Contacts of the helix formed by residues 299 - 320 (chain A) in PDB entry 1Y8Q
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 MET 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A VAL* 4.5 2.2 - - - +
160A GLY* 3.5 28.1 + - - +
161A TYR* 3.8 51.8 - - + +
296A PHE 4.8 5.2 - - - +
297A SER* 4.2 1.5 + - - -
298A GLU* 1.3 74.8 - - - +
300A ALA* 1.3 66.7 + - - +
301A PRO* 3.9 9.2 - - + -
302A VAL* 3.1 18.6 + - + +
303A CYS* 3.0 22.8 + - - -
7B LEU* 4.5 15.5 - - + -
39B THR* 5.6 2.0 - - + -
400B LEU* 5.4 2.0 - - + -
403B LEU* 4.4 16.4 - - + -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 4.7 2.1 - - - +
298A GLU 3.8 3.0 + - - -
299A MET* 1.3 70.3 - - - +
301A PRO* 1.3 70.8 - - + +
303A CYS* 3.2 10.9 + - - +
304A ALA* 3.1 22.2 + - - +
35B ASN* 3.9 11.1 - - - +
38B LEU* 3.7 42.2 - - + +
39B THR* 4.0 9.4 - - - +
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Residues in contact with PRO 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A MET* 3.3 13.5 - - + -
300A ALA* 1.3 93.4 - - + +
302A VAL* 1.3 60.7 + - - +
304A ALA* 3.3 5.5 + - + +
305A VAL* 3.1 28.0 + - - +
35B ASN* 4.7 4.0 - - + +
39B THR* 3.5 24.7 - - + +
396B GLY* 3.4 27.3 - - - +
399B VAL* 3.6 20.6 - - + -
400B LEU* 3.9 20.4 - - + -
403B LEU* 5.1 3.1 - - + -
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 3.6 15.5 - - + -
160A GLY 3.5 16.6 - - - +
161A TYR* 4.0 12.3 - - - +
162A HIS 3.5 26.7 - - - +
299A MET* 3.1 21.4 + - + +
301A PRO* 1.3 72.6 - - - +
303A CYS* 1.3 65.5 + - - +
305A VAL* 3.3 4.5 + - - +
306A VAL* 3.0 25.6 + - + +
331A PHE* 3.9 26.5 - - + -
400B LEU* 4.6 14.8 - - + -
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Residues in contact with CYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 3.8 16.2 - - - +
47A LEU* 3.7 31.6 - - - +
50A GLU* 3.5 11.2 - - + +
158A VAL* 4.0 18.4 - - - -
298A GLU* 4.3 16.6 - - - -
299A MET 3.0 23.0 + - - -
300A ALA* 3.2 10.3 + - - +
302A VAL* 1.3 76.5 - - - +
304A ALA* 1.3 55.4 + - - +
307A GLY* 2.8 31.7 + - - -
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 3.8 17.5 - - - +
300A ALA 3.1 12.7 + - - +
301A PRO 3.4 9.9 - - - +
302A VAL 3.1 0.2 - - - -
303A CYS* 1.3 75.7 - - - +
305A VAL* 1.3 60.4 + - - +
307A GLY 3.9 0.3 - - - -
308A GLY* 3.0 24.1 + - - -
34B LYS* 4.3 2.2 - - - +
35B ASN* 3.7 23.3 - - - +
392B ALA* 3.8 29.1 - - + +
396B GLY* 4.1 2.2 - - - -
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO 3.1 15.1 + - - +
302A VAL 3.3 5.4 + - - +
304A ALA* 1.3 74.0 - - - +
306A VAL* 1.3 68.1 + - + +
308A GLY* 2.9 12.3 + - - -
309A ILE* 3.0 23.8 + - + +
329A PHE* 5.0 0.9 - - + -
331A PHE* 3.9 42.4 - - + -
393B VAL* 3.8 32.7 - - + +
396B GLY 4.2 7.0 - - - -
397B LEU* 3.9 16.8 - - + -
400B LEU* 4.8 0.9 - - + -
429B LEU* 4.4 10.3 - - + -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.8 19.7 - - + -
157A ASP 4.3 2.5 - - - +
158A VAL* 4.1 7.4 - - + -
163A GLY* 3.7 28.9 - - - -
164A TYR 3.8 13.9 - - - +
165A THR* 3.7 21.1 - - + +
302A VAL* 3.0 15.2 + - + +
305A VAL* 1.3 75.7 - - - +
307A GLY* 1.3 57.5 + - - +
309A ILE* 4.5 5.4 - - - +
310A LEU* 2.9 28.3 + - + +
329A PHE* 4.7 4.0 - - + -
331A PHE* 4.2 20.9 - - + -
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Residues in contact with GLY 307 (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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47A LEU* 3.4 13.8 - - - +
50A GLU* 4.2 5.6 - - - -
51A ILE* 3.9 12.9 - - - +
54A ASN* 3.2 10.2 + - - -
303A CYS 2.8 21.3 + - - -
304A ALA 3.9 0.7 - - - -
306A VAL* 1.3 78.2 - - - +
308A GLY* 1.3 56.8 - - - +
311A ALA* 3.1 30.0 + - - +
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Residues in contact with GLY 308 (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 ASN* 3.8 9.4 - - - -
304A ALA 3.0 13.0 + - - -
305A VAL 2.9 7.3 + - - -
307A GLY* 1.3 76.9 - - - +
309A ILE* 1.3 63.9 + - - +
312A GLN* 3.0 12.2 + - - +
389B THR* 2.2 35.4 + - - -
392B ALA* 4.7 0.7 - - - -
393B VAL* 3.9 11.9 - - - -
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Residues in contact with ILE 309 (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 THR* 4.9 1.6 - - - +
305A VAL* 3.0 17.6 + - + +
306A VAL 4.1 2.2 - - - +
308A GLY* 1.3 75.9 - - - +
310A LEU* 1.3 64.2 + - - +
312A GLN* 3.1 17.9 + - - +
313A GLU* 3.0 24.9 + - + +
325A HIS* 4.4 13.2 - - + +
329A PHE* 3.8 50.9 - - + -
393B VAL* 3.6 25.1 - - + -
418B LEU* 4.4 16.2 - - + -
428B LEU* 4.3 17.3 - - + -
429B LEU* 5.7 1.8 - - + -
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Residues in contact with LEU 310 (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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47A LEU* 4.7 4.0 - - + -
51A ILE* 3.6 25.8 - - + -
130A CYS* 3.6 18.8 - - - -
131A LEU 5.3 0.2 - - - +
132A THR* 5.4 0.2 - - - +
154A PHE* 3.8 34.5 - - + -
155A THR 4.6 1.6 - - - +
156A GLY* 4.0 27.8 - - - +
165A THR* 3.6 25.3 - - + +
166A PHE 4.8 1.3 - - - +
306A VAL 2.9 18.0 + - - +
307A GLY 4.3 2.0 - - - +
309A ILE* 1.3 77.3 - - - +
311A ALA* 1.3 62.7 + - - +
313A GLU* 3.2 5.9 + - + +
314A ILE* 3.0 28.2 + - + +
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Residues in contact with ALA 311 (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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51A ILE* 4.4 9.1 - - + +
54A ASN* 3.5 30.1 - - + +
55A LEU* 3.9 16.5 - - + +
307A GLY 3.1 21.0 + - - +
308A GLY 4.1 1.8 - - - +
310A LEU* 1.3 76.9 - - - +
312A GLN* 1.3 62.1 + - - +
314A ILE* 3.2 7.3 + - - +
315A VAL* 3.0 28.8 + - + +
389B THR* 4.8 2.0 - - - +
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Residues in contact with GLN 312 (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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26A TRP* 6.3 0.9 - - + -
308A GLY 3.0 17.4 + - - +
309A ILE* 3.3 19.6 - - - +
311A ALA* 1.3 78.2 - - - +
313A GLU* 1.3 60.5 + - - +
315A VAL* 3.4 7.3 + - - +
316A LYS* 3.0 43.9 + - + +
325A HIS* 5.2 5.5 - - - -
144B TYR* 4.2 30.5 + - + +
387B ILE* 4.9 0.2 - - + -
389B THR* 2.9 38.7 + - + +
390B THR* 3.5 20.0 + - - +
393B VAL* 5.3 3.6 - - - +
418B LEU* 5.5 4.8 - - - +
428B LEU* 5.9 0.5 - - - +
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Residues in contact with GLU 313 (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 PHE* 3.8 17.5 - - + -
165A THR* 5.5 4.5 - - - +
309A ILE* 3.0 20.2 + - + +
310A LEU* 3.6 10.5 - - + +
312A GLN* 1.3 75.9 - - - +
314A ILE* 1.3 60.9 + - - +
316A LYS* 3.2 27.8 + - - +
317A ALA* 3.0 30.5 + - - +
324A PRO* 3.4 12.2 - - + +
325A HIS* 2.7 67.2 + - + +
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Residues in contact with ILE 314 (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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39A VAL* 4.5 7.2 - - + -
51A ILE* 4.3 16.4 - - + -
55A LEU* 4.1 16.2 - - + -
128A ALA* 4.4 14.6 - - + -
130A CYS* 3.9 36.3 - - + -
154A PHE* 3.7 26.2 - - + -
310A LEU* 3.0 19.4 + - + +
311A ALA* 3.2 6.9 + - - +
313A GLU* 1.3 78.1 - - - +
315A VAL* 1.3 58.2 + - - +
317A ALA* 3.5 1.0 + - - +
318A LEU* 3.0 54.3 + - + +
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Residues in contact with VAL 315 (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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26A TRP* 3.9 36.6 - - + -
34A LEU* 3.9 26.9 - - + +
54A ASN 6.0 0.2 - - - -
55A LEU* 4.1 12.1 - - + -
58A ALA* 4.0 25.4 - - + -
60A VAL* 5.5 0.2 - - + -
311A ALA* 3.0 20.1 + - + +
312A GLN* 3.8 6.5 - - - +
313A GLU 3.3 0.2 - - - -
314A ILE* 1.3 74.1 - - - +
316A LYS* 1.3 66.0 + - + +
318A LEU* 3.8 0.9 - - - +
319A SER* 2.8 32.8 + - - +
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Residues in contact with LYS 316 (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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172A HIS* 4.7 1.5 + - - -
312A GLN* 3.0 29.1 + - - +
313A GLU* 3.2 35.0 + - - +
314A ILE 3.3 0.2 - - - -
315A VAL* 1.3 77.0 - - + +
317A ALA* 1.3 57.7 + - - +
319A SER* 3.0 8.7 + - - -
320A GLN* 2.8 26.9 + - - -
321A ARG 3.4 19.8 + - - +
322A ASP* 4.3 20.1 - - + +
323A PRO 3.7 19.4 + - - +
324A PRO* 4.6 6.5 - - + -
325A HIS* 3.6 16.0 + - - -
144B TYR* 4.5 24.0 - - + +
420B LYS* 4.1 17.5 + - - +
421B GLN* 5.1 1.0 + - - +
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Residues in contact with ALA 317 (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 LYS* 3.6 16.2 + - + -
154A PHE* 3.7 22.7 - - + -
169A LEU* 3.8 22.2 - - + -
172A HIS* 3.3 29.5 - - + -
313A GLU 3.0 14.9 + - - +
314A ILE 3.8 1.3 - - - +
316A LYS* 1.3 78.9 - - - +
318A LEU* 1.3 64.1 + - + +
320A GLN* 3.3 6.9 + - - +
324A PRO* 4.9 1.5 - - - +
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Residues in contact with LEU 318 (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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33A ARG* 3.9 16.5 - - - +
34A LEU* 4.0 19.3 - - + -
37A SER* 3.8 29.4 + - - +
39A VAL* 3.7 26.5 - - + -
55A LEU* 5.8 0.2 - - + -
60A VAL* 4.5 3.8 - - + -
127A ASP* 4.0 18.6 - - + +
128A ALA* 3.7 22.7 - - + -
152A LYS* 4.8 10.4 + - + +
314A ILE* 3.0 29.3 + - + +
315A VAL* 3.9 3.4 - - + +
317A ALA* 1.3 78.9 - - + +
319A SER* 1.3 60.1 + - - +
320A GLN* 3.2 7.3 + - - +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 5.7 3.9 - - - +
30A ALA* 3.6 37.1 - - - +
33A ARG* 3.4 25.0 + - - -
34A LEU* 4.9 4.0 - - - +
315A VAL* 2.8 29.9 + - - +
316A LYS* 3.0 12.0 + - - -
318A LEU* 1.3 74.8 - - - +
320A GLN* 1.3 69.6 + - - +
321A ARG* 3.2 13.5 + - - +
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Residues in contact with GLN 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 3.7 24.8 + - - +
152A LYS* 5.0 6.4 - - - +
172A HIS* 4.3 8.0 + - + -
173A GLU* 3.5 36.1 + - - +
174A PHE* 3.7 12.6 - - - -
175A VAL* 3.0 27.9 + - - +
316A LYS 2.8 10.7 + - - -
317A ALA 3.3 13.7 + - - +
318A LEU 3.2 5.9 - - - +
319A SER* 1.3 80.3 - - - +
321A ARG* 1.3 55.5 + - - +
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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