Contacts of the helix formed by residues 147 - 169 (chain A) in PDB entry 1JS6
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 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLN* 3.3 2.6 - - - +
146A GLY* 1.3 80.7 - - - +
148A ALA* 1.3 59.5 + - - +
149A SER* 3.7 0.7 + - - -
150A GLU* 2.8 35.9 + - - +
151A ALA* 2.9 24.3 + - - +
302A HIS* 4.0 3.1 - - - -
309A PHE* 4.7 7.6 - - - -
312A SER* 3.5 16.0 + - - -
601A PLP 3.2 25.2 + - - -
352B PRO* 3.8 9.9 - - - +
354B GLY 5.4 2.5 - - - -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 1.3 72.1 - - - +
149A SER* 1.3 57.9 + - - +
151A ALA* 3.2 1.7 + - - +
152A THR* 2.9 33.6 + - - -
271A ASP* 4.6 3.8 - - - +
273A ALA* 3.9 12.6 - - + -
298A ASN* 3.4 21.7 - - - +
300A ASN* 3.3 27.2 + - - +
312A SER* 3.7 1.3 - - - -
601A PLP 2.8 25.4 + - + +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 4.1 4.0 - - - -
148A ALA* 1.3 78.1 - - - +
150A GLU* 1.3 60.3 + - - +
152A THR* 3.7 3.0 + - - -
153A LEU* 3.2 21.0 + - - +
194A SER* 3.2 36.4 - - - +
197A ARG* 5.8 0.9 - - - -
601A PLP 2.8 25.2 + - - -
351B LEU 5.3 2.5 - - - -
352B PRO* 4.7 4.3 - - - -
353B LEU* 3.2 31.2 - - - +
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 4.7 9.8 - - - +
146A GLY* 3.2 23.9 + - - +
147A SER* 2.8 28.2 + - - +
149A SER* 1.3 74.4 - - - +
151A ALA* 1.3 68.2 + - - +
153A LEU* 3.1 8.2 + - + +
154A VAL* 2.8 29.0 + - - +
309A PHE* 6.0 0.2 - - - -
351A LEU* 4.9 16.3 - - + +
352A PRO* 5.1 9.9 - - - +
150B GLU* 4.4 13.0 - - - +
351B LEU* 5.3 2.3 - - + +
352B PRO* 3.4 33.8 - - + +
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 4.0 12.5 - - + +
147A SER 2.9 12.4 + - - +
148A ALA 3.5 2.7 - - - +
150A GLU* 1.3 76.9 - - - +
152A THR* 1.3 63.0 + - - +
154A VAL* 3.2 3.5 + - - +
155A ALA* 3.0 23.2 + - - +
269A HIS* 4.5 2.0 - - - -
298A ASN* 3.3 40.8 - - + +
314A MET* 3.8 23.1 - - - +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 2.9 19.1 + - - -
149A SER* 3.9 7.2 - - - -
151A ALA* 1.3 76.7 - - - +
153A LEU* 1.3 62.1 + - - +
155A ALA* 3.3 4.0 + - - +
156A LEU* 3.0 21.7 + - - +
194A SER* 4.3 8.9 + - - -
195A VAL* 4.4 18.3 - - + +
198A ALA* 4.2 17.0 - - + -
238A PHE* 4.0 4.2 - - + -
240A VAL* 4.4 20.4 - - + -
269A HIS* 3.6 22.8 + - + -
271A ASP* 4.5 11.8 + - - +
298A ASN* 5.2 0.2 + - - -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A SER 3.2 12.1 + - - +
150A GLU* 3.1 10.2 + - + +
152A THR* 1.3 77.7 - - - +
154A VAL* 1.3 58.1 + - - +
156A LEU* 3.3 3.9 + - + +
157A LEU* 2.9 50.0 + - + +
198A ALA* 3.9 38.1 - - + +
201A ILE* 3.9 35.9 - - + -
202A GLY 4.7 0.7 - - - +
351A LEU* 3.5 26.9 - - + -
153B LEU* 6.1 1.1 - - + -
201B ILE* 6.0 0.7 - - + -
351B LEU* 4.9 10.3 - - + +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLN* 3.9 20.4 - - - +
150A GLU* 2.8 23.3 + - + +
151A ALA* 3.5 7.2 - - - +
153A LEU* 1.3 72.4 - - - +
155A ALA* 1.3 63.3 + - - +
157A LEU* 3.3 4.9 + - - +
158A ALA* 2.9 22.2 + - - +
314A MET* 4.4 9.2 - - + -
322A LEU* 3.7 30.5 - - + -
326A PHE* 4.0 13.1 - - + -
349A TRP 3.8 9.2 - - - +
350A GLN* 4.4 0.4 - - - -
351A LEU* 3.9 31.6 - - + +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 3.0 10.2 + - - +
152A THR 3.5 8.1 - - - +
154A VAL* 1.3 77.1 - - - +
156A LEU* 1.3 56.5 + - - +
158A ALA* 3.0 8.7 + - - +
159A ALA* 2.8 29.1 + - - +
238A PHE* 3.8 13.5 - - + -
267A TRP* 4.1 6.6 - - - +
269A HIS* 3.6 27.6 - - - +
296A SER* 3.7 10.5 - - - +
314A MET* 3.9 9.6 - - + -
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Residues in contact with LEU 156 (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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152A THR 3.0 16.3 + - - +
153A LEU* 3.7 8.3 - - + +
155A ALA* 1.3 76.2 - - - +
157A LEU* 1.3 63.1 + - + +
159A ALA* 3.2 1.2 + - - +
160A ARG* 2.7 31.8 + - + +
185A ALA* 4.7 4.5 - - + -
195A VAL* 5.1 2.9 - - + +
198A ALA* 4.1 8.5 - - + +
199A GLY* 3.9 28.0 - - - +
202A GLY* 4.1 25.6 - - - -
204A VAL* 4.4 11.9 - - + -
237A PHE* 3.9 15.8 - - + -
238A PHE* 3.6 38.1 - - + -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 2.9 34.9 + - + +
154A VAL 3.7 3.8 - - - +
155A ALA 3.3 0.2 - - - -
156A LEU* 1.3 74.3 - - + +
158A ALA* 1.3 65.8 + - - +
160A ARG* 3.6 39.5 + - - +
161A THR* 3.0 28.8 + - - -
201A ILE 5.6 0.4 - - - -
202A GLY* 4.4 14.1 - - - -
325A ALA* 3.7 4.4 - - + +
326A PHE* 4.4 13.5 - - + -
351A LEU* 3.7 25.1 - - + -
201B ILE* 3.5 32.5 - - + +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL 2.9 13.6 + - - +
155A ALA* 3.4 8.7 - - - +
157A LEU* 1.3 77.4 - - - +
159A ALA* 1.3 63.0 + - - +
161A THR* 3.5 2.4 + - - +
162A LYS* 3.0 24.3 + - - +
267A TRP* 3.7 16.4 - - + -
321A ASP 3.5 22.8 - - - +
322A LEU* 4.2 14.6 - - + +
325A ALA* 3.5 14.8 - - + +
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Residues in contact with ALA 159 (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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155A ALA 2.8 16.1 + - - +
156A LEU 3.5 4.5 - - - +
158A ALA* 1.3 74.0 - - - +
160A ARG* 1.3 67.9 + - - +
162A LYS* 3.1 4.7 + - - +
163A VAL* 3.0 23.7 + - - +
237A PHE* 3.9 14.3 - - + +
238A PHE* 3.8 11.7 - - + -
267A TRP* 3.6 40.1 - - + -
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Residues in contact with ARG 160 (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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156A LEU* 2.7 22.8 + - + +
157A LEU* 3.6 23.4 + - - +
159A ALA* 1.3 71.3 - - - +
161A THR* 1.3 70.7 + - - +
163A VAL* 3.1 6.0 - - - +
164A VAL* 3.1 29.5 + - + +
176A GLN* 5.4 8.2 + - - -
180A LEU* 3.6 33.7 - - + +
183A LEU* 3.9 7.4 - - + -
201A ILE 4.7 0.8 + - - -
202A GLY* 2.8 45.5 + - - -
204A VAL* 4.4 3.8 - - + -
237A PHE* 3.5 17.1 - - + -
160B ARG* 4.9 1.8 - - - +
200B LEU 3.7 12.5 + - - -
201B ILE* 2.9 31.1 + - - +
202B GLY 4.9 2.2 + - - -
203B GLY* 4.6 7.8 - - - +
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 3.0 17.9 + - - -
158A ALA 3.8 3.1 - - - +
160A ARG* 1.3 85.6 + - - +
162A LYS* 1.3 62.9 + - - +
164A VAL* 3.3 7.4 + - - +
165A ARG* 3.1 57.1 + - + +
324A GLY 4.2 0.4 - - - +
325A ALA* 3.8 26.7 + - - +
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Residues in contact with LYS 162 (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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158A ALA 3.0 17.7 + - - +
159A ALA* 3.6 5.8 - - - +
161A THR* 1.3 80.5 - - - +
163A VAL* 1.3 57.3 + - - +
165A ARG* 3.5 12.9 + - - +
166A ARG* 3.1 42.9 + - - +
265A ASP* 5.9 1.6 + - - -
267A TRP* 4.4 13.4 - - + -
295A ASP* 4.8 9.1 + - - -
318A ARG* 5.0 3.6 - - - +
321A ASP* 3.0 44.1 + - - +
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Residues in contact with VAL 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ALA 3.0 13.1 + - - +
160A ARG* 3.1 20.6 - - - +
162A LYS* 1.3 74.1 - - - +
164A VAL* 1.3 69.6 + - + +
166A ARG* 3.5 28.9 - - - +
167A LEU* 3.1 40.5 + - + +
179A VAL* 4.7 0.4 - - + -
183A LEU* 4.0 24.2 - - + -
235A ILE* 4.6 11.2 - - + -
236A PRO 5.3 0.9 - - - +
237A PHE* 4.2 20.4 - - + -
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 3.1 29.1 + - + +
161A THR* 3.8 6.7 - - - +
163A VAL* 1.3 78.9 - - + +
165A ARG* 1.3 59.3 + - + +
167A LEU* 3.9 0.7 - - - +
168A GLN* 3.0 53.5 + - + +
176A GLN* 4.2 35.9 - - + +
179A VAL* 4.0 26.5 - - + -
180A LEU* 4.7 3.4 - - + -
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A THR* 3.1 40.3 + - + +
162A LYS* 3.7 12.9 - - - +
164A VAL* 1.3 76.0 - - + +
166A ARG* 1.3 65.4 + - - +
168A GLN* 3.3 5.2 + - - +
169A ALA* 2.9 30.0 + - + +
320A THR 5.5 1.4 + - - -
324A GLY* 2.9 40.6 + - - -
327A LYS* 5.1 4.8 + - - +
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Residues in contact with ARG 166 (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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162A LYS* 3.1 36.0 + - - +
163A VAL* 3.5 30.1 - - - +
165A ARG* 1.3 80.0 - - - +
167A LEU* 1.3 72.8 + - + +
169A ALA* 3.5 5.3 + - - +
170A ALA* 3.5 20.8 + - - +
265A ASP* 3.3 37.0 + - - +
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Residues in contact with LEU 167 (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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163A VAL* 3.1 33.6 + - + +
164A VAL 4.0 2.7 - - - +
166A ARG* 1.3 91.9 - - + +
168A GLN* 1.3 56.3 + - - +
170A ALA* 3.5 5.4 + - - +
171A SER* 3.1 18.5 + - - -
174A LEU* 3.1 27.4 - - + +
179A VAL* 3.5 35.7 - - + -
235A ILE* 3.9 26.0 - - + -
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 3.0 40.8 + - + +
165A ARG* 4.1 5.2 - - - +
167A LEU* 1.3 71.4 - - - +
169A ALA* 1.3 56.8 + - - +
170A ALA 3.0 9.0 + - - -
171A SER 3.3 22.1 + - - +
172A PRO* 3.9 6.5 - - - +
174A LEU* 2.9 35.8 + - + +
175A THR* 3.7 2.3 - - - +
176A GLN* 3.4 22.3 - - - +
179A VAL* 5.0 1.6 - - + -
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 2.9 19.4 + - + +
166A ARG* 3.9 5.8 - - - +
168A GLN* 1.3 75.7 - - - +
170A ALA* 1.3 57.5 + - - +
172A PRO* 5.9 0.4 - - - -
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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