76.4 - - + +
136A ALA* 1.3 62.7 + - - +
138A ASN* 3.2 10.8 + - - +
139A ASP* 2.9 38.7 + - - +
173A LYS* 5.3 8.5 - - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL 2.9 17.2 + - - +
133A PHE 3.7 1.1 - - - +
135A ILE* 1.3 77.3 - - - +
137A SER* 1.3 57.3 + - - +
139A ASP* 3.4 9.3 + - - +
140A HIS* 2.9 28.8 + - - +
170A SER 4.3 4.6 - - - +
173A LYS* 4.2 16.1 - - + +
174A GLN* 4.0 16.8 - - - +
177A THR* 3.6 28.0 - - + +
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG* 3.4 24.1 + - - -
133A PHE* 2.9 24.6 + - - -
134A GLN* 3.4 8.7 - - - -
135A ILE 3.2 0.2 - - - -
136A ALA* 1.3 76.3 - - - +
138A ASN* 1.3 65.9 + - - +
140A HIS* 3.2 3.6 + - - +
141A ASP* 2.9 35.9 + - - +
174A GLN* 3.4 20.5 + - - +
314B ARG* 3.8 3.8 + - - -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 3.0 25.4 + - - +
135A ILE* 3.6 10.9 - - - +
137A SER* 1.3 78.9 + - - +
139A ASP* 1.3 65.8 + - - +
141A ASP* 3.2 15.3 + - - +
142A ALA* 3.0 23.4 + - - +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 2.9 35.7 + - - +
136A ALA* 3.6 8.4 - - - +
138A ASN* 1.3 78.8 - - - +
140A HIS* 1.3 57.3 + - - +
142A ALA* 3.3 8.2 + - - +
143A ALA* 2.9 28.1 + - - +
170A SER* 4.0 10.7 - - - -
173A LYS* 5.5 4.2 + - - +
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Residues in contact with HIS 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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15A ASP* 5.7 1.1 - - - -
136A ALA 2.9 18.4 + - - +
137A SER 3.2 4.0 + - - +
139A ASP* 1.3 71.9 - - - +
141A ASP* 1.3 74.3 + - - +
143A ALA* 3.2 1.0 + - - +
144A ILE* 2.9 28.0 + - + +
167A VAL* 4.1 4.9 - - + -
170A SER* 3.3 22.8 - - - +
171A ARG* 3.0 57.4 + - + +
174A GLN* 3.3 30.1 + - - +
299B ARG* 4.2 26.6 + - - -
314B ARG* 5.4 1.2 + - - -
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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
----------------------------------------------------------
137A SER* 2.9 25.3 + - - +
138A ASN* 3.2 16.5 + - - +
140A HIS* 1.3 81.9 + - - +
142A ALA* 1.3 63.1 + - - +
144A ILE* 3.3 7.8 - - - +
145A ASN* 3.0 36.9 + - - +
174A GLN* 4.9 0.3 - - - +
299B ARG* 4.5 5.0 + - - -
314B ARG* 3.0 36.9 + - - -
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Residues in contact with ALA 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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138A ASN 3.0 13.3 + - - +
139A ASP* 3.5 11.0 - - - +
141A ASP* 1.3 76.3 - - - +
143A ALA* 1.3 61.8 + - - +
145A ASN* 3.2 11.7 + - - +
146A ARG* 3.0 35.0 + - - +
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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
----------------------------------------------------------
139A ASP 2.9 12.8 + - - +
140A HIS 3.5 2.0 - - - +
142A ALA* 1.3 76.7 - - - +
144A ILE* 1.3 56.9 + - - +
146A ARG* 3.2 8.4 + - - +
147A TYR 2.9 22.2 + - - -
163A VAL* 4.3 2.0 - - - +
166A ASP* 4.1 9.6 - - + +
167A VAL* 3.3 27.0 - - + +
170A SER* 3.2 29.2 - - - +
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Residues in contact with ILE 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 HIS* 2.9 24.2 + - + +
141A ASP* 3.3 16.4 - - - +
143A ALA* 1.3 75.1 - - - +
145A ASN* 1.3 67.0 + - - +
147A TYR* 3.5 14.0 - - + +
148A SER* 2.9 37.7 + - - +
167A VAL* 3.9 5.3 - - + +
171A ARG* 4.0 20.6 - - - +
299B ARG* 4.0 39.7 - - - +
358B GLU* 4.2 10.1 - - + +
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Residues in contact with ASN 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 3.0 36.6 + - - +
142A ALA* 3.2 8.9 + - - +
144A ILE* 1.3 81.3 - - - +
146A ARG* 1.3 59.8 + - - +
148A SER* 3.2 9.5 + - - -
149A ARG* 3.0 36.5 + - - +
285B ASN* 5.3 2.8 + - - +
299B ARG* 5.0 11.6 - - - +
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 3.0 21.6 + - - +
143A ALA* 3.7 8.5 - - - +
145A ASN* 1.3 76.1 - - - +
147A TYR* 1.3 62.5 + - - +
149A ARG* 3.5 19.9 + - + +
150A LEU* 3.6 12.0 + - - +
163A VAL* 3.7 22.1 - - + +
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Residues in contact with TYR 147 (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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143A ALA 2.9 5.5 + - - -
144A ILE* 3.5 14.8 - - + +
145A ASN 3.1 0.2 - - - -
146A ARG* 1.3 76.0 - - - +
148A SER* 1.3 69.4 + - - +
150A LEU* 3.2 30.3 + - + +
160A LYS* 5.9 0.4 - - + -
163A VAL* 3.5 7.4 - - + +
164A THR* 3.7 35.0 - - + -
167A VAL* 3.6 20.9 - - + -
264B PRO* 3.8 22.4 + - + +
265B ASP* 3.6 13.0 - - - +
339B ARG* 3.2 39.0 + - - +
340B TYR* 5.6 0.2 - + - -
358B GLU* 2.9 46.2 + - + -
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ILE* 2.9 22.8 + - - +
145A ASN* 3.5 11.6 + - - -
147A TYR* 1.3 82.0 - - - +
149A ARG* 1.3 61.7 + - - +
150A LEU 3.1 4.2 + - - +
285B ASN* 2.7 32.0 + - - -
299B ARG* 5.9 0.3 - - - -
338B ARG* 3.5 24.7 + - - +
339B ARG* 4.9 0.9 + - - +
356B GLN* 3.2 25.2 + - - +
358B GLU* 6.2 0.2 - - - +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASN* 3.0 24.6 + - - +
146A ARG* 3.9 15.0 - - + +
147A TYR 3.2 0.6 - - - -
148A SER* 1.3 73.1 - - - +
150A LEU* 1.3 67.4 + - - +
151A SER* 3.5 2.3 + - - -
338B ARG* 3.9 26.8 - - - +
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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