Contacts of the helix formed by residues 251 - 272 (chain A) in PDB entry 1PFW
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 TYR 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ASP 3.4 19.3 - - - -
231A ILE* 2.8 30.0 + - + -
232A SER 3.8 3.1 - - - +
233A ARG* 3.3 47.6 + - + -
237A TYR* 3.7 13.0 - - - -
249A TYR 3.4 2.4 + - - -
250A PHE* 1.3 73.9 - - - +
252A VAL* 1.3 78.5 + - + +
253A TRP* 3.2 40.5 + + + -
254A LEU* 2.8 26.2 + - - +
255A ASP* 3.6 2.6 + - - +
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Residues in contact with VAL 252 (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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15A TYR* 5.2 6.3 - - + +
52A ASP* 3.3 31.0 - - - +
54A HIS* 3.7 29.8 - - + +
55A GLY* 5.2 2.0 - - - -
237A TYR* 3.1 17.3 + - - +
250A PHE 3.4 0.8 + - - -
251A TYR* 1.3 83.9 - - + +
253A TRP* 1.3 84.1 + - + +
254A LEU 3.1 0.7 + - - -
255A ASP* 3.2 12.1 + - - +
256A ALA* 2.7 28.2 + - + +
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Residues in contact with TRP 253 (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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15A TYR* 3.0 30.0 + + - -
52A ASP* 5.4 0.9 - - - -
231A ILE* 6.1 0.2 - - - -
251A TYR* 3.1 40.6 + + + -
252A VAL* 1.3 91.8 - - + +
254A LEU* 1.3 60.7 + - - +
256A ALA* 4.2 4.5 - - + -
257A PRO* 3.2 4.8 - - - +
297A ILE* 3.9 25.4 - - + -
300A PHE* 3.0 77.1 - + + -
304A PHE* 4.0 5.2 - - + -
553A MF3 3.3 37.9 - - + -
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Residues in contact with LEU 254 (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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106A SER* 4.5 9.4 - - - +
109A ILE* 5.6 1.1 - - + -
110A TYR* 5.4 2.9 - - + -
113A LEU* 5.0 6.1 - - + -
192A PHE* 5.9 0.4 - - + -
231A ILE* 4.0 43.7 - - + +
250A PHE* 4.1 32.1 - - + -
251A TYR* 2.8 15.7 + - - +
253A TRP* 1.3 78.7 - - - +
255A ASP* 1.3 64.3 + - - +
256A ALA 3.7 0.3 + - - -
257A PRO* 3.7 1.2 - - - +
258A ILE* 3.2 33.5 - - + +
304A PHE* 4.2 5.8 - - + -
308A MET* 3.3 36.8 - - - +
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Residues in contact with ASP 255 (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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54A HIS* 2.7 35.5 + - - +
97A THR* 3.7 10.9 + - - -
102A ASN* 3.0 28.0 - - - +
106A SER* 3.5 23.8 - - - +
239A GLY* 5.2 0.2 - - - -
240A PHE* 4.0 11.2 + - + -
250A PHE* 4.4 10.7 - - + +
251A TYR 3.6 1.9 + - - +
252A VAL* 3.2 18.6 + - - +
254A LEU* 1.3 82.9 - - + +
256A ALA* 1.3 72.7 + - - +
258A ILE* 3.3 4.4 + - - +
259A GLY 3.2 7.3 + - - -
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Residues in contact with ALA 256 (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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13A LEU* 3.2 11.6 - - - +
52A ASP* 3.7 21.3 - - - +
97A THR* 3.8 6.9 - - - +
252A VAL* 2.7 24.8 + - + +
253A TRP* 4.2 5.4 - - + -
255A ASP* 1.3 77.0 + - - +
257A PRO* 1.3 66.5 - - + +
259A GLY* 2.8 15.9 + - - -
553A MF3 3.1 29.3 - - - -
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Residues in contact with PRO 257 (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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253A TRP 3.2 15.7 - - - +
254A LEU 3.7 1.3 - - - +
256A ALA* 1.3 89.6 - - + +
258A ILE* 1.3 63.6 + - - +
259A GLY 2.8 5.8 - - - -
260A TYR* 2.9 28.4 + - + +
300A PHE* 3.5 24.9 - - + -
305A TRP* 3.4 42.4 - - + -
308A MET* 3.9 9.0 - - + -
553A MF3 3.3 21.7 - - - -
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Residues in contact with ILE 258 (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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102A ASN* 3.1 19.4 + - - +
105A LEU* 3.6 27.4 - - + -
106A SER* 3.6 28.3 - - - +
109A ILE* 3.8 29.8 - - + -
254A LEU* 3.2 32.8 - - + +
255A ASP 3.5 4.0 - - - +
256A ALA 3.1 1.0 - - - -
257A PRO* 1.3 77.3 - - - +
259A GLY* 1.3 56.0 + - - +
260A TYR 3.1 0.2 - - - -
261A MET* 2.9 9.0 + - - +
262A GLY 2.8 22.5 + - - -
305A TRP* 4.2 7.2 - - + -
308A MET* 3.9 14.4 - - + -
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Residues in contact with GLY 259 (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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13A LEU* 4.1 13.1 - - - +
50A ALA* 4.8 3.2 - - - +
96A SER 5.4 2.8 - - - +
97A THR* 4.2 6.7 - - - -
102A ASN* 3.5 17.0 - - - -
255A ASP 3.2 4.2 + - - -
256A ALA 2.8 12.5 + - - -
257A PRO 2.8 2.0 - - - -
258A ILE* 1.3 76.9 - - - +
260A TYR* 1.3 58.1 - - - +
262A GLY* 3.6 1.6 - - - -
263A SER* 2.8 31.4 + - - -
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Residues in contact with TYR 260 (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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8A LEU* 5.5 0.7 - - - +
10A THR* 3.5 32.9 + - + +
11A CYS 3.3 21.4 + - - -
12A ALA* 3.6 9.5 + - - -
13A LEU* 3.7 21.3 - - + -
48A ILE* 3.8 9.2 - - + +
256A ALA 4.1 0.8 + - - -
257A PRO* 2.9 22.5 + - + +
259A GLY* 1.3 76.1 - - - +
261A MET* 1.3 62.8 + - - +
263A SER* 3.6 4.8 + - - -
264A PHE* 3.3 21.0 + - - +
281A TRP* 4.4 16.8 - - + -
291A HIS* 3.6 21.7 - + - -
293A ILE* 4.3 3.1 - - - +
301A HIS* 2.7 30.7 + + - -
305A TRP* 4.0 7.4 - + - -
553A MF3 3.1 29.1 - - - -
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Residues in contact with MET 261 (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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105A LEU* 3.7 15.7 - - + -
109A ILE* 3.9 19.7 - - + -
258A ILE* 2.9 11.6 + - - +
260A TYR* 1.3 74.9 - - - +
262A GLY* 1.3 60.5 + - - +
264A PHE* 3.1 1.7 + - - -
265A LYS* 2.8 26.0 + - - +
277A PHE* 3.4 20.4 - - + -
281A TRP* 3.5 39.3 - - + -
305A TRP* 3.9 23.8 - - + -
309A LEU* 4.1 6.3 - - - -
314A PHE* 3.7 48.7 - - + -
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Residues in contact with GLY 262 (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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95A HIS* 4.2 5.2 - - - -
96A SER 5.8 0.4 - - - -
101A GLU* 3.6 19.1 - - - +
102A ASN* 4.3 10.1 - - - -
105A LEU* 3.6 14.5 - - - +
258A ILE 2.8 16.7 + - - -
259A GLY* 3.3 4.0 + - - -
261A MET* 1.3 72.6 - - - +
263A SER* 1.3 58.1 + - - +
265A LYS* 3.4 0.4 + - - -
266A ASN* 2.9 30.3 + - - +
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Residues in contact with SER 263 (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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48A ILE* 3.1 23.6 - - - +
49A CYS 3.0 23.7 + - - -
50A ALA* 4.5 2.0 - - - -
93A ASN* 2.9 30.1 + - - +
95A HIS* 3.5 25.5 + - - +
96A SER 5.7 0.2 + - - -
259A GLY 2.8 17.8 + - - -
260A TYR* 3.8 0.4 - - - -
262A GLY* 1.3 75.1 - - - +
264A PHE* 1.3 58.3 + - - +
266A ASN 3.4 0.5 + - - -
267A LEU* 3.0 13.5 + - - +
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Residues in contact with PHE 264 (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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8A LEU* 3.8 15.0 - - + -
46A ASN* 3.5 31.0 - - + -
48A ILE* 4.1 21.0 - - + +
260A TYR 3.3 10.9 + - - +
261A MET 3.1 8.0 + - - +
263A SER* 1.3 77.6 - - - +
265A LYS* 1.3 64.8 + - - +
267A LEU* 3.2 10.0 + - + +
268A CYS* 2.9 44.8 + - - -
271A ARG* 5.4 1.3 - - - -
276A SER* 3.7 20.4 - - - -
277A PHE* 3.8 11.0 - + - -
280A TYR* 3.7 35.9 - + + -
281A TRP* 3.5 22.7 - - - +
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Residues in contact with LYS 265 (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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101A GLU* 4.1 19.7 - - + +
104A GLN* 4.9 17.7 - - - +
105A LEU* 4.3 22.9 - - + -
261A MET 2.8 16.2 + - - +
262A GLY* 3.8 5.8 - - - +
264A PHE* 1.3 75.2 - - - +
266A ASN* 1.3 58.3 + - - +
268A CYS* 3.2 4.2 + - + +
269A ASP* 2.7 68.7 + - - +
277A PHE* 3.7 27.7 - - + -
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Residues in contact with ASN 266 (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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93A ASN* 2.9 21.0 + - - +
94A TYR 5.7 0.2 + - - -
95A HIS* 3.5 33.6 + - + +
101A GLU* 3.0 28.0 - - - +
262A GLY 2.9 18.5 + - - +
263A SER 3.5 4.3 - - - +
265A LYS* 1.3 78.3 - - - +
267A LEU* 1.3 56.3 + - - +
269A ASP* 3.3 3.1 + - - +
270A LYS* 2.9 68.5 + - - +
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Residues in contact with LEU 267 (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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46A ASN* 3.6 23.8 - - - +
48A ILE* 3.8 21.1 - - + -
92A ASP* 3.5 25.4 - - + +
93A ASN* 3.6 15.6 + - + +
263A SER 3.0 14.0 + - - +
264A PHE* 3.5 15.0 - - + +
266A ASN* 1.3 76.6 - - - +
268A CYS* 1.3 63.9 + - - +
270A LYS* 3.3 9.4 + - + +
271A ARG* 3.1 63.3 + - + +
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Residues in contact with CYS 268 (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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264A PHE* 2.9 50.2 + - - +
265A LYS* 3.6 9.2 - - + +
267A LEU* 1.3 77.5 - - - +
269A ASP* 1.3 65.1 + - - +
271A ARG* 3.1 6.8 + - - +
272A GLY 3.0 4.2 + - - -
273A ASP* 2.9 48.1 + - + +
276A SER* 3.8 10.5 - - - -
277A PHE* 3.7 22.2 - - + +
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Residues in contact with ASP 269 (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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101A GLU* 4.4 9.3 - - - +
265A LYS* 2.7 60.4 + - - +
266A ASN* 3.7 5.6 - - - +
268A CYS* 1.3 76.5 - - - +
270A LYS* 1.3 61.2 + - + +
272A GLY* 3.2 12.7 + - - +
273A ASP 4.7 4.4 - - - +
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Residues in contact with LYS 270 (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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93A ASN* 2.8 29.0 - - - +
94A TYR 5.8 0.4 + - - -
266A ASN* 2.9 45.3 + - - +
267A LEU* 3.8 10.8 - - + +
268A CYS 3.2 0.2 - - - -
269A ASP* 1.3 78.1 - - + +
271A ARG* 1.3 60.9 + - + +
272A GLY 3.5 0.3 + - - -
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Residues in contact with ARG 271 (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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46A ASN* 3.2 28.3 + - - +
92A ASP* 4.1 17.0 + - - +
264A PHE* 5.4 2.2 - - - -
267A LEU* 3.1 50.9 + - + +
268A CYS* 3.1 9.6 + - - +
270A LYS* 1.3 76.5 - - + +
272A GLY* 1.3 62.4 + - - +
273A ASP* 3.4 16.8 + - + +
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Residues in contact with GLY 272 (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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268A CYS 3.0 2.8 + - - -
269A ASP* 3.2 13.9 + - - -
270A LYS 3.2 1.2 - - - -
271A ARG* 1.3 78.5 - - - +
273A ASP* 1.3 62.0 + - - +
274A SER* 3.6 5.6 + - - -
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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
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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