Contacts of the helix formed by residues 355 - 367 (chain H) in PDB entry 5U0A
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 355 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327G GLU 3.5 11.2 - - - -
328G VAL* 3.2 16.6 - - - +
330G PRO* 3.9 17.4 - - - +
338H ALA* 4.2 2.6 - - - +
353H TYR* 3.2 2.2 - - - +
354H ASP* 1.3 81.4 - - - +
356H TYR* 1.3 63.8 + - - +
357H PRO* 4.0 2.3 - - - +
358H ALA* 3.1 24.2 + - - +
359H LEU* 3.0 28.4 + - - +
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Residues in contact with TYR 356 (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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325G LEU* 6.1 0.2 - - + -
328G VAL* 2.9 37.0 + - + +
329G TRP* 3.6 29.2 - + + -
264H LEU* 4.0 21.1 - - + -
280H LEU* 4.7 8.1 - - + -
281H PRO* 2.5 45.8 + - + -
282H ASP 3.9 10.7 + - - -
283H LEU* 4.1 1.4 + - - -
284H VAL* 3.4 33.0 - - + -
338H ALA* 3.6 18.7 + - + -
340H VAL* 4.4 3.6 + - - +
355H SER* 1.3 70.6 - - - +
357H PRO* 1.3 64.8 - - + +
359H LEU* 3.1 5.9 + - - +
360H ILE* 2.9 34.0 + - + +
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Residues in contact with PRO 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G VAL 3.9 0.4 - - - +
329G TRP* 4.7 7.4 - - + -
330G PRO* 3.8 29.6 - - + +
261H ARG* 4.0 23.6 - - - +
355H SER* 3.7 3.1 - - - +
356H TYR* 1.3 94.8 - - + +
358H ALA* 1.3 56.6 + - - +
360H ILE* 3.9 8.4 - - + +
361H ASP* 2.9 41.7 + - - +
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Residues in contact with ALA 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353H TYR* 4.3 12.9 - - + -
354H ASP* 5.0 2.7 - - + +
355H SER* 3.1 28.2 + - - +
356H TYR 3.2 0.8 - - - -
357H PRO* 1.3 78.3 - - - +
359H LEU* 1.3 58.1 + - - +
361H ASP* 3.5 5.0 + - - +
362H ALA* 2.9 30.4 + - - +
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Residues in contact with LEU 359 (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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284H VAL* 3.4 33.7 - - + +
286H ILE* 3.9 20.6 - - + -
336H GLY 3.7 19.7 - - - +
337H TYR* 3.9 16.6 - - - +
338H ALA* 3.9 2.5 - - + +
353H TYR* 3.6 34.4 - - + +
355H SER 3.0 13.4 + - - +
356H TYR* 3.1 8.5 + - - +
358H ALA* 1.3 75.4 - - - +
360H ILE* 1.3 66.7 + - + +
362H ALA* 3.2 0.9 + - - -
363H MET* 2.9 37.4 + - + +
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Residues in contact with ILE 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G TRP* 6.2 1.3 - - + -
257H ALA* 3.9 23.1 - - + +
260H LEU* 3.8 14.6 - - + -
261H ARG* 3.6 36.3 - - + +
264H LEU* 3.9 16.6 - - + -
286H ILE* 3.9 23.1 - - + -
356H TYR* 2.9 22.3 + - + +
357H PRO* 3.9 7.2 - - + +
359H LEU* 1.3 75.3 - - + +
361H ASP* 1.3 62.4 + - - +
363H MET* 4.3 0.2 - - - +
364H VAL* 2.9 42.1 + - + +
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Residues in contact with ASP 361 (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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253H ARG* 5.0 1.2 + - - -
257H ALA* 5.1 7.3 - - - +
357H PRO* 2.9 26.8 + - - +
358H ALA* 3.9 5.8 - - - +
360H ILE* 1.3 81.9 - - - +
362H ALA* 1.3 58.2 + - - +
364H VAL* 4.3 3.3 - - - +
365H ALA* 2.9 32.1 + - - +
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Residues in contact with ALA 362 (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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353H TYR* 3.6 37.5 - - + +
358H ALA 2.9 18.8 + - - +
359H LEU 3.2 3.1 + - - +
361H ASP* 1.3 78.2 - - - +
363H MET* 1.3 61.5 + - + +
365H ALA* 3.5 4.0 + - - +
366H ALA* 2.9 27.9 + - - +
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Residues in contact with MET 363 (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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4H VAL* 5.7 1.3 - - + -
286H ILE* 3.7 33.2 - - + +
288H VAL* 3.7 14.9 - - + +
334H ILE* 4.0 27.4 - - + +
335H ARG 3.5 26.7 - - - +
353H TYR* 3.4 42.8 - - + +
359H LEU* 2.9 30.0 + - + +
360H ILE 4.3 1.1 - - - +
362H ALA* 1.3 77.1 - - + +
364H VAL* 1.3 68.2 + - + +
366H ALA* 3.1 5.7 + - + +
367H ALA* 3.1 18.0 + - - +
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Residues in contact with VAL 364 (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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4H VAL* 5.9 2.9 - - + -
253H ARG* 3.8 45.7 + - + +
256H VAL* 4.0 19.1 - - + -
257H ALA* 4.0 29.4 - - + +
260H LEU* 4.2 9.4 - - + -
360H ILE* 2.9 26.7 + - + +
361H ASP* 4.3 2.9 - - - +
363H MET* 1.3 76.8 - - - +
365H ALA* 1.3 62.7 + - - +
367H ALA* 3.0 22.5 + - - +
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Residues in contact with ALA 365 (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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253H ARG* 3.6 24.1 - - - +
361H ASP 2.9 21.4 + - - +
362H ALA* 3.9 4.9 - - - +
364H VAL* 1.3 77.7 - - - +
366H ALA* 1.3 60.6 + - - +
367H ALA 3.4 3.1 + - - -
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Residues in contact with ALA 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H VAL* 4.7 3.4 - - + +
290H PHE* 5.3 2.6 - - - -
334H ILE* 3.6 47.8 - - + +
362H ALA 2.9 18.0 + - - +
363H MET* 3.4 10.5 - - + +
364H VAL 3.1 0.4 - - - -
365H ALA* 1.3 78.9 - - - +
367H ALA* 1.3 57.6 + - - +
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Residues in contact with ALA 367 (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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2H THR 6.1 0.2 - - - +
4H VAL* 4.3 7.0 - - + -
239H LEU* 3.7 31.4 - - + +
288H VAL* 3.8 19.5 - - + -
290H PHE* 6.1 2.5 - - - -
363H MET 3.1 12.1 + - - +
364H VAL* 3.0 17.6 + - - +
365H ALA 4.5 2.7 - - - -
366H ALA* 1.3 81.4 - - - +
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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