Contacts of the helix formed by residues 354 - 367 (chain N) in PDB entry 5G04
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 354 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280N GLU* 3.6 23.8 - - - -
281N TYR* 4.7 0.2 - - - -
347N ILE* 2.7 40.8 + - - +
350N ASP* 3.8 9.9 - - - -
351N PHE* 3.4 5.5 - - - +
353N ASP* 1.3 85.6 + - - +
355N ARG* 1.3 63.0 + - - +
356N PRO* 3.4 7.4 - - - +
357N ALA* 3.2 23.8 + - - +
358N ILE* 3.5 6.9 + - - +
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Residues in contact with ARG 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351N PHE* 3.7 39.4 - - + -
352N PRO 6.0 0.4 - - - -
353N ASP* 3.4 5.3 - - - -
354N SER* 1.3 77.7 + - - +
356N PRO* 1.4 67.4 - - + +
358N ILE* 3.2 25.5 - - + +
359N GLU* 3.3 28.8 + - - +
405N LYS* 5.7 2.8 + - - +
409N VAL* 4.0 25.9 - - - +
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Residues in contact with PRO 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281N TYR* 2.8 50.8 + - + +
353N ASP* 4.8 2.5 - - - +
354N SER* 3.5 10.8 - - - +
355N ARG* 1.4 95.9 - - + +
357N ALA* 1.3 54.5 + - - +
359N GLU* 3.4 12.0 + - + +
360N ASP* 3.1 22.0 + - - +
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Residues in contact with ALA 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280N GLU* 4.4 8.7 - - + -
281N TYR* 2.9 25.7 - - + -
340N ARG* 3.5 19.7 - - - +
347N ILE* 4.1 23.3 - - + -
354N SER* 3.2 16.2 + - - +
356N PRO* 1.3 75.9 - - - +
358N ILE* 1.3 57.1 + - - +
360N ASP* 3.3 7.8 + - - +
361N LEU* 3.2 21.0 + - - +
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Residues in contact with ILE 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344N LEU* 4.2 11.4 - - + -
347N ILE* 3.6 24.2 - - + -
348N VAL* 5.1 1.6 - - + -
351N PHE* 5.5 3.1 - - + -
354N SER 3.5 6.8 + - - +
355N ARG* 3.2 26.9 - - + +
357N ALA* 1.3 74.5 - - - +
359N GLU* 1.3 59.2 + - + +
361N LEU* 3.5 25.8 - - + +
362N LYS* 2.9 28.1 + - - +
406N ALA* 3.5 47.3 - - + +
409N VAL* 3.9 25.6 - - + -
410N LEU* 4.5 6.2 - - + +
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Residues in contact with GLU 359 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355N ARG* 3.3 45.7 + - - +
356N PRO* 3.4 13.6 + - + +
357N ALA 3.3 0.8 - - - -
358N ILE* 1.3 75.6 - - + +
360N ASP* 1.3 61.7 + - - +
362N LYS* 3.5 23.0 + - - +
363N TYR* 3.1 25.8 + - - +
409N VAL* 4.0 21.5 - - + -
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Residues in contact with ASP 360 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281N TYR* 3.1 20.3 + - - +
284N SER 3.1 2.0 - - - +
285N PHE 2.9 28.2 + - - -
286N LEU* 3.4 29.7 + - + +
336N TYR* 3.3 26.4 + - + +
356N PRO 3.1 8.3 + - - +
357N ALA 3.3 6.7 + - - +
359N GLU* 1.3 74.5 - - - +
361N LEU* 1.3 54.3 + - - +
363N TYR* 3.3 8.3 + - - +
364N CYS* 2.8 33.8 + - - +
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Residues in contact with LEU 361 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337N ALA* 3.9 11.2 - - - +
340N ARG* 3.7 37.2 - - + +
341N ILE* 4.0 12.3 - - + +
344N LEU* 3.9 29.8 - - + -
347N ILE* 6.0 1.1 - - + -
357N ALA 3.2 8.6 + - - +
358N ILE* 3.5 20.9 - - + +
360N ASP* 1.3 72.3 - - - +
362N LYS* 1.3 54.9 + - - +
364N CYS* 2.8 10.6 + - - +
365N LEU* 2.6 72.3 + - + +
374N LEU* 5.0 4.0 - - + -
410N LEU* 4.6 8.3 - - + -
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Residues in contact with LYS 362 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358N ILE 2.9 20.6 + - - +
359N GLU* 3.5 27.0 + - - +
360N ASP 3.3 0.2 - - - -
361N LEU* 1.3 69.1 - - - +
363N TYR* 1.3 83.4 + - - +
365N LEU* 3.1 11.8 + - - +
366N GLU* 3.1 38.6 + - - +
409N VAL* 3.9 17.3 - - + -
410N LEU* 2.2 48.0 - - + +
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Residues in contact with TYR 363 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286N LEU* 3.7 28.9 - - + -
290N HIS* 4.5 5.7 + - - -
333N TYR* 3.2 32.0 + + - -
359N GLU 3.1 14.6 + - - +
360N ASP 3.6 8.1 - - - +
362N LYS* 1.3 88.6 - - - +
364N CYS* 1.3 62.0 + - - +
366N GLU* 3.7 5.8 + - + +
367N ARG* 2.9 60.2 + - - +
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Residues in contact with CYS 364 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286N LEU* 5.3 1.3 - - - -
332N PHE* 5.1 0.2 - - - -
333N TYR* 3.2 57.2 - - - -
336N TYR* 4.1 14.8 - - + -
337N ALA* 3.8 22.6 - - + +
360N ASP 2.8 12.9 + - - +
361N LEU* 2.8 14.3 + - - +
363N TYR* 1.3 80.1 - - - +
365N LEU* 1.3 53.5 + - - +
367N ARG 2.4 30.0 - - - +
368N THR 3.8 4.0 - - - +
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Residues in contact with LEU 365 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337N ALA* 4.7 10.5 - - + -
341N ILE* 5.0 4.7 - - + -
361N LEU* 2.6 42.7 + - + +
362N LYS 3.1 6.4 + - - +
364N CYS* 1.3 73.2 - - - +
366N GLU* 1.3 70.1 + - - +
367N ARG 3.2 1.6 - - - -
368N THR* 3.3 22.7 + - - +
370N GLN* 5.3 15.2 + - + +
371N ARG* 4.2 23.0 + - - +
374N LEU* 3.7 33.7 - - + -
410N LEU* 4.0 26.9 - - + -
411N ASP* 5.2 2.5 - - - +
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Residues in contact with GLU 366 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362N LYS* 3.1 44.9 + - - +
363N TYR* 4.2 7.4 - - + +
364N CYS 3.5 0.2 - - - -
365N LEU* 1.3 80.3 - - - +
367N ARG* 1.3 63.0 + - + +
368N THR* 3.2 12.3 + - - +
371N ARG* 3.7 16.5 + - - +
410N LEU* 4.3 5.4 - - - +
411N ASP 5.6 3.0 + - - -
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Residues in contact with ARG 367 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290N HIS* 5.0 1.4 + - - -
329N GLN* 3.8 12.1 + - - -
333N TYR* 2.7 67.5 + - + +
334N ARG* 4.6 4.6 + - - +
363N TYR* 2.9 45.3 + - + +
364N CYS 2.4 22.2 + - - +
366N GLU* 1.3 78.6 - - + +
368N THR* 1.3 63.4 + - - +
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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
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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