Contacts of the helix formed by residues 139 - 160 (chain L) in PDB entry 3E8E
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 139 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L ARG 4.3 0.4 + - - -
138L PHE* 1.3 76.9 - - - +
140L GLU* 1.3 59.7 + - - +
141L PRO* 3.4 13.3 - - - +
142L HIS* 3.1 22.7 + - - +
143L ALA* 2.9 26.9 + - - +
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Residues in contact with GLU 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L PHE 5.5 0.4 - - - +
139L SER* 1.3 71.5 - - - +
141L PRO* 1.3 67.8 - - + +
143L ALA* 4.5 3.6 - - - -
144L ARG* 2.8 39.6 + - - +
232L ALA* 5.0 6.1 - - + -
260L HIS* 3.7 8.3 + - - +
261L PHE* 3.5 7.2 - - + -
262L SER* 2.7 49.3 + - - -
265L LEU* 3.4 25.7 - - + +
296L TRP* 3.2 24.1 + - + +
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Residues in contact with PRO 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139L SER* 3.4 13.9 - - - +
140L GLU* 1.3 95.2 - - + +
142L HIS* 1.3 59.0 + - - +
144L ARG* 3.5 22.7 + - + +
145L PHE* 3.1 23.7 + - - +
313L PRO* 5.6 0.9 - - - -
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Residues in contact with HIS 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L ILE* 4.9 6.5 - - + -
138L PHE* 3.8 31.8 - + + +
139L SER* 3.1 21.6 + - - +
141L PRO* 1.3 77.2 - - - +
143L ALA* 1.3 63.7 + - - +
145L PHE* 3.3 12.6 + - - +
146L TYR* 3.1 53.2 + + - -
313L PRO* 3.2 38.4 + - + +
314L PHE* 3.7 23.4 - + + +
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Residues in contact with ALA 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L PHE* 4.1 6.0 - - + +
139L SER 2.9 19.1 + - - +
140L GLU* 3.9 6.1 - - - +
142L HIS* 1.3 72.6 - - - +
144L ARG* 1.3 53.0 + - - +
146L TYR* 3.3 2.2 + - - -
147L ALA* 2.8 34.7 + - - +
228L ILE* 4.8 2.0 - - + +
231L MET* 3.3 46.4 - - + +
232L ALA* 4.4 7.4 - - + +
296L TRP* 4.1 9.4 - - + -
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Residues in contact with ARG 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140L GLU* 2.8 28.7 + - - +
141L PRO* 3.5 37.2 - - - +
143L ALA* 1.3 72.4 - - - +
145L PHE* 1.3 65.3 + - - +
147L ALA* 3.6 1.0 - - - +
148L ALA* 2.9 24.6 + - - +
296L TRP* 2.6 71.8 + - + +
297L PHE* 4.1 10.9 - - + -
299L THR* 3.9 22.3 + - - +
300L THR* 3.6 24.0 - - - +
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Residues in contact with PHE 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L PRO 3.1 14.5 + - - +
142L HIS 3.3 9.2 + - - +
144L ARG* 1.3 78.2 - - - +
146L TYR* 1.3 72.8 + + - +
148L ALA* 3.6 5.7 + - - +
149L GLN* 3.1 44.8 + - - +
178L GLY 3.5 19.3 - - - -
179L TYR* 3.7 40.4 - + - -
305L ILE* 4.6 12.5 - - + +
310L VAL* 4.2 25.4 - - + -
311L GLU 4.6 0.7 - - - -
312L ALA* 3.8 13.2 - - + -
313L PRO* 3.3 28.0 - - + -
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Residues in contact with TYR 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128L MET* 3.6 20.4 - - + -
138L PHE* 3.6 25.4 - + - -
142L HIS* 3.1 44.1 + + - -
143L ALA 3.3 5.9 + - - +
144L ARG 3.2 0.2 - - - -
145L PHE* 1.3 90.9 - + - +
147L ALA* 1.3 66.5 + - - +
149L GLN* 3.1 20.5 + - - +
150L ILE* 3.3 17.1 + - + +
174L ILE* 3.9 19.0 - - + +
178L GLY 3.7 22.3 + - - -
180L ILE* 3.7 15.1 - - + +
227L LEU* 6.1 0.2 - - + -
231L MET* 3.8 15.0 - - - -
313L PRO* 4.7 1.3 - - + +
314L PHE* 3.7 22.3 + - - +
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Residues in contact with ALA 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L ALA 2.8 21.9 + - - +
144L ARG* 3.3 9.2 + - - +
146L TYR* 1.3 72.5 - - - +
148L ALA* 1.3 57.7 + - - +
150L ILE* 3.1 7.6 + - - +
151L VAL* 3.0 32.0 + - - +
224L LEU* 4.3 7.6 - - + +
227L LEU* 5.5 0.2 - - - -
228L ILE* 3.8 32.8 - - + -
231L MET* 4.1 4.9 - - + +
296L TRP* 4.0 2.0 - - + -
297L PHE* 4.0 11.9 - - + -
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Residues in contact with ALA 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144L ARG* 2.9 16.6 + - + +
145L PHE 3.8 2.0 - - - +
146L TYR 3.2 0.2 - - - -
147L ALA* 1.3 77.5 - - - +
149L GLN* 1.3 59.9 + - - +
152L LEU* 3.2 18.0 + - - +
297L PHE* 4.0 3.3 - - + -
300L THR* 3.9 7.6 - - + -
302L TRP* 3.2 38.6 - - + -
305L ILE* 3.4 31.9 - - + -
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Residues in contact with GLN 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L PHE* 3.6 25.9 - - + -
145L PHE* 3.1 51.7 + - - +
146L TYR* 3.1 16.7 + - - +
148L ALA* 1.3 75.5 - - - +
150L ILE* 1.3 56.1 + - - +
152L LEU* 3.4 3.5 + - - +
153L THR* 2.7 36.5 + - - -
179L TYR* 3.5 15.5 - - - -
180L ILE* 2.6 40.0 + - + +
305L ILE* 3.8 18.2 - - + -
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Residues in contact with ILE 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L TYR 3.6 13.5 - - - +
147L ALA 3.1 7.0 + - - +
149L GLN* 1.3 76.3 - - + +
151L VAL* 1.3 60.0 + - - +
153L THR* 4.0 4.0 - - - +
154L PHE* 2.8 62.6 + - + -
167L LEU* 3.7 9.6 - - + -
172L LEU* 3.9 17.3 - - + -
180L ILE* 4.2 12.3 - - + -
182L VAL* 3.9 28.5 - - + -
224L LEU* 3.9 14.6 - - + -
227L LEU* 4.0 18.6 - - + -
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Residues in contact with VAL 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L ALA 3.0 16.6 + - - +
148L ALA 3.7 7.2 - - - +
150L ILE* 1.3 74.5 - - - +
152L LEU* 1.3 59.9 + - - +
155L GLU* 2.9 29.1 + - - +
221L TRP* 3.8 10.8 - - + -
224L LEU* 3.6 26.5 - - + -
288L VAL* 3.8 23.6 - - + -
291L ILE* 3.8 18.4 - - + -
292L LYS* 4.3 9.0 - - + -
297L PHE* 4.4 5.8 - - + -
302L TRP* 3.6 27.4 - - + -
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Residues in contact with LEU 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L PHE* 3.8 18.3 - - + -
102L PHE* 3.9 13.5 - - + -
148L ALA 3.2 16.6 + - - +
149L GLN 3.7 5.4 - - - +
151L VAL* 1.3 78.1 - - - +
153L THR* 1.3 58.1 + - - +
155L GLU* 3.3 20.9 + - - +
156L TYR* 2.9 30.0 + - - +
292L LYS* 4.1 8.5 - - - +
302L TRP* 3.8 38.4 - - + +
305L ILE* 3.9 24.0 - - + -
306L TYR* 4.0 13.2 - - + +
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Residues in contact with THR 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L PHE* 3.7 11.5 - - + -
102L PHE* 3.5 23.2 - - - +
103L LEU* 3.4 32.5 - - + -
149L GLN 2.7 22.9 + - - -
150L ILE* 3.7 9.5 - - + +
152L LEU* 1.3 77.4 - - - +
154L PHE* 1.3 61.7 + - + +
156L TYR* 3.6 2.1 - - - +
157L LEU* 3.0 38.0 + - + +
182L VAL* 4.3 13.9 - - + +
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Residues in contact with PHE 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ILE* 2.8 46.5 + - + +
153L THR* 1.3 77.1 - - + +
155L GLU* 1.3 60.1 + - - +
157L LEU* 4.3 11.9 - - + +
158L HIS* 2.8 41.8 + - + +
164L TYR* 3.9 26.0 - + + -
167L LEU* 3.8 26.5 - - + -
182L VAL* 6.3 2.5 - - + -
220L ASP* 3.4 50.3 - - + -
221L TRP* 3.6 31.0 - + + -
224L LEU* 4.6 2.7 - - + -
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Residues in contact with GLU 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L VAL* 3.6 26.4 - - - +
19L LEU* 4.6 13.9 - - + +
151L VAL 2.9 17.9 + - - +
152L LEU* 3.5 14.5 - - - +
154L PHE* 1.3 74.9 - - - +
156L TYR* 1.3 62.9 + - - +
158L HIS* 4.1 2.7 - - - +
159L SER* 3.2 23.9 + - - -
221L TRP* 4.2 6.1 - - - -
288L VAL* 3.8 29.7 - - + +
289L ASN* 5.5 0.3 - - - +
292L LYS* 3.1 31.6 + - - -
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Residues in contact with TYR 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18L PHE* 4.9 6.7 - + - -
19L LEU* 5.7 7.6 - - + -
22L ALA* 4.1 27.6 + - + +
26L PHE* 5.1 2.4 - - - +
97L ALA 4.8 1.0 + - - -
98L VAL* 3.8 8.0 - - + -
99L ASN* 3.0 39.0 + - - +
100L PHE* 3.5 43.3 - + + -
103L LEU* 4.3 7.0 - - + -
152L LEU 2.9 17.3 + - - +
153L THR* 3.6 4.0 - - + +
155L GLU* 1.3 76.4 - - - +
157L LEU* 1.3 83.5 - - + +
159L SER* 2.6 25.8 + - - -
160L LEU* 3.6 33.5 + - + +
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Residues in contact with LEU 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L VAL* 4.5 2.2 - - + -
103L LEU* 4.4 7.0 - - + -
153L THR* 3.0 37.3 + - + +
154L PHE* 4.1 16.8 - - + +
156L TYR* 1.3 94.8 - - + +
158L HIS* 1.3 62.5 + - + +
160L LEU* 3.2 9.8 + - - +
162L LEU* 3.0 58.2 + - + +
164L TYR* 4.5 19.7 - - + +
182L VAL* 6.0 0.7 - - + -
185L PHE* 4.3 29.4 - - + -
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Residues in contact with HIS 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L PHE* 2.8 33.1 + + + +
155L GLU* 4.2 3.1 - - - +
157L LEU* 1.3 70.5 - - + +
159L SER* 1.3 57.1 + - - +
160L LEU 3.1 4.5 - - - -
161L ASP* 2.8 17.3 + - - +
162L LEU 3.2 22.0 - - - -
163L ILE* 4.7 0.2 - - - -
217L LYS* 3.4 65.3 + - + +
220L ASP* 2.8 32.4 + - + +
221L TRP* 3.5 33.4 + + + -
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Residues in contact with SER 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L LEU* 3.7 33.9 + - - +
22L ALA* 6.1 1.0 - - - +
23L LYS* 3.8 21.1 - - - +
155L GLU 3.2 14.8 + - - -
156L TYR* 2.6 25.3 + - - -
158L HIS* 1.3 75.7 - - - +
160L LEU* 1.3 64.7 + - - +
161L ASP* 3.4 3.4 + - - +
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Residues in contact with LEU 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L LEU 5.2 0.9 - - - +
22L ALA* 4.4 2.7 - - + +
23L LYS* 3.5 45.1 - - + +
26L PHE* 3.8 33.4 - - + -
98L VAL* 4.9 0.7 - - + -
156L TYR* 3.6 48.2 - - + +
157L LEU 3.2 6.9 + - - +
158L HIS 3.1 1.0 - - - -
159L SER* 1.3 82.0 + - - +
161L ASP* 1.3 66.5 + - - +
162L LEU* 3.2 17.4 + - + +
190L ARG* 3.0 28.7 + - - +
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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
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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) + - + + + + + -
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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