Contacts of the helix formed by residues 308 - 331 (chain A) in PDB entry 1W6J
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 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLU* 4.8 0.5 - - - +
303A TYR* 3.2 20.8 + - - -
306A HIS 3.6 1.8 + - - -
307A HIS* 1.3 70.7 + - - +
309A ALA* 1.3 63.7 + - - +
310A HIS* 3.5 8.8 + - - +
311A LEU* 3.1 30.6 + - - +
312A ARG* 3.0 22.0 + - - +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A HIS* 3.3 21.7 + - + +
308A SER* 1.3 71.8 - - - +
310A HIS* 1.3 57.3 + - - +
312A ARG* 3.4 2.5 + - - +
313A GLN* 3.0 30.3 + - - +
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Residues in contact with HIS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A SER* 3.2 6.8 - - - +
309A ALA* 1.3 76.5 - - - +
311A LEU* 1.3 78.8 + - + +
313A GLN* 3.5 16.5 + - - +
314A ARG* 3.3 35.2 + - - +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLU* 4.4 12.3 - - + -
217A LEU* 3.5 22.8 - - + +
303A TYR* 4.3 15.5 - - - +
308A SER* 3.1 22.6 + - - +
310A HIS* 1.3 84.3 - - + +
312A ARG* 1.3 59.8 - - - +
314A ARG* 3.2 38.1 + - - +
315A ALA* 2.9 23.4 + - - +
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE* 5.1 0.8 - - - +
213A PRO* 3.8 15.0 - - + +
214A GLU* 2.9 42.7 + - - +
244A TYR* 4.2 3.6 - - - -
245A ALA* 4.2 24.8 + - + +
247A ARG* 3.9 13.5 - - - +
303A TYR* 4.9 1.4 - - - -
304A GLU* 2.8 43.4 + - - +
307A HIS* 3.7 38.7 + - + +
308A SER 3.0 16.0 + - - +
309A ALA* 3.7 4.7 - - - +
311A LEU* 1.3 74.5 - - - +
313A GLN* 1.3 55.6 + - - +
315A ALA* 3.1 3.1 + - - +
316A VAL* 2.8 45.7 + - + +
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Residues in contact with GLN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ALA 3.0 18.9 + - - +
310A HIS* 3.5 16.3 + - - +
312A ARG* 1.3 75.7 - - - +
314A ARG* 1.3 60.5 + - - +
316A VAL* 3.6 7.3 + - - +
317A GLN* 3.2 23.7 + - - +
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.9 29.2 + - + +
310A HIS* 3.3 25.4 + - + +
311A LEU* 3.2 37.2 + - - +
312A ARG 3.2 0.4 - - - -
313A GLN* 1.3 77.5 - - - +
315A ALA* 1.3 63.6 + - - +
317A GLN* 3.5 5.9 + - - +
318A LYS* 3.2 21.8 + - - +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PRO* 3.6 35.7 - - + +
214A GLU* 4.0 3.6 - - + +
216A TRP* 5.5 1.3 - - + +
217A LEU* 3.7 22.8 - - + +
311A LEU 2.9 13.4 + - - +
312A ARG* 3.1 9.8 + - - +
314A ARG* 1.3 73.7 - - - +
316A VAL* 1.3 59.9 + - - +
318A LYS* 3.1 4.4 + - - +
319A LEU* 2.8 35.0 + - - +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PRO* 5.5 0.2 - - + -
242A TYR* 3.5 28.3 - - + +
245A ALA* 3.5 33.7 - - + -
246A VAL* 4.5 10.3 - - + -
312A ARG* 2.8 29.4 + - + +
313A GLN* 3.8 8.3 - - - +
315A ALA* 1.3 73.4 - - + +
317A GLN* 1.3 62.3 + - - +
319A LEU* 3.5 9.9 + - + +
320A TYR* 3.1 22.2 + - - +
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Residues in contact with GLN 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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313A GLN 3.2 17.5 + - - +
314A ARG* 3.7 7.4 - - - +
315A ALA 3.2 0.2 - - - -
316A VAL* 1.3 78.9 - - - +
318A LYS* 1.3 62.1 + - - +
320A TYR* 3.4 18.7 + - - +
321A GLU* 2.9 51.7 + - - +
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Residues in contact with LYS 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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216A TRP* 2.8 39.8 + - + +
217A LEU* 4.1 19.8 - - + +
218A PHE 4.8 2.2 + - - -
220A ASP* 4.7 5.1 + - - -
225A HIS* 4.6 3.6 + - - -
314A ARG 3.2 10.5 + - - +
315A ALA* 3.1 8.8 + - - +
317A GLN* 1.3 76.4 - - - +
319A LEU* 1.3 66.9 + - - +
321A GLU* 3.2 13.0 + - - +
322A HIS* 3.1 54.5 + - + +
434A TYR* 3.6 16.1 + - - -
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Residues in contact with LEU 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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213A PRO* 3.8 17.7 - - + +
216A TRP* 3.4 44.4 - - + +
238A LEU* 3.5 25.3 - - + +
241A SER* 3.8 12.8 - - - -
242A TYR* 3.4 42.0 - - + +
245A ALA* 5.2 0.7 - - + -
315A ALA 2.8 22.8 + - - +
316A VAL* 3.7 9.6 - - - +
318A LYS* 1.3 70.8 - - - +
320A TYR* 1.3 63.6 + - - +
322A HIS* 3.1 3.7 + - - -
323A ILE* 3.0 26.9 + - - +
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Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TYR* 4.1 9.3 - + + -
316A VAL* 3.1 12.0 + - + +
317A GLN* 3.5 26.2 - - - +
318A LYS 3.2 0.2 - - - -
319A LEU* 1.3 78.8 - - - +
321A GLU* 1.3 59.5 + - + +
323A ILE* 3.2 9.8 + - + +
324A VAL* 2.9 49.1 + - + +
346A VAL* 4.1 12.3 - - + -
347A ARG* 3.9 12.7 + - - -
350A VAL* 3.7 37.6 - - + +
351A ASP* 2.7 38.7 + - - -
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLN* 2.9 46.1 + - - +
318A LYS* 3.2 13.6 + - - +
320A TYR* 1.3 77.9 - - + +
322A HIS* 1.3 63.3 + - - +
324A VAL* 3.4 9.1 + - - +
325A ALA* 2.9 28.2 + - - +
328A ARG* 4.9 1.2 + - - -
432A LYS* 5.2 10.9 + - - -
433A TYR* 3.9 14.0 + - + +
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Residues in contact with HIS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TRP* 4.1 11.0 - + - -
235A GLN* 4.7 0.7 - - - +
238A LEU* 3.8 22.7 - - + +
318A LYS* 3.1 50.1 + - + +
319A LEU 3.1 7.6 + - - +
321A GLU* 1.3 78.8 - - + +
323A ILE* 1.3 58.3 + - - +
325A ALA* 3.5 7.7 - - - +
326A ASP* 3.1 26.5 + - - +
432A LYS* 3.6 22.0 + - + -
433A TYR* 3.7 32.1 - + + +
434A TYR* 3.8 29.8 + + - -
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Residues in contact with ILE 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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238A LEU* 3.7 19.1 - - + +
239A PRO* 3.9 24.7 - - + -
242A TYR* 4.2 11.4 - - + -
319A LEU 3.0 17.5 + - - +
320A TYR* 3.2 7.8 + - - +
322A HIS* 1.3 74.3 - - - +
324A VAL* 1.3 64.5 + - - +
326A ASP* 3.3 5.5 + - - +
327A ASP* 3.1 28.5 + - - +
343A ASN* 3.7 36.1 - - + +
346A VAL* 3.9 26.9 - - + -
347A ARG* 4.3 11.7 - - - -
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 2.9 54.6 + - + +
321A GLU* 3.4 8.0 + - - +
323A ILE* 1.3 73.3 - - - +
325A ALA* 1.3 56.7 + - - +
327A ASP* 3.4 3.8 + - - +
328A ARG* 2.9 50.6 + - + +
347A ARG* 3.7 30.5 - - - +
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Residues in contact with ALA 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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321A GLU 2.9 18.5 + - - +
322A HIS 3.5 6.7 - - - +
323A ILE 3.2 0.2 - - - -
324A VAL* 1.3 74.4 - - - +
326A ASP* 1.3 60.0 + - - +
328A ARG* 3.1 15.9 + - - +
329A PHE* 2.9 40.4 + - + -
433A TYR* 3.5 41.5 - - + -
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN* 3.6 23.7 - - - +
322A HIS 3.1 10.3 + - - +
323A ILE* 3.3 5.1 + - - +
325A ALA* 1.3 77.6 - - - +
327A ASP* 1.3 57.9 + - - +
329A PHE* 3.2 6.7 + - - -
330A THR* 2.7 38.2 + - - +
334A SER* 2.6 31.2 + - - -
343A ASN* 3.1 17.2 + - - +
435A ARG* 4.9 0.9 + - - +
451A TRP* 3.3 34.5 + - - -
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Residues in contact with ASP 327 (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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323A ILE* 3.1 11.1 + - - +
324A VAL 3.5 8.5 - - - +
326A ASP* 1.3 76.7 - - - +
328A ARG* 1.3 60.8 + - - +
330A THR* 4.0 4.0 + - - -
331A LYS* 3.1 6.2 + - - -
332A SER* 3.0 34.7 + - - +
334A SER* 5.6 1.4 - - - -
343A ASN* 3.2 21.8 + - - -
347A ARG* 2.9 34.3 + - - +
360A GLU* 4.3 2.8 - - - +
361A HIS* 2.9 34.8 + - - -
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Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLU 4.9 0.8 + - - -
324A VAL* 2.9 42.6 + - + +
325A ALA* 3.4 17.7 - - - +
327A ASP* 1.3 77.2 - - + +
329A PHE* 1.3 89.0 + - + +
330A THR 3.2 1.6 + - - -
331A LYS* 3.7 9.9 + - - +
428A PRO* 4.7 7.9 + - - +
429A ASP* 5.4 3.6 + - - -
433A TYR* 3.9 26.3 + - - -
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Residues in contact with PHE 329 (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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325A ALA* 2.9 21.1 + - + +
326A ASP* 3.2 6.7 + - - +
328A ARG* 1.3 102.5 - - + +
330A THR* 1.3 59.5 + - + +
331A LYS* 3.7 1.1 - - - -
427A PRO* 3.5 29.2 - - + -
428A PRO* 3.5 31.9 - - + -
430A TYR* 4.4 9.4 - - - -
433A TYR* 3.8 37.5 - + + -
435A ARG* 3.8 34.3 + - + +
438A ARG* 3.9 17.9 + - - +
448A ASP 4.2 3.1 - - - +
449A CYS 4.1 3.5 - - - +
450A GLY* 5.0 0.2 - - - -
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP* 2.7 28.6 + - - +
327A ASP* 4.0 1.0 - - - -
329A PHE* 1.3 84.0 - - + +
331A LYS* 1.3 71.0 + - - +
332A SER 3.6 2.4 + - - -
333A ILE* 3.0 18.6 + - - +
334A SER* 2.8 29.3 + - - -
435A ARG* 4.5 0.9 - - - +
448A ASP 3.2 17.2 - - - +
449A CYS 3.4 18.6 - - - +
451A TRP* 3.6 25.4 - - + +
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ASP 3.1 7.9 + - - -
328A ARG 3.7 7.8 + - - +
329A PHE 5.6 0.4 - - - -
330A THR* 1.3 80.2 - - - +
332A SER* 1.3 64.9 + - - +
333A ILE* 3.3 0.7 + - + -
360A GLU* 3.4 22.5 - - - +
364A ARG* 3.1 36.3 + - - +
448A ASP* 3.3 38.4 + - + +
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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