Contacts of the helix formed by residues 359 - 375 (chain D) in PDB entry 5C5B
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 359 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265D ASP* 3.5 26.7 - - - -
267D ASP* 4.1 4.8 + - - -
340D TYR* 3.6 14.0 - - - -
357D ALA* 3.4 2.1 - - - +
358D GLU* 1.3 89.6 - - - +
360D ARG* 1.3 64.9 + - - +
361D LYS* 3.4 6.9 + - - +
362D GLU* 3.1 26.2 + - - +
363D ASN* 3.2 22.5 + - - +
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Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ASP* 3.1 16.6 + - - +
268D VAL* 4.7 12.3 + - + +
271D PRO* 4.1 29.2 - - + +
273D ILE* 5.0 2.4 - - + +
340D TYR* 3.4 29.5 - - + +
359D SER* 1.3 71.2 - - - +
361D LYS* 1.3 59.0 + - - +
363D ASN* 3.3 5.1 + - - +
364D GLU* 2.9 65.0 + - + +
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Residues in contact with LYS 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ASP* 3.0 28.7 + - + +
271D PRO* 4.4 8.3 - - + +
272D GLN* 3.2 34.3 + - + +
273D ILE* 4.3 11.2 - - + -
280D LYS* 6.0 0.2 - - - +
359D SER* 3.3 3.8 + - - +
360D ARG* 1.3 80.0 - - - +
362D GLU* 1.3 61.3 + - + +
364D GLU* 3.4 1.4 + - - +
365D GLU* 2.9 62.5 + - + +
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Residues in contact with GLU 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D LYS* 4.4 10.2 + - - +
282D GLY* 5.1 3.6 - - - -
283D TYR 3.9 23.8 + - - +
284D LEU* 4.3 0.2 - - - -
357D ALA* 3.2 10.3 - - + +
358D GLU* 3.0 37.9 + - - +
359D SER* 3.1 15.9 + - - +
361D LYS* 1.3 77.6 - - + +
363D ASN* 1.3 61.8 + - - +
365D GLU* 4.3 4.9 - - - -
366D TRP* 2.9 58.5 + - + +
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Residues in contact with ASN 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D ALA* 4.4 9.7 - - - +
340D TYR* 3.3 31.4 - - + +
341D CYS 4.0 1.0 - - - -
342D PHE* 3.2 26.9 - - - +
357D ALA* 3.8 11.6 - - + +
359D SER 3.2 19.6 + - - +
360D ARG* 3.4 6.8 + - - +
362D GLU* 1.3 76.1 - - - +
364D GLU* 1.3 73.9 + - - +
366D TRP* 3.3 4.4 + - - +
367D ILE* 3.0 46.5 + - - +
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ILE* 3.7 31.3 - - + +
275D ARG* 2.8 33.6 + - - +
360D ARG* 2.9 54.9 + - + +
361D LYS 3.8 0.9 - - - +
363D ASN* 1.3 82.7 + - - +
365D GLU* 1.3 57.4 + - - +
367D ILE* 3.4 8.2 + - - +
368D CYS* 2.9 35.5 + - - -
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Residues in contact with GLU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D GLN 3.6 3.6 - - - +
273D ILE* 3.8 11.0 - - + -
274D ASN* 2.8 39.9 + - - +
277D LEU* 3.7 20.7 - - + +
280D LYS* 3.4 27.2 + - - +
361D LYS* 2.9 55.7 + - + +
364D GLU* 1.3 74.6 - - - +
366D TRP* 1.3 60.8 + - - +
368D CYS* 3.9 2.0 - - - +
369D ALA* 2.9 30.5 + - - +
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Residues in contact with TRP 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D LYS* 3.3 56.7 - - + +
282D GLY* 3.9 12.6 - - - +
284D LEU* 3.5 36.8 - - + +
302D PHE* 3.5 31.4 - - + -
303D PHE* 4.4 0.9 - - - -
304D THR* 4.0 16.4 - - + -
309D LEU* 4.1 12.3 - - + -
342D PHE* 3.7 20.6 - + + -
362D GLU* 2.9 47.1 + - + +
363D ASN 3.6 3.6 - - - +
365D GLU* 1.3 74.8 - - - +
367D ILE* 1.3 64.9 + - - +
369D ALA* 3.2 2.7 + - + +
370D ILE* 2.9 41.7 + - + +
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Residues in contact with ILE 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D VAL* 3.2 32.9 - - + +
331D MET* 4.7 1.8 - - - -
332D ALA* 3.6 29.4 - - + +
342D PHE* 3.9 22.2 - - + -
363D ASN* 3.0 43.0 + - - +
364D GLU* 3.6 7.9 - - - +
366D TRP* 1.3 77.5 - - - +
368D CYS* 1.3 60.0 + - - +
371D ASN* 2.9 41.6 + - - +
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Residues in contact with CYS 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D ILE* 5.2 0.2 - - - -
274D ASN 4.5 0.9 - - - +
275D ARG* 3.3 68.2 - - - +
364D GLU 2.9 25.1 + - - +
365D GLU* 3.9 5.4 - - - +
367D ILE* 1.3 79.8 - - - +
369D ALA* 1.3 58.1 + - - +
371D ASN* 3.4 8.3 + - - +
372D ASN* 2.9 38.0 + - - +
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Residues in contact with ALA 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D LEU* 3.3 29.1 - - + +
278D ILE 5.2 0.4 - - - -
279D GLN* 5.0 4.7 - - - +
280D LYS* 4.3 19.7 - - + -
304D THR* 5.5 0.9 - - + -
365D GLU 2.9 19.3 + - - +
366D TRP* 3.4 8.3 - - + +
368D CYS* 1.3 76.9 - - - +
370D ILE* 1.3 59.2 + - + +
372D ASN* 3.2 3.5 + - - +
373D ILE* 2.9 37.7 + - + +
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Residues in contact with ILE 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D THR* 4.4 5.2 - - + -
309D LEU* 4.3 11.7 - - + -
325D LEU* 3.7 46.5 - - + +
328D CYS* 5.6 3.8 - - + -
329D SER 5.1 3.4 - - - +
330D VAL* 3.6 34.1 - - + +
342D PHE* 5.1 4.7 - - + -
344D ILE* 4.5 8.3 - - + -
366D TRP* 2.9 40.4 + - + +
369D ALA* 1.3 75.4 - - - +
371D ASN* 1.3 57.6 + - - +
373D ILE* 3.5 6.0 + - - +
374D SER* 3.0 27.5 + - - -
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Residues in contact with ASN 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D SER* 4.6 4.0 - - - -
330D VAL* 3.3 27.9 + - - +
367D ILE* 2.9 38.3 + - - +
368D CYS* 3.6 9.4 - - - +
370D ILE* 1.3 76.8 - - - +
372D ASN* 1.3 64.5 + - - +
374D SER* 2.4 29.4 + - - +
375D ARG 3.3 7.4 + - - -
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Residues in contact with ASN 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ARG 2.9 27.7 + - - +
276D ASN* 3.4 11.9 + - - +
277D LEU 2.9 28.6 + - - +
278D ILE* 4.8 10.7 - - + +
368D CYS* 2.9 21.4 + - - +
369D ALA 3.2 0.6 + - - +
371D ASN* 1.3 79.9 - - - +
373D ILE* 1.3 62.8 + - - +
374D SER 3.4 0.2 + - - -
375D ARG* 3.6 15.9 + - - +
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Residues in contact with ILE 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ILE* 3.2 33.0 - - + +
304D THR* 3.6 35.0 - - + -
307D GLY* 3.6 31.0 - - - +
325D LEU* 4.0 24.0 - - + +
326D ASP* 5.3 3.0 - - - +
369D ALA* 2.9 21.3 + - + +
370D ILE* 3.8 5.6 - - - +
372D ASN* 1.3 73.5 - - - +
374D SER* 1.3 68.2 + - - +
375D ARG* 4.5 0.3 - - - -
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Residues in contact with SER 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325D LEU 3.6 17.7 + - - -
326D ASP* 4.5 5.5 - - - +
327D ASN* 3.9 14.6 + - - +
328D CYS* 3.2 30.5 + - - -
370D ILE* 3.0 14.4 + - - -
371D ASN* 2.4 30.9 + - - +
373D ILE* 1.3 79.7 - - - +
375D ARG* 1.3 73.7 + - - +
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Residues in contact with ARG 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ASN* 5.6 8.5 - - - +
371D ASN 3.3 6.2 + - - -
372D ASN* 3.8 15.6 - - - +
373D ILE 3.5 1.0 - - - -
374D SER* 1.3 88.9 + - - +
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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