Contacts of the helix formed by residues 313 - 336 (chain A) in PDB entry 5ULW
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 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A CYS* 3.3 8.8 - - - -
312A SER* 1.3 73.2 + - - +
314A GLU* 1.3 50.1 + - - +
315A VAL* 3.0 6.7 - - - -
316A GLU* 2.4 53.3 + - - +
317A ALA* 2.6 17.0 + - - +
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Residues in contact with GLU 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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311A CYS 4.1 4.0 - - - +
312A SER* 2.6 34.1 + - - +
313A SER* 1.3 67.7 - - - +
315A VAL* 1.3 59.7 + - - +
317A ALA* 3.8 9.7 - - - +
318A LYS* 3.4 18.2 + - - +
388A MET* 4.5 8.2 - - + +
391A PHE* 3.2 30.2 - - + -
395A VAL* 4.3 17.1 - - + +
396A ASN 5.1 4.0 - - - +
397A VAL* 3.5 31.9 - - + -
403A LEU* 5.7 1.2 - - - +
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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
----------------------------------------------------------
313A SER* 3.0 1.7 - - - -
314A GLU* 1.3 79.3 - - - +
316A GLU* 1.3 61.4 + - - +
318A LYS* 3.4 18.4 - - - +
319A ASN* 3.5 6.2 + - - +
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A CYS* 4.6 3.8 - - - -
313A SER* 2.4 49.3 + - - +
315A VAL* 1.3 67.1 - - - +
317A ALA* 1.3 55.1 + - - +
318A LYS 3.1 1.3 - - - -
319A ASN* 2.7 29.9 + - + +
320A LYS* 3.0 11.5 + - - +
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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
----------------------------------------------------------
311A CYS* 3.7 24.9 - - - +
313A SER 2.6 12.1 + - - +
314A GLU* 3.8 10.8 - - - +
316A GLU* 1.3 70.3 - - - +
318A LYS* 1.3 62.4 + - - +
320A LYS* 3.2 4.5 + - - +
321A ILE* 2.9 30.4 + - - +
388A MET* 5.5 0.4 - - + -
391A PHE* 3.9 32.3 - - + -
406A LEU* 3.9 11.0 - - + -
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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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314A GLU 3.4 10.2 + - - +
315A VAL* 3.4 14.4 - - - +
316A GLU 3.1 0.8 - - - -
317A ALA* 1.3 77.4 - - - +
319A ASN* 1.3 60.6 + - - +
321A ILE* 3.8 3.1 - - - +
322A GLU* 3.1 21.8 + - - +
384A VAL* 4.6 7.4 - - + +
388A MET* 3.8 31.4 - - + -
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Residues in contact with ASN 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 VAL 3.5 5.7 + - - +
316A GLU* 2.7 22.3 + - + +
318A LYS* 1.3 71.2 - - - +
320A LYS* 1.3 65.6 + - - +
322A GLU* 3.0 16.6 + - - +
323A GLU* 3.0 13.0 + - - +
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Residues in contact with LYS 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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306A ASP* 6.1 3.1 - - + +
308A PHE* 5.0 12.6 - - + -
311A CYS* 5.9 1.3 - - - -
316A GLU 3.0 9.2 + - - +
317A ALA* 3.2 9.4 + - - +
319A ASN* 1.3 75.1 - - - +
321A ILE* 1.3 59.1 + - - +
323A GLU* 3.0 10.1 + - - +
324A LEU* 2.9 34.3 + - + +
406A LEU* 4.2 15.9 - - + -
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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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317A ALA 2.9 18.7 + - - +
318A LYS* 3.8 4.7 - - - +
320A LYS* 1.3 74.5 - - - +
322A GLU* 1.3 59.0 + - - +
324A LEU* 3.9 9.1 - - + +
325A LEU* 3.0 29.3 + - + +
344A LEU* 5.7 5.4 - - + -
384A VAL* 4.7 11.0 - - + -
387A LEU* 4.1 37.2 - - + +
388A MET* 4.0 21.8 - - - -
391A PHE* 4.1 23.1 - - + -
406A LEU* 3.8 20.4 - - + -
408A VAL* 4.6 12.0 - - + +
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Residues in contact with GLU 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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318A LYS 3.1 14.4 + - - +
319A ASN* 3.0 12.8 + - - +
321A ILE* 1.3 78.8 - - - +
323A GLU* 1.3 56.8 + - - +
325A LEU* 3.5 7.1 + - - +
326A ALA* 3.0 28.1 + - - +
380A MET* 4.2 12.0 - - - +
384A VAL* 4.8 14.4 - - + -
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Residues in contact with GLU 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 ASN 3.0 9.1 + - - +
320A LYS* 3.0 12.2 + - - +
322A GLU* 1.3 74.3 - - - +
324A LEU* 1.3 69.1 + - + +
326A ALA* 3.1 18.9 + - - +
327A SER* 3.5 6.9 + - - -
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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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304A GLU* 3.8 16.5 - - + +
305A GLU 3.7 35.9 - - - +
306A ASP* 4.2 8.7 - - + +
320A LYS* 2.9 22.1 + - + +
321A ILE* 3.9 8.7 - - + +
323A GLU* 1.3 77.4 - - - +
325A LEU* 1.3 63.9 + - - +
326A ALA 3.1 0.2 + - - -
327A SER* 3.4 3.6 + - - -
328A LEU* 3.3 24.4 + - - +
406A LEU* 3.4 37.5 - - + +
407A SER* 4.0 8.7 - - - +
408A VAL* 4.2 18.6 - - + +
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Residues in contact with LEU 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 ILE 3.0 20.1 + - - +
322A GLU* 3.9 3.6 - - - +
324A LEU* 1.3 75.5 - - - +
326A ALA* 1.3 64.5 + - - +
328A LEU* 3.4 8.3 + - - +
329A LEU* 2.8 67.0 + - + +
380A MET* 4.1 21.8 - - - +
383A MET* 3.5 29.8 - - + -
384A VAL* 4.4 10.1 - - + -
387A LEU* 4.2 18.6 - - + -
408A VAL* 5.0 4.4 - - + +
410A PHE* 3.8 21.5 - - + -
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Residues in contact with ALA 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 GLU 3.0 11.3 + - - +
323A GLU* 3.1 14.1 + - - +
325A LEU* 1.3 78.8 - - - +
327A SER* 1.3 65.0 + - - +
329A LEU* 3.2 15.3 + - - +
330A ASN* 3.5 5.7 + - - +
380A MET* 3.3 31.3 - - + +
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Residues in contact with SER 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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304A GLU* 3.6 27.1 + - - -
323A GLU 3.5 5.2 + - - -
324A LEU 3.4 4.2 + - - -
326A ALA* 1.3 78.1 - - - +
328A LEU* 1.3 65.6 + - - +
330A ASN* 2.9 18.6 + - - +
331A ARG* 3.0 20.2 + - - +
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Residues in contact with LEU 328 (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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302A PHE* 3.7 15.7 - - + +
303A SER* 3.6 24.5 - - - +
304A GLU* 3.3 30.9 + - + +
324A LEU 3.3 15.2 + - - +
325A LEU* 3.8 5.6 - - - +
326A ALA 3.3 0.2 - - - -
327A SER* 1.3 76.1 - - - +
329A LEU* 1.3 57.9 + - - +
331A ARG* 3.2 12.2 + - - +
332A VAL* 2.8 37.0 + - - +
408A VAL* 3.4 45.1 - - + +
410A PHE* 3.8 16.2 - - + -
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Residues in contact with LEU 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 LEU* 2.8 44.1 + - + +
326A ALA 3.3 4.9 - - - +
327A SER 3.1 0.2 - - - -
328A LEU* 1.3 76.3 - - - +
330A ASN* 1.3 62.8 + - - +
332A VAL* 5.0 3.4 - - + -
333A CYS* 2.9 29.3 + - - +
379A VAL* 3.9 25.6 - - + -
380A MET* 3.7 40.6 - - + -
383A MET* 5.2 3.8 - - + -
410A PHE* 4.3 12.3 - - + -
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Residues in contact with ASN 330 (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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326A ALA 3.5 4.7 + - - +
327A SER* 2.9 13.5 + - - +
329A LEU* 1.3 77.3 - - - +
331A ARG* 1.3 63.8 + - + +
333A CYS* 3.7 8.2 - - - +
334A GLN* 3.1 23.7 + - - +
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Residues in contact with ARG 331 (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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100A THR* 5.2 5.8 - - - +
103A ARG* 3.1 42.2 - - - +
302A PHE* 3.3 40.8 - - + +
303A SER 3.1 20.0 + - - -
304A GLU* 2.8 40.7 + - - +
327A SER* 3.0 18.8 + - - +
328A LEU* 3.6 12.7 - - - +
330A ASN* 1.3 77.7 - - + +
332A VAL* 1.3 62.9 + - - +
334A GLN* 3.1 16.2 + - - +
335A ASP* 3.2 11.4 + - - +
843T G 3.1 23.6 + - - -
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Residues in contact with VAL 332 (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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302A PHE* 3.7 41.7 - - + -
328A LEU 2.8 23.6 + - - +
329A LEU* 4.3 2.9 - - - +
331A ARG* 1.3 71.0 - - - +
333A CYS* 1.3 65.5 + - - +
335A ASP* 3.1 19.2 + - + +
336A GLY 3.6 3.3 + - - -
337A ARG 3.7 11.8 - - - +
339A PRO* 3.4 34.5 - - + -
410A PHE* 4.2 20.0 - - + -
413A LEU* 5.8 2.0 - - + -
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Residues in contact with CYS 333 (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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329A LEU 2.9 20.4 + - - +
330A ASN* 3.7 7.2 - - - +
332A VAL* 1.3 76.8 - - - +
334A GLN* 1.3 68.7 + - - +
336A GLY* 3.0 16.3 + - - -
337A ARG 5.5 0.7 - - - -
371A LYS 4.6 16.4 - - - +
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Residues in contact with GLN 334 (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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330A ASN 3.1 15.1 + - - +
331A ARG* 3.1 11.2 + - - +
333A CYS* 1.3 80.1 - - - +
335A ASP* 1.3 63.5 + - - +
336A GLY* 3.2 1.9 + - - -
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Residues in contact with ASP 335 (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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298A PRO* 4.9 3.6 - - - +
299A PRO* 5.4 2.4 - - - +
302A PHE* 3.6 28.3 - - + -
331A ARG 3.2 3.9 + - - +
332A VAL 3.1 11.4 + - - +
333A CYS 3.0 1.6 + - - -
334A GLN* 1.3 78.9 - - - +
336A GLY* 1.3 58.6 + - - +
337A ARG* 2.8 55.2 + - - +
413A LEU* 3.8 1.2 - - - +
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Residues in contact with GLY 336 (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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332A VAL 3.6 1.0 + - - -
333A CYS 3.0 15.5 + - - -
334A GLN 3.2 2.4 + - - -
335A ASP* 1.3 78.7 - - - +
337A ARG* 1.3 61.1 + - - +
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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