Contacts of the helix formed by residues 309 - 329 (chain H) in PDB entry 5U07
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 GLY 309 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLY 3.8 5.7 + - - -
301G GLU* 3.2 19.3 - - - -
302G THR* 3.7 20.1 - - - +
303G ALA 5.3 1.0 - - - +
308H ASP* 1.3 86.6 + - - +
310H TYR* 1.3 63.9 + - - -
311H THR 3.4 3.7 + - - -
312H LEU* 4.1 7.3 + - - +
313H ARG* 4.1 14.9 + - - +
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Residues in contact with TYR 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLY* 3.7 11.4 - - - -
32G GLY* 3.5 31.3 - - - -
301G GLU* 3.5 4.9 + - - -
195H HIS* 3.3 55.8 - + + +
196H GLY 5.2 0.9 + - - -
230H THR* 4.1 18.4 - - + +
304H LEU* 3.7 28.7 + - + +
305H TYR 3.9 3.6 + - - -
306H GLY* 3.0 41.5 + - - -
308H ASP 3.9 4.3 - - - -
309H GLY* 1.3 71.7 - - - -
311H THR* 1.3 59.0 + - - +
312H LEU 3.4 0.4 - - - -
313H ARG* 3.8 8.1 - - - +
314H ALA* 2.8 32.7 + - + +
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Residues in contact with THR 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298G PRO 5.5 0.2 - - - +
301G GLU* 2.3 38.1 + - + +
302G THR* 4.3 5.9 - - - +
9H ILE* 5.5 4.7 - - + -
11H THR* 3.5 19.5 - - + -
230H THR* 4.2 6.5 - - + -
282H ASP* 3.3 27.6 - - + +
310H TYR* 1.3 77.6 - - - +
312H LEU* 1.3 64.5 + - - +
314H ALA* 3.6 4.4 - - - +
315H CYS* 2.9 40.9 + - - -
341H GLU* 5.2 5.2 + - - -
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Residues in contact with LEU 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G THR* 5.9 4.5 - - + -
309H GLY 4.1 5.6 + - - +
310H TYR 3.4 0.2 - - - -
311H THR* 1.3 82.7 + - - +
313H ARG* 1.3 66.2 + - + +
315H CYS* 3.3 4.4 + - + +
316H GLN* 3.0 54.3 + - + +
341H GLU* 4.5 24.2 - - + +
343H LYS* 4.6 18.2 - - + -
344H THR* 4.3 12.1 - - - +
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Residues in contact with ARG 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304H LEU* 4.3 29.3 - - + +
305H TYR* 4.2 19.4 - - - +
306H GLY* 3.7 35.8 + - - +
308H ASP* 5.1 12.8 + - - +
309H GLY 4.1 14.6 - - - +
310H TYR* 3.4 9.8 + - - +
311H THR 3.3 0.6 - - - -
312H LEU* 1.3 80.1 - - + +
314H ALA* 1.3 57.6 + - - +
316H GLN* 3.5 12.6 + - - +
317H GLU* 3.0 29.1 + - - +
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Residues in contact with ALA 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 4.6 14.6 - - + -
194H VAL* 4.2 20.0 - - + -
230H THR* 5.1 1.8 - - - +
300H PHE* 3.7 23.1 - - + -
304H LEU* 4.3 3.5 - - - +
310H TYR 2.8 20.2 + - - +
311H THR* 3.6 5.8 - - - +
313H ARG* 1.3 76.2 - - - +
315H CYS* 1.3 59.5 + - - +
317H GLU* 3.1 3.3 + - - +
318H LEU* 2.9 30.0 + - - +
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Residues in contact with CYS 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ILE* 5.0 12.8 - - - -
282H ASP* 5.3 3.8 - - - -
283H LEU* 4.0 31.2 - - + +
311H THR* 2.9 24.8 + - - +
312H LEU* 3.8 4.9 - - + +
314H ALA* 1.3 75.3 - - - +
316H GLN* 1.3 63.8 + - + +
318H LEU* 3.3 6.8 + - - +
319H ASN* 2.9 24.8 + - - +
341H GLU* 2.9 37.9 - - - +
346H LEU* 4.0 9.0 - - + +
349H LEU* 5.4 0.2 - - - +
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Residues in contact with GLN 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H LEU* 3.0 50.9 + - + +
313H ARG* 3.9 11.2 - - - +
315H CYS* 1.3 77.4 - - + +
317H GLU* 1.3 58.3 + - - +
319H ASN* 3.4 7.7 + - - +
320H ASN* 2.9 30.4 + - - +
344H THR* 4.0 18.1 + - + +
346H LEU* 4.5 6.7 - - + -
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Residues in contact with GLU 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H ALA* 3.8 27.7 - - + +
300H PHE* 4.1 14.6 - - + -
302H THR* 5.3 2.9 + - - -
304H LEU* 5.5 9.6 - - + -
313H ARG 3.0 18.0 + - - +
314H ALA* 3.1 4.9 + - - +
316H GLN* 1.3 75.8 - - - +
318H LEU* 1.3 60.8 + - - +
320H ASN* 3.4 9.3 + - - +
321H TYR* 2.9 30.5 + - - +
324H ARG* 4.3 16.4 + - - -
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Residues in contact with LEU 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H HIS* 4.6 7.2 - - + -
9H ILE* 4.3 15.3 - - + -
232H TYR* 3.8 29.2 - - + -
283H LEU* 4.5 12.1 - - + -
285H HIS* 4.7 5.4 - - + -
296H PHE* 3.8 26.1 - - + -
299H ALA* 4.9 1.8 - - - -
300H PHE* 4.0 15.3 - - + -
314H ALA 2.9 14.9 + - - +
315H CYS* 3.9 6.1 - - - +
317H GLU* 1.3 76.1 - - - +
319H ASN* 1.3 58.9 + - - +
321H TYR* 3.9 4.9 - - - +
322H ALA* 2.9 30.5 + - - +
349H LEU* 3.9 30.7 - - + -
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Residues in contact with ASN 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315H CYS 2.9 9.8 + - - +
316H GLN* 3.5 6.1 + - - +
318H LEU* 1.3 77.7 - - - +
320H ASN* 1.3 65.0 + - - +
322H ALA* 3.1 2.9 + - - +
323H GLU* 2.9 20.3 + - - +
344H THR* 4.8 3.8 - - - +
346H LEU* 3.1 53.9 - - + +
347H ALA* 3.7 3.8 - - - +
348H ALA* 3.1 27.1 + - - +
349H LEU* 4.1 12.4 + - + -
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Residues in contact with ASN 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H GLN 2.9 18.1 + - - +
317H GLU* 3.8 13.5 + - - +
319H ASN* 1.3 76.8 - - - +
321H TYR* 1.3 62.9 + - - +
323H GLU* 3.2 9.8 + - - +
324H ARG* 2.3 60.3 + - - +
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Residues in contact with TYR 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D THR* 5.1 1.0 - - - +
280D LEU* 4.7 4.9 + - - +
282D ASP* 4.0 9.6 + - - -
340D VAL* 4.1 25.8 - - + +
295H SER 4.8 1.2 + - - -
296H PHE* 3.9 29.2 - + - -
298H PRO* 3.6 26.4 - - + +
299H ALA* 3.5 32.5 - - + -
317H GLU* 2.9 20.2 + - - +
318H LEU* 3.9 2.5 - - - +
320H ASN* 1.3 76.9 - - - +
322H ALA* 1.3 57.6 + - - +
324H ARG* 3.3 24.3 + - - +
325H LEU* 2.9 61.1 + - + +
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Residues in contact with ALA 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285H HIS* 5.4 0.9 - - - +
296H PHE* 3.8 27.3 - - + -
318H LEU 2.9 19.7 + - - +
319H ASN 3.1 5.1 + - - +
321H TYR* 1.3 78.5 - - - +
323H GLU* 1.3 61.9 + - - +
325H LEU* 3.3 2.6 + - - +
326H ARG* 2.9 23.7 + - - +
335H ARG* 5.3 6.0 + - - +
348H ALA* 4.2 8.3 - - + +
349H LEU* 3.5 24.5 - - + -
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Residues in contact with GLU 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D ASN* 5.4 0.9 + - - -
319H ASN* 2.9 8.6 + - - +
320H ASN* 3.2 12.8 + - - +
322H ALA* 1.3 75.7 - - - +
324H ARG* 1.3 92.0 + - - +
326H ARG* 3.0 18.4 + - - +
327H GLU* 3.0 37.7 + - - +
348H ALA* 3.4 23.5 - - + +
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Residues in contact with ARG 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D VAL* 2.5 39.4 + - + +
341D GLU* 5.5 0.4 - - - +
342D ASN* 3.7 23.0 - - - +
343D LYS* 3.2 29.6 - - - +
317H GLU* 4.3 15.4 + - - -
320H ASN* 2.3 52.1 + - - +
321H TYR* 3.9 22.2 - - + +
323H GLU* 1.3 94.2 + - - +
325H LEU* 1.3 59.0 + - - +
327H GLU* 2.9 18.9 - - - +
328H VAL* 2.9 31.2 + - - +
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Residues in contact with LEU 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 3.7 28.9 - - + +
340D VAL* 3.7 26.9 - - + -
294H ILE* 3.7 23.6 - - + -
296H PHE* 3.7 21.3 - - + -
321H TYR* 2.9 51.9 + - + +
322H ALA* 3.9 4.7 - - - +
324H ARG* 1.3 77.4 - - - +
326H ARG* 1.3 59.2 + - - +
328H VAL* 4.4 3.8 - - + +
329H TRP* 2.7 34.1 + - - +
335H ARG* 5.4 0.4 - - - -
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Residues in contact with ARG 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H ALA 2.9 16.4 + - - +
323H GLU* 3.0 13.4 + - - +
325H LEU* 1.3 76.9 - - - +
327H GLU* 1.3 62.7 + - - +
329H TRP 3.5 17.2 - - - +
330H PRO* 3.6 7.0 - - + +
331H ASP* 4.1 9.2 - - - +
335H ARG* 3.6 42.0 - - - +
347H ALA* 4.8 4.6 + - - +
348H ALA* 4.0 35.9 + - - +
350H GLY* 5.2 4.8 - - - +
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Residues in contact with GLU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D THR 5.4 0.9 - - - +
340D VAL 5.9 0.2 - - - -
342D ASN* 3.7 27.4 + - - +
354D ASP* 4.0 15.5 - - + +
355D SER* 3.3 15.4 - - - -
323H GLU* 3.0 30.1 + - - +
324H ARG* 2.9 33.5 - - - +
326H ARG* 1.3 80.0 - - - +
328H VAL* 1.3 70.0 + - + +
329H TRP 3.5 0.2 + - - -
330H PRO* 3.9 7.8 - - - +
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Residues in contact with VAL 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ALA* 5.8 0.4 - - + -
339D THR 3.5 22.9 - - - +
340D VAL* 4.3 11.7 - - + -
354D ASP 3.7 12.6 - - - +
355D SER* 3.1 11.9 - - - -
356D TYR* 3.1 68.0 + - + +
357D PRO* 3.5 2.4 - - - +
324H ARG 2.9 21.2 + - - +
325H LEU* 4.1 5.8 - - + +
327H GLU* 1.3 84.6 - - + +
329H TRP* 1.3 58.8 + - + +
330H PRO* 3.3 3.7 - - - +
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Residues in contact with TRP 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D ARG* 3.7 38.6 - - + -
264D LEU* 4.8 10.1 - - + -
265D SER* 3.9 26.0 - - - -
280D LEU* 3.7 37.7 - - + -
356D TYR* 4.2 26.9 - + + -
357D PRO* 4.7 8.1 - - + -
289H ARG* 3.5 29.0 - - - +
291H ASP* 4.1 19.8 + - + +
292H ARG* 4.8 7.5 - - + +
294H ILE* 4.2 7.0 - - + +
325H LEU* 2.7 21.1 + - + +
326H ARG 3.5 3.5 - - - +
328H VAL* 1.3 74.4 - - + +
330H PRO* 1.3 69.0 + - + +
331H ASP* 2.9 19.8 - - - +
335H ARG* 5.0 0.2 + - - -
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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