Contacts of the helix formed by residues 308 - 326 (chain B) in PDB entry 1U54
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ILE* 3.4 17.8 - - - +
282B ASP* 3.4 24.9 - - - -
283B HIS* 4.6 2.5 - - - -
300B GLU* 4.0 6.8 + - - +
306B THR* 5.1 3.0 - - - +
307B PHE* 1.3 78.7 - - - +
309B HIS* 1.3 55.9 + - - +
310B ALA* 3.6 8.8 + - - +
311B SER* 2.8 22.3 + - - -
312B ASP* 2.7 34.3 + - - +
372B PRO* 5.3 1.7 - - - +
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Residues in contact with HIS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 3.0 61.8 + - + +
247B ARG* 4.0 19.3 + - - +
248B PHE 3.6 20.0 + - - -
249B ILE* 3.2 7.5 - - - +
277B LEU* 3.2 32.0 - - + +
282B ASP 5.3 1.3 - - - -
308B SER* 1.3 72.4 - - - +
310B ALA* 1.3 60.3 + - - +
312B ASP* 3.4 9.1 + - - +
313B THR* 3.2 24.4 + - - -
378B PHE* 4.3 5.3 - - - -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER* 3.0 7.4 + - - +
309B HIS* 1.3 75.7 - - - +
311B SER* 1.3 64.9 + - - +
313B THR* 3.2 10.1 - - - -
314B TRP 3.1 13.7 + - - -
372B PRO* 3.4 41.5 - - + +
375B ARG* 3.0 22.4 + - + +
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ALA* 4.1 5.0 - - - +
300B GLU* 3.7 18.6 + - - -
301B SER* 3.9 17.9 - - - -
307B PHE* 3.5 17.0 - - - -
308B SER* 2.8 32.4 + - - -
310B ALA* 1.3 79.9 - - - +
312B ASP* 1.3 61.0 + - - +
314B TRP* 3.3 5.4 + - - +
315B MET* 3.2 26.1 + - - +
375B ARG* 3.9 4.8 - - - +
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Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B MET* 3.5 18.7 - - + +
248B PHE 4.6 1.4 - - - +
249B ILE* 3.5 14.2 - - - +
250B HIS* 3.0 21.6 + - - -
251B ARG* 2.9 29.0 + - - +
253B LEU* 4.1 5.6 - - - +
308B SER 2.7 17.1 + - - +
309B HIS* 3.4 13.7 + - - +
311B SER* 1.3 72.6 + - - +
313B THR* 1.3 60.9 + - - +
315B MET* 3.2 9.6 + - - +
316B PHE* 2.8 27.5 + - - +
378B PHE* 4.1 14.3 - - + -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 5.0 0.7 + - - -
309B HIS 3.2 10.6 + - - -
310B ALA* 3.2 12.8 - - - -
312B ASP* 1.3 76.2 - - - +
314B TRP* 1.3 66.4 + - - +
316B PHE* 3.1 4.5 + - - +
317B GLY 3.0 18.2 + - - -
367B CYS* 3.3 34.5 - - + +
375B ARG* 4.1 4.9 - - + -
376B PRO* 3.2 33.2 + - + +
377B THR* 5.0 0.7 - - - -
378B PHE* 3.9 17.6 - - - -
381B LEU* 3.8 10.7 - - + +
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Residues in contact with TRP 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 5.5 0.8 + - - -
296B TRP 3.8 7.5 - - - -
297B CYS 3.5 10.1 + - - -
298B ALA* 3.5 27.1 - - + -
299B PRO* 3.4 29.6 - - + -
310B ALA 3.1 2.4 + - - -
311B SER 3.4 9.2 - - - +
312B ASP 3.2 0.2 - - - -
313B THR* 1.3 81.4 - - - +
315B MET* 1.3 59.2 + - - +
317B GLY 3.0 15.4 + - - -
318B VAL* 3.3 13.1 + - + +
343B ILE* 4.3 17.9 - - + -
349B ARG* 3.4 31.9 - - - -
367B CYS 3.3 11.9 - - - +
368B TRP* 3.2 58.9 + + + -
369B ALA 4.4 0.9 - - - -
370B HIS* 4.6 0.4 - - - -
375B ARG* 3.3 30.7 - - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ARG* 3.8 29.4 - - - +
252B ASP* 4.3 1.8 - - - -
253B LEU* 3.5 27.7 - - + +
256B ARG* 5.8 0.9 - - - +
292B VAL* 3.8 27.6 - - + -
296B TRP* 3.2 47.8 - - + +
297B CYS* 4.3 8.7 - - - +
298B ALA 5.0 1.1 - - - +
307B PHE* 4.6 9.4 - - + -
311B SER* 3.2 17.6 + - - +
312B ASP* 3.2 8.7 + - - +
314B TRP* 1.3 75.6 - - + +
316B PHE* 1.3 57.8 + - - +
317B GLY 3.3 0.2 - - - -
318B VAL* 3.5 6.6 + - - +
319B THR* 2.8 31.0 + - - -
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ALA 3.6 21.3 - - - -
236B VAL* 3.5 35.0 - - + -
237B ALA* 3.9 7.2 - - + -
253B LEU* 3.9 11.4 - - + +
312B ASP 2.8 13.2 + - - +
313B THR 3.1 7.2 + - - +
315B MET* 1.3 75.2 - - - +
317B GLY* 1.3 62.2 + - - +
319B THR* 3.4 7.7 + - + -
320B LEU* 3.2 54.8 + - + +
323B MET* 5.9 0.2 - - - -
367B CYS* 3.9 14.1 - - - -
378B PHE* 3.7 24.0 - + + -
381B LEU* 4.0 24.9 - - + -
385B LEU* 4.0 8.1 - - + -
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Residues in contact with GLY 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR 3.0 11.1 + - - -
314B TRP 3.0 4.8 + - - -
316B PHE* 1.3 75.4 - - - +
318B VAL* 1.3 64.5 + - - +
319B THR 3.3 0.2 + - - -
320B LEU* 3.3 6.8 + - - +
321B TRP* 3.2 17.2 + - - +
364B MET* 4.0 7.3 - - - +
367B CYS* 3.7 23.7 - - - -
368B TRP* 3.3 20.3 - - - -
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Residues in contact with VAL 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ALA 4.0 12.6 - - - +
296B TRP* 3.3 37.9 - - + +
314B TRP* 3.3 26.6 + - + +
315B MET* 3.7 7.4 - - - +
316B PHE 3.4 0.2 - - - -
317B GLY* 1.3 74.8 - - - +
319B THR* 1.3 55.8 + - - +
320B LEU 3.4 0.2 - - - -
321B TRP* 3.5 4.4 + - - +
322B GLU* 3.1 25.9 + - - +
330B PRO* 3.9 24.7 - - + -
350B LEU* 4.4 7.6 - - + -
368B TRP* 3.5 18.3 - - + +
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Residues in contact with THR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 5.4 2.0 - - + -
253B LEU* 3.2 23.6 + - + +
254B ALA* 3.4 16.7 - - - -
255B ALA* 4.2 2.9 - - - +
258B LEU* 3.5 33.7 - - + -
296B TRP* 4.5 0.7 - - - -
315B MET 2.8 20.0 + - - -
316B PHE* 3.6 15.9 - - + -
317B GLY 3.1 0.4 - - - -
318B VAL* 1.3 74.8 - - - +
320B LEU* 1.3 60.5 + - - +
322B GLU* 3.4 10.0 - - - +
323B MET* 3.0 30.8 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ALA* 3.3 33.2 - - + -
316B PHE* 3.2 46.3 + - + +
317B GLY* 3.3 8.3 + - - +
319B THR* 1.3 74.4 - - - +
321B TRP* 1.3 60.1 + - - +
323B MET* 3.1 16.7 + - + +
324B PHE* 2.8 41.0 + - + -
360B ILE* 5.4 2.7 - - + +
363B VAL* 4.1 21.3 - - + -
364B MET* 3.9 25.6 - - + +
367B CYS* 5.2 0.2 - - - -
385B LEU* 4.4 7.2 - - + -
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Residues in contact with TRP 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B GLY 3.2 12.7 + - - +
318B VAL 3.5 8.3 - - - +
319B THR 3.4 0.2 - - - -
320B LEU* 1.3 74.4 - - - +
322B GLU* 1.3 66.8 + - + +
324B PHE 3.1 0.3 + - - -
325B THR* 2.8 50.9 + - + +
328B GLN* 3.7 35.0 - - + -
329B GLU 4.3 2.7 - - - -
330B PRO* 3.4 46.0 - - + -
331B TRP 5.1 0.2 - - - -
350B LEU* 3.6 38.2 - - + +
351B PRO* 2.8 37.7 + - + -
353B PRO* 3.6 15.0 - - + +
364B MET* 3.8 18.1 - - - +
368B TRP* 4.5 1.8 - + + -
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LEU* 3.7 24.7 - - - +
217B LEU* 3.9 3.0 - - - +
255B ALA* 3.5 28.7 + - + +
256B ARG 4.8 0.7 + - - -
296B TRP* 2.9 40.8 + - - +
318B VAL 3.1 13.0 + - - +
319B THR* 3.4 9.8 - - - +
320B LEU 3.2 0.2 - - - -
321B TRP* 1.3 86.9 - - + +
323B MET* 1.3 63.1 + - - +
325B THR* 3.5 5.1 + - - -
326B TYR 3.1 3.8 + - - -
327B GLY* 2.8 27.6 + - - +
328B GLN 3.6 22.2 - - - +
329B GLU* 5.2 0.9 - - - +
330B PRO* 4.4 4.7 - - + +
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Residues in contact with MET 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B LEU* 4.3 19.5 - - + -
217B LEU* 3.7 14.1 - - + +
229B LEU* 3.2 55.7 - - + +
232B TYR* 3.4 24.7 - - + +
233B ALA* 3.5 13.9 - - + +
236B VAL* 5.3 1.8 - - - -
255B ALA* 5.3 1.8 - - + -
258B LEU* 4.5 9.9 - - + -
316B PHE* 5.9 0.2 - - - -
319B THR* 3.0 28.2 + - + +
320B LEU* 3.1 25.3 + - + +
322B GLU* 1.3 77.6 - - - +
324B PHE* 1.3 63.9 + - + +
326B TYR* 3.3 14.6 + - - -
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LEU* 3.8 29.2 - - + -
229B LEU* 3.9 33.9 - - + -
230B SER* 4.5 8.3 - - - -
233B ALA* 5.0 1.6 - - + -
320B LEU* 2.8 48.5 + - + +
321B TRP 4.1 0.2 - - - +
323B MET* 1.3 75.7 - - + +
325B THR* 1.3 58.3 + - - +
326B TYR* 3.1 26.9 - - - -
353B PRO* 3.8 28.8 - - + +
354B GLU 4.4 4.9 - - - +
356B CYS* 4.0 18.7 - - + +
357B PRO* 5.0 0.2 - - + -
360B ILE* 3.9 36.8 - - + -
364B MET* 4.1 7.0 - - + -
385B LEU* 6.3 0.2 - - + -
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Residues in contact with THR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN* 5.0 0.2 + - - -
321B TRP* 2.8 53.8 + - + +
322B GLU* 3.5 4.0 + - - -
324B PHE* 1.3 73.9 - - - +
326B TYR* 1.3 72.7 + - - +
328B GLN* 3.2 51.5 + - - +
353B PRO* 3.7 22.0 - - + -
354B GLU 5.9 0.2 - - - -
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Residues in contact with TYR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 3.8 16.2 - - + +
218B ARG* 4.1 2.6 + - - +
221B GLN* 2.9 57.1 + - + +
224B PHE* 3.3 44.6 + + + -
225B LEU* 5.2 0.5 - - - -
226B LEU* 4.4 17.8 - - - +
229B LEU* 3.9 15.3 - - + +
322B GLU 3.1 4.6 + - - -
323B MET 3.3 10.5 + - - -
324B PHE* 3.1 28.0 - + - -
325B THR* 1.3 83.0 - - - +
327B GLY* 1.3 60.5 + - - +
328B GLN* 4.9 1.4 - - - +
354B GLU 5.2 6.1 - - - -
355B ASP* 5.5 9.5 - - + +
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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
------------------------------------------------------------
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