Contacts of the helix formed by residues 130 - 151 (chain E) in PDB entry 4O9U
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 ASP 130 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B NAP 4.3 2.6 - - - -
120E ILE* 4.5 13.7 - - - +
121E PRO 5.0 1.5 - - - +
122E ARG* 3.4 28.6 + - - +
126E ALA 2.6 15.4 + - - +
127E GLN* 3.3 32.0 + - + +
128E SER 3.7 0.2 - - - -
129E MET* 1.3 68.7 - - - +
131E ALA* 1.3 64.1 + - - +
132E LEU* 3.7 20.1 - - - +
133E SER* 3.3 32.9 + - - +
134E SER* 3.3 12.6 + - - -
329E ASN* 4.1 3.5 + - - +
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Residues in contact with ALA 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E PHE* 4.4 19.0 - - + -
117E MET* 3.7 33.9 + - + +
120E ILE* 5.5 1.6 - - - +
129E MET 2.8 6.5 + - - -
130E ASP* 1.3 69.8 + - - +
132E LEU* 1.3 65.2 + - - +
133E SER 3.2 0.7 - - - -
134E SER* 2.9 22.3 + - - +
135E GLN* 3.1 17.5 + - + +
326E TYR* 4.7 11.4 - - + -
329E ASN* 3.6 9.6 - - - +
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E PHE* 5.0 9.7 - - + -
117E MET 5.1 4.1 + - - +
118E GLU* 3.7 37.5 - - + +
120E ILE* 4.5 11.4 - - + +
122E ARG* 3.3 36.3 - - - +
130E ASP* 3.7 7.2 + - - +
131E ALA* 1.3 78.7 - - - +
133E SER* 1.3 59.3 + - - +
135E GLN* 5.1 0.6 - - - +
136E ALA* 3.3 26.5 + - - +
177E VAL* 3.9 4.6 - - - +
500E NAD 3.4 25.5 + - - +
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Residues in contact with SER 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO* 4.1 19.3 - - - -
500B NAP 4.3 14.9 + - - -
122E ARG* 4.5 6.1 + - - -
127E GLN 5.8 0.2 - - - -
130E ASP* 3.3 32.5 + - - -
131E ALA 3.2 0.8 - - - -
132E LEU* 1.3 77.3 - - - +
134E SER* 1.3 57.3 + - - +
137E THR* 2.6 35.8 + - - -
177E VAL* 3.2 17.2 - - - +
161F ALA* 6.5 0.9 - - - -
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Residues in contact with SER 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO* 5.6 1.1 - - - -
130E ASP 3.3 5.2 + - - -
131E ALA* 2.9 11.0 + - - -
133E SER* 1.3 79.8 - - - +
135E GLN* 1.3 83.6 + - - +
137E THR* 3.3 17.5 - - - -
138E VAL* 3.5 14.0 + - - +
325E MET* 3.7 30.7 - - - +
329E ASN* 2.9 26.1 + - - -
162F ALA* 4.7 4.0 - - - -
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E ARG* 3.7 22.9 + - - +
94E PHE* 4.5 18.6 - - + -
131E ALA 3.1 15.2 + - - +
132E LEU* 5.1 0.7 - - - +
134E SER* 1.3 99.1 + - - +
136E ALA* 1.3 61.5 + - - +
137E THR 3.1 1.8 - - - -
138E VAL* 3.3 6.6 + - - +
139E ALA* 3.1 25.6 + - - +
315E PRO* 3.8 15.5 - - + +
322E ALA* 3.3 42.7 + - - +
325E MET* 4.2 2.2 - - - +
326E TYR* 3.7 23.7 - - + +
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Residues in contact with ALA 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU 3.3 20.9 + - - +
135E GLN* 1.3 75.0 - - - +
137E THR* 1.3 59.3 + - - +
139E ALA* 3.9 7.9 - - - -
140E GLY* 3.1 22.2 + - - -
177E VAL* 3.6 19.5 - - + -
178E ALA* 3.2 27.2 - - + +
284E LEU* 5.7 0.7 - - + -
500E NAD 4.3 10.5 - - - +
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Residues in contact with THR 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO* 3.5 19.2 - - + +
133E SER 2.6 22.7 + - - -
134E SER* 3.3 11.0 - - - +
136E ALA* 1.3 75.7 - - - +
138E VAL* 1.3 65.4 + - - +
141E TYR* 3.2 8.5 + - - +
177E VAL* 4.0 2.9 - - - +
181E MET* 2.9 58.1 - - + +
325E MET* 4.6 11.0 - - + -
154F PHE* 4.5 14.6 - - + -
158F LEU* 5.2 6.5 - - + -
160F THR* 5.3 2.9 - - + -
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Residues in contact with VAL 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E SER 3.5 14.8 + - - +
135E GLN* 3.3 10.2 + - - +
137E THR* 1.3 75.2 - - - +
139E ALA* 1.3 62.8 + - - +
141E TYR* 3.4 5.7 - - - +
142E LEU* 3.3 21.2 + - + +
314E LEU 4.4 1.8 - - - +
315E PRO* 3.8 20.9 - - + -
318E LEU* 3.6 33.2 - - + -
322E ALA* 3.9 27.6 - - + -
325E MET* 4.3 6.3 - - - -
154F PHE* 3.9 23.6 - - + -
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Residues in contact with ALA 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLN 3.1 15.7 + - - +
136E ALA* 3.9 6.5 - - - +
138E VAL* 1.3 74.9 - - - +
140E GLY* 1.3 54.7 + - - +
141E TYR 3.2 0.2 + - - -
142E LEU* 3.3 3.5 + - - +
143E ALA* 2.8 34.5 + - - +
284E LEU* 3.4 32.9 - - + +
314E LEU* 3.6 26.7 - - + +
315E PRO* 4.9 4.0 - - + -
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Residues in contact with GLY 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E ALA 3.1 14.0 + - - -
139E ALA* 1.3 76.2 - - - +
141E TYR* 1.3 63.2 + - - +
143E ALA* 3.4 15.9 - - - +
144E ALA* 3.4 1.9 + - - +
178E ALA* 3.4 29.0 - - - +
181E MET* 3.8 8.2 - - - +
182E ALA* 3.3 20.8 - - - -
255E THR* 6.2 0.4 - - - -
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Residues in contact with TYR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E THR 3.2 12.9 + - - +
138E VAL 3.4 7.9 - - - +
139E ALA 3.1 0.6 - - - -
140E GLY* 1.3 74.3 - - - +
142E LEU* 1.3 77.3 + - + +
144E ALA* 2.9 22.3 + - - +
145E ILE* 3.1 42.3 + - + +
181E MET* 3.6 5.5 - - + +
185E THR* 4.2 24.1 + - + +
318E LEU* 3.7 40.4 - - + -
148F ALA* 3.9 5.8 + - - +
153F ARG 3.7 3.2 + - - -
154F PHE* 3.4 28.7 - + + -
155F PHE* 3.5 31.2 + - - +
156F PRO* 4.1 17.0 - - + -
189F LEU* 4.9 2.5 - - + -
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E VAL 3.3 6.3 + - - +
139E ALA 3.3 6.6 + - - +
141E TYR* 1.3 87.0 - - + +
143E ALA* 1.3 55.8 + - - +
145E ILE* 3.9 8.7 - - + -
146E HIS* 2.8 57.1 + - + +
314E LEU* 3.3 35.0 - - + +
317E GLU* 3.8 17.9 - - + +
318E LEU* 3.7 39.9 - - + -
148F ALA 4.3 7.0 - - - +
149F ARG* 4.1 19.7 - - - +
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E ALA 2.8 18.2 + - - +
140E GLY* 3.4 13.9 - - - +
141E TYR 3.1 0.2 - - - -
142E LEU* 1.3 77.6 - - - +
144E ALA* 1.3 59.5 + - - +
146E HIS* 4.3 3.1 - - - +
147E ALA* 3.4 19.4 + - - +
182E ALA* 4.5 2.0 - - + -
253E ILE* 4.1 23.4 - - + +
255E THR* 6.1 0.7 - - + -
282E VAL* 3.8 19.0 - - + +
284E LEU* 3.9 17.9 - - + -
314E LEU* 5.0 2.2 - - - +
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E GLY 3.4 3.7 + - - +
141E TYR 2.9 9.6 + - - +
143E ALA* 1.3 77.3 - - - +
145E ILE* 1.3 66.9 + - - +
146E HIS 3.3 0.4 - - - -
147E ALA* 3.1 8.3 + - - +
148E ALA* 3.1 22.9 + - - +
155E PHE* 4.8 2.9 - - + -
182E ALA* 4.0 15.3 - - - +
185E THR* 3.6 28.0 - - + -
186E ALA* 4.3 8.1 - - + +
189E LEU* 4.5 6.8 - - + +
253E ILE* 4.5 6.5 - - + +
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Residues in contact with ILE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E TYR* 3.1 48.1 + - + +
142E LEU* 3.1 11.2 + - + +
144E ALA* 1.3 77.0 - - - +
146E HIS* 1.3 56.7 + - - +
148E ALA* 3.3 3.9 + - - -
149E ARG* 3.0 26.0 + - - +
185E THR* 4.4 4.7 - - + -
189E LEU* 5.7 2.7 - - + -
145F ILE* 3.5 16.3 - - + +
148F ALA* 3.6 10.1 - - + +
149F ARG* 3.3 39.5 - - + +
189F LEU* 3.7 30.5 - - + -
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Residues in contact with HIS 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LEU* 2.8 44.1 + - + +
143E ALA* 4.3 4.3 - - - +
145E ILE* 1.3 76.5 - - - +
147E ALA* 1.3 53.9 + - - +
149E ARG* 4.0 8.5 - - - +
150E LEU* 2.8 52.0 + - + +
282E VAL* 5.7 3.8 - - + -
309E TYR* 3.9 33.9 + + + -
314E LEU* 4.8 6.3 - - + +
317E GLU* 3.0 26.8 + - - -
149F ARG* 3.3 47.6 + - + +
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Residues in contact with ALA 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ALA 3.4 16.4 + - - +
144E ALA* 3.1 14.6 + - - +
146E HIS* 1.3 80.6 - - - +
148E ALA* 1.3 56.7 + - - +
151E SER* 2.9 29.6 + - - -
155E PHE* 3.2 18.6 - - + -
251E VAL* 3.9 21.4 - - + +
253E ILE* 4.3 4.7 - - + -
280E VAL* 4.6 6.2 - - - +
282E VAL* 4.2 9.4 - - + -
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ALA 3.1 6.1 + - - +
145E ILE* 3.9 3.1 - - - +
147E ALA* 1.3 74.6 - - - +
149E ARG* 1.3 65.3 + - - +
150E LEU 3.3 0.4 - - - -
151E SER* 3.9 12.0 - - - +
155E PHE* 3.6 11.7 - - + -
189E LEU* 3.7 30.5 - - + -
141F TYR* 4.0 12.1 + - - +
142F LEU* 3.9 13.2 - - - +
145F ILE* 3.5 26.8 - - + +
318F LEU* 4.9 0.2 - - - +
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Residues in contact with ARG 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ILE 3.0 17.4 + - - +
146E HIS* 3.1 15.2 + - - +
148E ALA* 1.3 79.3 - - - +
150E LEU* 1.3 82.7 + - + +
151E SER 4.6 1.7 - - - +
142F LEU* 5.2 5.7 - - - +
145F ILE* 3.2 13.8 - - + +
146F HIS* 3.2 36.7 + - + -
149F ARG* 2.8 54.3 - - + +
309F TYR* 4.7 7.7 + - - -
317F GLU* 4.7 16.5 + - - +
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E HIS* 2.8 25.9 + - + +
149E ARG* 1.3 109.8 - - + +
151E SER* 1.3 66.4 + - - +
152E PRO* 3.4 2.8 - - - +
280E VAL* 4.5 19.4 - - + +
282E VAL* 6.3 1.8 - - + -
300E VAL* 5.5 15.7 - - + -
307E ARG* 3.5 38.7 + - + +
309E TYR* 4.2 34.3 - - + -
149F ARG* 5.6 0.4 - - - +
317F GLU 5.3 0.9 - - - +
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Residues in contact with SER 151 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ALA 2.9 23.1 + - - -
148E ALA* 3.9 7.0 - - - +
149E ARG 3.6 2.3 - - - +
150E LEU* 1.3 77.4 - - - +
152E PRO* 1.3 66.2 - - - +
153E ARG* 2.9 31.4 + - - +
155E PHE* 3.3 20.1 - - - -
168E ALA* 4.9 1.0 - - - +
250E ASP* 5.5 1.2 - - - +
251E VAL* 4.4 4.1 - - - +
278E GLY 5.2 0.3 + - - -
280E VAL* 3.7 12.3 - - - +
142F LEU* 5.2 0.5 - - - +
317F GLU 4.4 2.6 - - - +
318F LEU* 3.3 14.9 - - - +
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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