Contacts of the helix formed by residues 304 - 326 (chain A) in PDB entry 1W7L
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 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ARG* 4.1 1.8 - - - +
295A GLU* 3.4 17.2 + - - -
298A LEU* 3.2 32.9 + - - +
299A PHE* 5.0 0.9 - - - -
300A ARG 4.3 3.2 + - - -
301A GLN 2.8 18.5 + - - -
303A SER* 1.3 79.7 + - - +
305A TYR* 1.3 59.2 + - - +
306A PHE* 3.9 2.1 + - - +
307A VAL* 3.2 20.1 + - - +
308A GLN* 2.9 31.2 + - - +
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Residues in contact with TYR 305 (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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40A PHE* 4.9 1.6 - - - -
43A PRO* 3.6 41.0 - - + +
45A PHE* 3.8 15.7 - + + -
248A THR 3.6 23.6 - - - -
249A PHE* 4.2 3.6 - + - -
250A SER* 2.7 30.5 + - - -
294A ARG* 3.6 4.1 - - - +
295A GLU* 2.9 22.7 + - - +
304A SER* 1.3 71.8 - - - +
306A PHE* 1.3 67.7 + + - +
307A VAL 3.1 0.2 - - - -
308A GLN* 4.4 10.3 - - + +
309A PHE* 2.8 76.5 + + + +
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Residues in contact with PHE 306 (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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79A PHE* 3.9 14.8 - + - -
218A TRP* 3.6 65.7 - + + +
248A THR* 3.5 41.7 - - + -
249A PHE* 4.0 8.3 - + - -
292A PHE* 4.0 4.5 - + - -
295A GLU* 2.9 46.2 + - + +
299A PHE* 5.0 8.5 - + + -
304A SER* 4.6 2.7 - - - +
305A TYR* 1.3 85.0 - + - +
307A VAL* 1.3 61.0 + - + +
310A PRO* 3.3 21.1 - - - +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG* 4.1 21.3 - - - +
301A GLN 3.6 10.5 - - - +
302A PRO* 4.2 19.5 - - + +
304A SER* 3.2 19.6 + - - +
305A TYR 3.1 0.6 - - - -
306A PHE* 1.3 81.1 - - + +
308A GLN* 1.3 66.6 + - - +
309A PHE 3.4 0.4 + - - -
310A PRO* 3.6 8.4 - - - +
311A GLN* 3.6 36.3 + - - +
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Residues in contact with GLN 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ARG* 5.4 1.2 + - - -
302A PRO 3.2 23.5 + - - +
303A SER* 3.5 26.0 + - - +
304A SER 2.9 17.7 + - - +
305A TYR* 4.2 9.7 + - + +
307A VAL* 1.3 75.0 - - + +
309A PHE* 1.3 63.8 + - + +
311A GLN* 3.3 10.0 + - - +
312A ALA* 3.1 21.9 + - - +
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Residues in contact with PHE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 3.6 32.3 - + - -
219A MET* 3.6 37.2 - - + -
247A LYS 5.6 1.6 - - - -
248A THR 5.4 1.3 - - - -
250A SER* 3.2 23.3 - - - -
305A TYR* 2.8 62.4 + + + +
308A GLN* 1.3 75.5 - - - +
310A PRO* 1.3 57.0 - - + +
312A ALA* 3.1 8.4 + - + +
313A MET* 2.9 52.1 + - + +
338A TYR* 5.1 3.4 - + - -
402A VAL* 3.9 7.6 - - + -
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Residues in contact with PRO 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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218A TRP* 3.2 25.4 - - + +
219A MET* 4.6 6.3 - - + -
220A VAL* 3.8 21.8 - - + +
221A TYR* 3.5 14.3 - - + -
305A TYR 3.5 8.3 - - - +
306A PHE* 3.3 20.0 - - - +
307A VAL 3.6 7.4 - - - +
309A PHE* 1.3 96.3 - - + +
311A GLN* 1.3 52.4 + - + +
313A MET* 4.5 1.8 - - + -
314A GLN* 2.8 37.6 + - - +
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Residues in contact with GLN 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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307A VAL* 3.6 31.4 - - - +
308A GLN* 3.3 12.6 + - - +
309A PHE 3.2 0.4 - - - -
310A PRO* 1.3 77.1 - - + +
312A ALA* 1.3 65.8 + - - +
314A GLN* 3.4 8.7 + - - +
315A ARG* 3.4 32.2 + - - +
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Residues in contact with ALA 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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308A GLN 3.1 12.1 + - - +
309A PHE* 3.5 11.7 - - + +
311A GLN* 1.3 77.6 - - - +
313A MET* 1.3 75.2 + - + +
315A ARG* 3.2 41.5 + - - +
316A CYS* 3.2 15.6 + - - -
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Residues in contact with MET 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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40A PHE* 4.0 12.8 - - + -
219A MET* 3.8 20.2 - - + -
221A TYR* 4.0 10.3 - - - +
309A PHE* 2.9 49.7 + - + +
310A PRO 4.0 2.5 - - - +
312A ALA* 1.3 85.8 - - + +
314A GLN* 1.3 59.4 + - - +
316A CYS* 3.1 24.7 + - - +
317A ARG* 2.8 28.9 + - - +
401A PHE* 3.6 6.2 - - + -
402A VAL* 3.6 36.8 - - + -
403A LYS 4.8 0.9 - - - +
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Residues in contact with GLN 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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221A TYR* 3.3 17.2 - - + +
222A ASP* 2.9 44.2 + - - +
310A PRO 2.8 22.5 + - - +
311A GLN* 3.6 10.1 - - - +
313A MET* 1.3 72.8 - - - +
315A ARG* 1.3 57.0 + - + +
317A ARG* 3.3 26.1 + - - +
318A ASP* 2.9 42.7 + - - +
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Residues in contact with ARG 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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311A GLN* 3.4 14.5 + - - +
312A ALA* 3.2 45.0 + - - +
313A MET 3.2 0.4 - - - -
314A GLN* 1.3 73.9 - - - +
316A CYS* 1.3 61.7 + - - +
318A ASP* 3.3 9.7 + - - +
319A HIS* 2.9 30.9 + - - +
322A ARG* 4.8 1.6 + - - +
405A GLU* 5.9 0.6 + - - -
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Residues in contact with CYS 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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312A ALA 3.2 14.9 + - - -
313A MET* 3.1 29.9 + - - +
315A ARG* 1.3 79.0 - - - +
317A ARG* 1.3 56.1 + - - +
319A HIS* 3.4 3.9 + - - +
320A MET* 2.9 30.3 + - - +
401A PHE* 3.3 23.2 - - - +
403A LYS 3.9 16.8 - - - -
405A GLU* 5.9 4.0 - - - -
408A LEU* 3.9 20.0 - - + +
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Residues in contact with ARG 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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221A TYR* 3.6 17.7 - - - +
222A ASP* 2.8 45.6 + - - -
313A MET 2.8 16.1 + - - +
314A GLN* 3.4 21.9 + - - +
316A CYS* 1.3 72.9 - - - +
318A ASP* 1.3 81.3 + - - +
320A MET* 3.2 3.3 + - - +
321A ILE* 2.9 45.7 + - + +
333A ILE* 3.7 9.8 - - - +
334A PRO* 2.9 41.9 + - + -
335A GLN* 4.7 0.4 - - - +
340A LEU* 4.3 0.8 - - + +
401A PHE* 3.6 35.8 - - + -
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Residues in contact with ASP 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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314A GLN* 2.9 31.6 + - - +
315A ARG* 3.7 8.7 - - - +
317A ARG* 1.3 104.5 + - - +
319A HIS* 1.3 62.2 + - - +
321A ILE* 3.3 10.2 + - - +
322A ARG* 3.0 53.8 + - - +
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Residues in contact with HIS 319 (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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315A ARG 2.9 17.5 + - - +
316A CYS* 3.5 7.9 - - - +
318A ASP* 1.3 78.3 - - - +
320A MET* 1.3 58.4 + - - +
322A ARG* 3.3 14.8 + - + +
323A SER* 2.9 35.4 + - - -
405A GLU* 5.5 1.5 - - + +
408A LEU* 3.8 32.7 - - + +
409A GLN* 4.8 5.2 - - + -
411A MET* 4.2 4.6 - - + +
412A ASP* 2.6 31.5 + - - -
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Residues in contact with MET 320 (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 LEU* 3.9 10.1 - - + -
316A CYS 2.9 16.6 + - - +
317A ARG 3.7 3.8 - - - +
319A HIS* 1.3 76.9 - - - +
321A ILE* 1.3 56.2 + - - +
323A SER 3.2 0.3 + - - -
324A LEU* 2.9 51.4 + - + +
340A LEU* 4.2 9.2 - - + -
399A PHE* 3.7 27.8 - - - -
400A CYS 3.4 21.1 - - - +
401A PHE* 3.6 22.7 - - + -
408A LEU* 3.8 14.1 - - + +
411A MET* 3.7 32.8 - - + +
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Residues in contact with ILE 321 (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 LEU* 4.4 13.2 - - + -
317A ARG* 2.9 45.7 + - + +
318A ASP* 3.3 9.4 + - - +
320A MET* 1.3 72.2 - - - +
322A ARG* 1.3 61.3 + - + +
324A LEU* 5.4 0.2 - - - -
325A GLN* 3.0 46.4 + - - +
331A PRO* 3.6 24.9 - - + +
333A ILE* 3.8 36.8 - - + -
334A PRO* 4.4 1.6 - - + -
340A LEU* 3.8 15.9 - - + -
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Residues in contact with ARG 322 (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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315A ARG* 4.8 2.0 + - - +
318A ASP* 3.0 47.2 + - - +
319A HIS* 3.7 16.0 - - + +
321A ILE* 1.3 77.4 - - + +
323A SER* 1.3 63.7 + - - +
325A GLN* 3.5 14.9 - - - +
326A SER* 3.1 26.9 + - - -
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Residues in contact with SER 323 (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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319A HIS* 2.9 28.7 + - - -
320A MET 3.7 2.9 - - - -
322A ARG* 1.3 77.5 - - - +
324A LEU* 1.3 62.2 + - - +
326A SER* 3.3 19.1 - - - -
327A VAL* 4.1 5.2 + - - +
411A MET* 3.8 8.3 - - - -
412A ASP* 2.6 29.2 + - - -
415A LEU* 3.7 21.9 - - - +
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Residues in contact with LEU 324 (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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320A MET* 2.9 41.2 + - + +
321A ILE 4.4 1.3 - - - +
323A SER* 1.3 68.4 - - - +
325A GLN* 1.3 63.9 + - - +
326A SER 2.9 6.1 + - - -
327A VAL* 3.0 13.7 + - - +
329A LEU* 3.6 43.7 + - + +
331A PRO* 4.4 4.9 - - + -
340A LEU* 3.8 7.4 - - + -
342A THR* 3.8 12.1 - - + -
376A LEU* 5.4 2.0 - - + -
399A PHE* 3.6 41.7 - - + -
411A MET* 4.5 9.9 - - + -
415A LEU* 4.1 24.0 - - + -
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Residues in contact with GLN 325 (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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153A GLU* 4.3 18.2 - - - +
154A LEU* 3.6 41.8 - - + +
321A ILE* 3.0 27.2 + - - +
322A ARG* 3.5 15.5 - - - +
324A LEU* 1.3 75.2 - - - +
326A SER* 1.3 60.5 + - - +
327A VAL 3.3 1.6 + - - -
328A GLY* 3.6 9.4 + - - -
329A LEU 3.3 13.3 + - - +
331A PRO* 3.9 5.6 - - + +
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Residues in contact with SER 326 (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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322A ARG 3.1 12.4 + - - -
323A SER* 3.3 15.7 - - - -
324A LEU 2.9 1.0 - - - -
325A GLN* 1.3 78.2 - - - +
327A VAL* 1.3 64.2 + - - +
328A GLY 3.6 0.4 - - - -
419A LYS* 3.8 28.3 + - - +
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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) + - + + + + + -
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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