Contacts of the helix formed by residues 152 - 174 (chain A) in PDB entry 4PYP
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 LEU 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR* 3.9 24.9 - - + -
12A LEU* 6.5 0.4 - - + -
149A PRO* 3.1 30.9 + - + -
151A ALA* 1.3 80.2 - - + +
153A ARG* 1.3 58.7 + - - +
154A GLY 3.3 1.8 - - - -
155A ALA* 4.2 9.9 - - + +
156A LEU* 3.1 46.7 + - + +
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Residues in contact with ARG 153 (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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144A VAL 4.6 0.2 - - - +
145A GLY* 3.0 40.3 + - - -
148A SER* 3.5 22.8 + - - +
149A PRO 3.1 17.1 + - - +
150A THR* 3.3 40.7 + - - +
151A ALA 3.0 1.6 - - - -
152A LEU* 1.3 77.3 - - - +
154A GLY* 1.3 63.9 + - - +
156A LEU* 4.0 1.7 - - - +
157A GLY* 3.5 15.6 + - - -
212A ARG* 3.0 28.3 - - - +
243A GLU* 3.5 8.7 + - - -
247A GLU* 3.9 13.5 + - - -
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Residues in contact with GLY 154 (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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150A THR 4.5 0.8 + - - -
151A ALA 3.7 7.1 + - - -
152A LEU 3.3 0.4 - - - -
153A ARG* 1.3 76.2 - - - +
155A ALA* 1.3 57.5 + - - +
156A LEU 3.0 9.8 + - - -
157A GLY* 3.3 10.6 + - - -
158A THR* 3.4 8.8 + - - -
329A GLN* 6.3 1.1 - - - -
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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
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151A ALA 4.9 1.2 + - - -
152A LEU* 3.9 12.6 + - + +
154A GLY* 1.3 74.5 - - - +
156A LEU* 1.3 66.6 + - + +
158A THR* 2.9 24.8 + - - +
159A LEU* 5.1 2.8 - - - +
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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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12A LEU* 4.3 17.3 - - + -
16A VAL* 4.5 8.3 - - + -
144A VAL* 3.7 16.9 - - + +
148A SER* 3.3 30.7 - - - +
149A PRO* 5.3 0.7 - - + -
152A LEU* 3.1 35.0 + - + +
153A ARG* 4.4 2.2 - - - +
154A GLY 3.0 1.0 + - - -
155A ALA* 1.3 85.7 - - + +
157A GLY* 1.3 60.6 + - - +
158A THR* 2.9 6.2 + - - -
159A LEU* 3.3 34.2 + - + +
160A HIS 4.6 0.3 + - - -
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Residues in contact with GLY 157 (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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141A PRO* 6.1 5.2 - - - -
144A VAL* 4.8 7.6 - - - +
153A ARG 3.5 9.2 + - - -
154A GLY 3.3 7.7 + - - -
156A LEU* 1.3 75.3 - - - +
158A THR* 1.3 64.6 + - - +
159A LEU 3.0 1.9 + - - -
160A HIS* 3.0 21.4 + - - +
161A GLN* 3.8 13.5 + - - +
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Residues in contact with THR 158 (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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154A GLY 3.4 8.0 + - - -
155A ALA* 2.9 32.2 + - - +
157A GLY* 1.3 76.8 - - - +
159A LEU* 1.3 61.6 + - + +
161A GLN* 3.4 16.8 + - - +
162A LEU* 3.1 41.0 + - + +
325A LEU* 3.6 35.7 - - + +
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Residues in contact with LEU 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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16A VAL* 3.7 28.3 - - + -
17A GLY* 6.0 1.3 - - - -
20A VAL* 3.6 24.3 - - + +
23A SER* 3.7 2.4 + - - -
155A ALA 5.1 1.6 - - - +
156A LEU* 3.6 25.8 - - + +
157A GLY 3.0 1.6 - - - -
158A THR* 1.3 78.1 - - + +
160A HIS* 1.3 58.8 + - - +
162A LEU* 4.3 20.6 - - + -
163A GLY* 2.7 28.2 + - - -
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Residues in contact with HIS 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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20A VAL* 4.5 3.7 - - - +
23A SER* 3.3 28.2 + - - -
26A PHE* 5.3 2.2 - + - -
136A THR* 4.2 9.6 - - + -
137A THR* 3.6 39.6 - - + +
140A VAL* 3.8 18.1 - - + +
141A PRO* 3.7 26.9 - - + +
144A VAL* 6.2 0.9 - - + -
156A LEU 4.6 0.4 + - - -
157A GLY* 3.0 13.0 + - - +
159A LEU* 1.3 77.1 - - - +
161A GLN* 1.3 67.0 + - + +
164A ILE* 3.2 41.5 + - + +
601A BNG 6.5 0.9 - - + -
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Residues in contact with GLN 161 (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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154A GLY 5.8 0.2 + - - -
157A GLY 3.8 9.6 + - - +
158A THR* 3.6 26.2 + - - +
160A HIS* 1.3 77.0 - - + +
162A LEU* 1.3 56.5 + - - +
163A GLY 3.0 1.3 - - - -
164A ILE* 2.7 34.1 + - - +
165A VAL* 3.1 15.1 + - - +
321A THR* 4.6 11.6 - - + +
325A LEU* 3.4 28.4 - - - +
389A PHE* 6.2 0.2 - - - -
601A BNG 3.9 56.8 - - + +
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Residues in contact with LEU 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 THR* 3.1 37.7 + - + +
159A LEU* 4.0 19.5 - - + +
161A GLN* 1.3 78.3 - - + +
163A GLY* 1.3 62.7 + - - +
165A VAL* 4.6 4.3 - - - +
166A VAL* 3.0 35.3 + - + +
318A THR* 5.0 10.1 - - + -
321A THR* 4.2 16.3 - - + +
322A VAL* 3.6 30.1 - - + -
325A LEU* 4.8 3.6 - - + -
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Residues in contact with GLY 163 (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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20A VAL* 4.4 4.0 - - - -
23A SER* 3.1 26.5 - - - -
24A LEU* 3.1 28.0 - - - +
159A LEU 2.7 17.7 + - - -
161A GLN 2.9 0.4 + - - -
162A LEU* 1.3 74.3 - - - +
164A ILE* 1.3 57.9 + - - +
166A VAL* 4.9 0.7 - - - -
167A GLY 2.9 20.4 + - - -
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Residues in contact with ILE 164 (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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23A SER* 3.4 18.8 - - - +
26A PHE* 3.4 39.5 - - + -
27A GLY* 2.9 11.4 - - - -
30A THR* 5.6 0.7 - - + +
137A THR* 5.4 1.3 - - + -
160A HIS* 3.2 40.6 + - + +
161A GLN* 2.7 15.7 + - - +
163A GLY* 1.3 70.5 - - - -
165A VAL* 1.3 56.7 + - + +
167A GLY 3.0 0.3 + - - -
168A ILE* 2.7 48.8 + - + +
601A BNG 4.9 21.3 - - + -
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Residues in contact with VAL 165 (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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161A GLN* 3.1 12.5 + - - +
162A LEU* 4.1 5.8 - - - +
164A ILE* 1.3 78.9 - - + +
166A VAL* 1.3 55.6 + - - +
168A ILE* 3.2 12.7 + - + +
169A LEU 3.0 21.1 + - - -
314A GLY 5.0 0.2 - - - +
317A ASN* 3.0 28.3 - - + +
318A THR* 3.2 38.9 + - + +
321A THR* 3.4 26.5 - - + +
380A GLU* 4.3 2.0 - - - +
601A BNG 4.3 15.3 - - + +
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Residues in contact with VAL 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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24A LEU* 4.3 11.0 - - + -
162A LEU* 3.0 26.5 + - + +
163A GLY* 4.2 2.0 - - - +
165A VAL* 1.3 73.2 - - - +
167A GLY* 1.3 68.1 + - - +
169A LEU* 3.0 19.8 + - + +
170A ILE* 3.1 30.6 + - + +
318A THR* 4.0 20.6 - - + -
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Residues in contact with GLY 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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24A LEU* 3.7 14.1 - - - +
27A GLY* 3.1 15.0 - - - -
28A TYR* 3.2 17.5 + - - +
163A GLY 2.9 18.7 + - - -
164A ILE 3.0 5.3 + - - -
166A VAL* 1.3 77.9 - - - +
168A ILE* 1.3 58.4 + - - +
170A ILE* 3.6 9.3 + - - +
171A ALA 3.3 11.6 + - - -
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Residues in contact with ILE 168 (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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27A GLY* 3.1 16.1 + - - +
30A THR* 4.9 6.3 - - + -
31A GLY* 4.1 16.2 - - - +
164A ILE* 2.7 39.7 + - + +
165A VAL* 3.2 12.6 - - + +
166A VAL 3.0 0.4 - - - -
167A GLY* 1.3 71.1 - - - +
169A LEU* 1.3 66.8 + - + +
170A ILE 3.0 3.2 + - - -
171A ALA* 3.1 15.0 + - - +
172A GLN* 3.1 37.0 + - + +
291A PHE* 4.2 18.2 - - + -
314A GLY* 4.9 3.6 - - - +
317A ASN* 5.2 3.1 - - - +
601A BNG 4.1 30.1 - - - +
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Residues in contact with LEU 169 (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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165A VAL 3.0 11.5 + - - +
166A VAL* 3.0 12.4 + - + +
168A ILE* 1.3 77.8 - - - +
170A ILE* 1.3 62.7 + - + +
172A GLN* 3.6 11.5 + - - +
173A VAL* 3.0 43.6 + - + +
311A ILE* 4.5 1.8 - - + +
314A GLY* 3.3 8.5 - - - +
315A ILE* 3.3 55.2 - - + +
318A THR* 4.1 10.3 - - + +
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Residues in contact with ILE 170 (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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24A LEU* 5.3 6.7 - - + -
28A TYR* 3.7 21.1 - - + -
166A VAL* 3.1 34.3 + - + +
167A GLY* 3.8 10.8 - - - +
168A ILE 3.0 0.4 - - - -
169A LEU* 1.3 82.1 - - + +
171A ALA* 1.3 59.1 + - - +
173A VAL* 3.2 4.6 + - - -
174A PHE* 2.7 61.0 + - + +
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Residues in contact with ALA 171 (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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28A TYR* 3.8 17.9 - - + +
31A GLY 3.2 26.2 - - - +
32A VAL* 3.4 32.5 - - + +
35A ALA* 5.0 0.2 - - - +
167A GLY 3.3 10.0 + - - +
168A ILE 3.1 7.6 + - - +
170A ILE* 1.3 80.3 - - - +
172A GLN* 1.3 56.9 + - - +
174A PHE* 3.9 1.6 - - - +
175A GLY* 3.1 23.6 + - - -
189A LEU* 4.8 3.6 - - - +
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Residues in contact with GLN 172 (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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31A GLY* 3.8 4.0 + - - +
34A ASN* 3.8 14.3 + - - +
35A ALA* 4.4 10.2 - - - +
168A ILE* 3.1 15.9 + - - +
169A LEU* 3.7 10.6 - - - +
171A ALA* 1.3 74.7 - - - +
173A VAL* 1.3 62.4 + - - +
175A GLY* 2.8 22.2 + - - -
176A LEU* 3.5 3.1 + - - +
291A PHE* 3.6 22.2 - - - -
307A VAL* 5.4 1.4 - - - +
310A THR* 3.3 32.0 - - + +
311A ILE* 3.8 21.0 - - + +
313A SER* 3.6 14.6 + - - -
314A GLY* 2.9 28.7 + - - -
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Residues in contact with VAL 173 (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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169A LEU* 3.0 32.1 + - + +
170A ILE* 3.8 4.9 - - - +
172A GLN* 1.3 70.4 - - - +
174A PHE* 1.3 71.3 + - + +
175A GLY 2.8 5.8 + - - -
176A LEU* 3.0 29.7 + - + +
179A ILE* 3.9 14.0 - - + +
311A ILE* 3.5 32.1 - - + -
315A ILE* 6.0 0.2 - - + -
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Residues in contact with PHE 174 (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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28A TYR* 3.2 28.9 - + - +
170A ILE* 2.7 39.0 + - + +
171A ALA 4.1 2.0 - - - +
173A VAL* 1.3 80.7 - - + +
175A GLY* 1.3 58.8 + - - +
176A LEU 3.2 0.4 - - - -
179A ILE* 3.5 22.1 - - + +
180A MET* 3.3 24.9 + - - +
189A LEU* 3.3 25.9 - - + +
192A ILE* 4.3 17.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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