Contacts of the helix formed by residues 154 - 175 (chain C) in PDB entry 4J1R
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 PRO 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C TYR* 3.5 29.2 - - + +
152C THR* 3.5 3.3 - - + +
153C LEU* 1.4 90.2 - - + +
155C VAL* 1.3 66.7 + - + +
156C ILE* 3.0 18.2 - - + -
157C TYR* 2.9 29.2 + - + +
158C VAL* 3.4 7.1 + - - +
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C THR* 6.3 2.5 - - + -
153C LEU 3.4 3.9 + - - +
154C PRO* 1.3 71.2 - - + +
156C ILE* 1.3 63.0 + - - +
158C VAL* 3.2 11.5 + - + +
159C LYS* 2.9 46.0 + - - +
251C LEU* 5.7 5.6 - - + -
310C PRO* 4.1 30.5 - - + -
312C GLU* 5.7 0.2 - - - +
339C PHE* 4.1 16.6 - - + -
342C GLU* 5.7 0.7 - - - +
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Residues in contact with ILE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C PRO* 2.9 17.9 + - + -
155C VAL* 1.3 78.4 - - - +
157C TYR* 1.3 66.2 + - + +
159C LYS* 3.4 5.8 + - + +
160C LEU* 3.2 30.6 + - + +
342C GLU* 3.5 33.8 + - + +
343C LEU* 4.1 20.6 - - + -
348C VAL* 4.6 9.6 - - + -
349C LYS 4.9 7.0 - - - +
350C LEU* 6.2 0.4 - - + -
351C PRO* 4.0 31.2 - - + -
356C THR* 6.4 0.7 - - + -
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C TYR* 4.6 7.2 - - - -
153C LEU* 3.8 21.8 - - + -
154C PRO* 2.9 37.4 + - + +
156C ILE* 1.3 79.5 - - + +
158C VAL* 1.3 60.6 + - - +
160C LEU* 3.3 18.5 + - + +
161C TYR* 3.0 61.0 + + + -
194C ALA* 5.2 6.7 - - + -
350C LEU* 5.7 0.2 - - + -
351C PRO* 3.3 45.7 - - + +
352C ASN* 4.9 6.2 + - - +
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LEU* 3.7 33.2 - - + +
154C PRO 3.7 9.4 - - - +
155C VAL* 3.5 12.6 - - + +
157C TYR* 1.3 77.2 - - - +
159C LYS* 1.3 63.2 + - - +
161C TYR* 4.0 0.6 - - - +
162C MET* 3.0 33.4 + - + +
247C LEU* 3.7 31.0 - - + -
250C LEU* 4.1 28.9 - - + +
251C LEU* 4.5 10.3 - - + -
339C PHE* 4.0 8.5 - - + -
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Residues in contact with LYS 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 2.9 38.5 + - - +
156C ILE* 3.7 5.6 - - + +
157C TYR 3.4 0.2 - - - -
158C VAL* 1.3 75.4 - - - +
160C LEU* 1.3 63.6 + - - +
163C TYR* 3.1 23.6 + - - +
312C GLU* 4.8 9.2 + - - -
338C SER 5.7 0.2 + - - -
339C PHE* 3.3 44.6 + - + +
340C PHE* 3.1 18.1 - - + -
342C GLU* 2.5 50.1 + - + +
343C LEU* 3.8 19.7 - - + -
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Residues in contact with LEU 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ILE* 3.2 22.7 + - + +
157C TYR* 3.5 22.2 - - + +
158C VAL 3.2 0.2 - - - -
159C LYS* 1.3 80.4 - - - +
161C TYR* 1.3 68.4 + - + +
163C TYR* 3.8 1.8 - - - +
164C GLN* 3.2 35.5 + - - +
194C ALA* 4.0 15.5 - - + -
343C LEU* 4.0 23.1 - - + -
350C LEU* 3.7 27.8 - - + -
356C THR* 4.8 4.0 - - + -
357C PRO* 4.6 17.5 - - + -
359C LEU* 4.4 19.0 - - + +
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Residues in contact with TYR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 4.5 15.9 - - + -
142C VAL* 4.9 10.6 - - + +
153C LEU* 4.3 15.0 - - + -
157C TYR* 3.0 47.8 + + + +
158C VAL* 4.1 3.1 - - - +
160C LEU* 1.3 86.8 - - + +
162C MET* 1.3 65.4 + - + +
164C GLN* 3.4 8.4 + - - +
165C LEU* 3.0 21.8 + - - +
187C LEU* 6.2 0.9 - - + -
189C LEU* 3.6 43.7 - - + +
191C PRO* 5.8 3.5 - - - +
194C ALA* 4.2 25.9 - - + +
196C LEU* 3.6 19.1 - - + +
250C LEU* 5.1 8.5 - - + -
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Residues in contact with MET 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C VAL* 3.0 25.3 + - + +
161C TYR* 1.3 77.3 - - - +
163C TYR* 1.3 64.8 + - - +
165C LEU* 3.0 20.1 + - + +
166C PHE* 2.9 55.5 + - + -
187C LEU* 6.0 0.7 - - - -
243C ALA 3.3 23.8 - - - +
246C VAL* 4.0 14.6 - - - -
247C LEU* 3.8 43.1 - - + -
250C LEU* 4.3 7.0 - - + -
339C PHE* 4.9 0.7 - - + -
340C PHE* 3.8 17.9 - - + -
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Residues in contact with TYR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C LYS 3.1 20.4 + - - +
160C LEU 3.8 2.9 - - - +
162C MET* 1.3 77.8 - - - +
164C GLN* 1.3 64.3 + - - +
166C PHE* 3.2 5.6 + - - +
167C ARG* 3.0 36.4 + - - +
335C CYS* 3.6 41.5 - - + -
340C PHE* 3.5 24.4 - + + -
343C LEU* 3.9 12.8 - - + -
344C ARG* 4.2 9.3 + - + -
359C LEU* 2.9 55.6 + - + -
360C PHE* 4.4 9.3 - + - -
362C PHE* 3.1 22.8 - + - -
377C LEU* 4.4 4.9 + - + +
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Residues in contact with GLN 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ASN* 3.0 38.0 + - - +
160C LEU* 3.2 26.7 + - - +
161C TYR* 3.9 2.6 - - - +
163C TYR* 1.3 77.6 - - + +
165C LEU* 1.3 62.8 + - - +
167C ARG* 3.4 5.6 + - - +
168C SER* 3.1 21.0 + - - -
194C ALA 2.9 24.2 + - - -
195C VAL* 3.4 10.9 - - - +
196C LEU* 2.9 41.4 + - + +
357C PRO* 4.4 6.0 - - - +
359C LEU* 4.2 23.9 - - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C TYR 3.0 13.3 + - - +
162C MET* 3.0 36.0 + - + +
164C GLN* 1.3 76.1 - - - +
166C PHE* 1.3 65.9 + - + +
168C SER* 2.9 26.4 + - - +
169C LEU* 3.0 29.6 + - + +
182C ILE* 4.5 14.6 - - + -
187C LEU* 3.9 37.5 - - + -
196C LEU* 3.9 8.0 - - + +
198C LEU* 4.7 2.5 - - + -
243C ALA* 3.9 20.0 - - + -
246C VAL* 4.8 2.7 - - + -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C MET* 2.9 54.3 + - + -
163C TYR* 3.2 2.2 + - - +
165C LEU* 1.3 74.9 - - + +
167C ARG* 1.3 52.6 + - - +
169C LEU* 4.1 9.4 - - + -
170C ALA* 2.7 35.9 + - - +
240C VAL* 5.1 6.1 - - + -
243C ALA* 3.8 21.8 - - + -
316C LEU* 4.7 4.5 - - + -
320C LEU* 3.7 29.2 - - + -
331C PRO* 3.4 17.7 - - + +
334C ALA* 3.7 27.6 - - + -
335C CYS* 3.4 20.9 - - - -
340C PHE* 3.9 24.0 - + - -
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Residues in contact with ARG 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C HIS* 3.8 10.4 + - + -
107C CYS* 4.1 6.0 - - - -
108C ASN* 3.6 17.8 + - - +
163C TYR* 3.0 41.4 + - + +
164C GLN* 3.5 9.9 - - - +
165C LEU 3.2 0.2 - - - -
166C PHE* 1.3 73.7 - - - +
168C SER* 1.3 65.8 + - - +
170C ALA* 3.3 7.7 + - - +
171C TYR* 3.0 21.8 + - - +
332C LEU* 6.3 0.2 - - - -
335C CYS* 4.1 9.6 - - - -
358C ALA 3.4 7.7 + - - -
359C LEU* 3.1 24.7 + - - +
360C PHE 3.8 0.4 - - - +
361C ASN* 3.0 41.4 + - - -
362C PHE* 3.9 18.0 - - + -
366C GLU* 3.1 38.7 + - - +
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C HIS* 4.0 10.1 - - - -
108C ASN* 3.4 27.1 + - - -
109C ILE* 3.6 13.2 - - - -
164C GLN 3.1 9.3 + - - -
165C LEU* 2.9 21.8 + - - +
167C ARG* 1.3 79.4 - - - +
169C LEU* 1.3 56.7 + - - +
171C TYR* 3.3 4.8 - - - +
172C ILE* 2.9 34.3 + - - +
196C LEU* 5.1 0.3 - - - +
198C LEU* 3.7 21.4 + - - +
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C LEU* 3.0 26.6 + - + +
166C PHE* 3.5 13.5 - - + +
168C SER* 1.3 73.7 + - - +
170C ALA* 1.3 60.5 + - - +
171C TYR 3.1 1.6 - - - -
172C ILE* 3.8 12.1 - - + -
173C HIS* 2.9 52.7 + - + +
182C ILE* 3.8 17.7 - - + -
198C LEU* 3.8 25.1 - - + -
239C ASP* 4.2 25.1 - - + +
240C VAL* 4.7 2.9 - - + +
243C ALA* 4.3 15.7 - - + -
331C PRO* 4.0 12.8 - - + -
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Residues in contact with ALA 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C PHE 2.7 21.2 + - - +
167C ARG* 3.5 7.9 - - - +
169C LEU* 1.3 71.8 - - - +
171C TYR* 1.3 62.9 + - - +
173C HIS* 4.1 2.7 - - - +
174C SER* 3.3 22.2 + - - -
331C PRO* 3.4 18.3 - - + +
332C LEU* 4.0 31.0 - - + +
366C GLU* 4.6 14.1 - - + +
369C SER* 5.7 5.5 - - - -
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Residues in contact with TYR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LYS 3.9 2.9 + - - -
104C LEU* 3.5 27.0 - - + -
105C ASP* 2.9 38.8 + - - +
106C HIS* 3.7 29.8 - + + +
109C ILE* 3.5 19.3 - - + -
167C ARG 3.0 12.8 + - - +
168C SER* 3.3 10.1 - - - +
170C ALA* 1.3 77.3 - - - +
172C ILE* 1.3 60.8 + - - +
174C SER* 2.5 26.9 + - - -
175C PHE* 3.2 33.2 - + - -
363C THR* 5.1 4.0 - - + -
365C GLN* 4.2 15.0 - - + -
366C GLU* 3.9 19.7 - - + +
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LEU* 3.9 22.2 - - + -
109C ILE* 3.7 23.1 - - + -
168C SER 2.9 20.6 + - - +
169C LEU* 3.5 29.4 - - + +
171C TYR* 1.3 76.5 - - - +
173C HIS* 1.3 70.4 + - - +
174C SER 3.2 0.2 - - - -
175C PHE* 3.4 13.0 + - - +
177C ILE* 3.0 45.3 + - + +
179C HIS* 4.1 23.6 - - + +
198C LEU* 4.1 8.7 - - + -
201C PHE* 4.2 9.6 - - + -
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Residues in contact with HIS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169C LEU* 2.9 34.5 + - + +
170C ALA* 4.1 4.5 - - - +
172C ILE* 1.3 82.1 - - + +
174C SER* 1.3 64.1 + - - +
176C GLY* 3.0 13.7 + - - -
177C ILE 3.0 17.9 + - - +
236C SER* 3.2 45.1 + - - +
239C ASP* 3.1 33.2 - - + +
240C VAL* 4.7 2.9 - - + +
331C PRO* 3.5 27.9 - - + +
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Residues in contact with SER 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C ALA 3.3 11.3 + - - -
171C TYR* 2.5 22.7 + - - -
173C HIS* 1.3 78.4 - - - +
175C PHE* 1.3 59.5 + - - +
176C GLY 3.2 0.7 + - - -
365C GLN* 3.0 47.5 + - - +
366C GLU* 5.4 0.9 - - - -
368C SER* 4.4 12.9 + - - -
369C SER* 5.7 3.8 - - - -
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Residues in contact with PHE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LYS* 4.7 29.8 - - + +
104C LEU* 4.1 8.5 - - + -
171C TYR* 3.2 66.4 - + - -
172C ILE* 3.4 8.7 + - - +
173C HIS 3.2 0.6 - - - -
174C SER* 1.3 79.8 + - - +
176C GLY* 1.3 56.0 + - - +
177C ILE* 3.7 21.8 - - + -
206C GLN* 3.0 29.1 + - - +
365C GLN* 3.8 23.6 - - + -
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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