Contacts of the helix formed by residues 356 - 369 (chain H) in PDB entry 2R9R
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 356 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343H TYR* 3.5 18.4 - - - -
354H PHE 3.2 2.6 - - - -
355H PRO* 1.3 81.0 - - - +
357H ILE* 1.3 64.5 + - - +
358H PRO* 3.4 13.0 - - - +
359H ASP* 2.6 32.4 + - - +
360H ALA* 3.0 21.1 + - - +
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Residues in contact with ILE 357 (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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336H ILE* 5.0 2.0 - - + +
339H SER* 4.1 0.2 - - - -
340H SER* 3.7 34.5 - - - +
343H TYR* 3.7 31.4 - - + -
344H PHE* 3.9 28.5 - - + -
356H SER* 1.3 69.9 - - - +
358H PRO* 1.3 74.8 - - + +
360H ALA* 2.8 16.9 + - - +
361H PHE* 3.2 29.9 + - + -
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Residues in contact with PRO 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H SER* 3.4 14.1 - - - +
357H ILE* 1.3 94.5 - - + +
359H ASP* 1.3 62.1 + - - +
361H PHE* 3.0 36.2 + - + +
500H PGW 3.0 34.8 - - + +
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Residues in contact with ASP 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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355H PRO* 3.7 33.3 - - + +
356H SER* 2.6 27.3 + - - +
357H ILE 3.1 1.0 - - - -
358H PRO* 1.3 79.1 - - - +
360H ALA* 1.3 62.0 + - - +
361H PHE 3.3 0.9 + - - -
362H TRP* 3.5 10.6 + - - +
376H MET* 3.6 14.2 - - + +
500H PGW 3.4 37.3 + - - +
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Residues in contact with ALA 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H SER* 3.2 29.7 + - - +
342H VAL* 4.0 4.3 - - + -
343H TYR* 5.0 0.4 - - + -
354H PHE* 3.6 31.4 - - + -
356H SER 3.0 10.7 + - - +
357H ILE* 2.8 12.0 + - - +
359H ASP* 1.3 76.5 - - - +
361H PHE* 1.3 64.5 + - - +
362H TRP 3.1 0.2 - - - -
363H TRP* 2.8 14.4 + - - +
364H ALA* 3.0 10.0 + - - +
376H MET* 4.0 2.4 - - - +
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Residues in contact with PHE 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H VAL* 3.7 14.3 - - + +
336H ILE* 4.0 30.5 - - + -
339H SER* 3.1 20.2 + - - -
357H ILE* 3.2 27.5 + - + -
358H PRO* 3.0 36.4 + - + +
360H ALA* 1.3 74.3 - - - +
362H TRP* 1.3 64.2 + - - +
364H ALA* 3.0 14.0 + - - +
365H VAL* 3.0 17.4 + - - +
500H PGW 3.3 54.7 - - + -
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Residues in contact with TRP 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359H ASP 3.5 11.6 + - - +
361H PHE* 1.3 79.7 - - - +
363H TRP* 1.3 63.4 + - - +
365H VAL* 3.3 8.6 + - + +
366H VAL* 3.0 38.6 + - + +
373H TYR* 3.4 38.4 - + - -
375H ASP* 2.8 34.1 + - - -
376H MET* 3.8 17.7 - - + -
500H PGW 3.2 35.9 - - + +
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Residues in contact with TRP 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H PHE 3.8 13.0 - - - -
339H SER* 4.9 0.7 - - - -
342H VAL* 3.6 37.5 - - + -
354H PHE* 3.6 20.4 - + + -
360H ALA 2.8 14.1 + - - +
362H TRP* 1.3 78.7 - - - +
364H ALA* 1.3 68.7 + - + +
366H VAL* 3.4 8.5 + - + +
367H SER* 2.7 55.1 + - - -
376H MET* 3.3 39.8 + - + -
377H VAL* 4.5 1.2 - - - +
378H PRO* 3.8 22.7 - - + +
386H VAL* 4.3 2.2 - - + -
387H GLY* 3.6 33.9 - - - -
390H CYS* 3.9 22.2 - - + -
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Residues in contact with ALA 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H VAL* 3.8 23.6 - - - +
338H PHE* 4.7 4.5 - - + -
339H SER* 3.4 23.1 - - - +
360H ALA 3.0 4.0 + - - +
361H PHE 3.0 9.9 + - - +
363H TRP* 1.3 91.4 - - + +
365H VAL* 1.3 59.1 + - - +
367H SER* 3.2 1.0 + - - -
368H MET* 2.9 37.4 + - - +
390H CYS* 4.3 4.3 - - - -
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Residues in contact with VAL 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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331H LEU* 5.1 10.5 - - + -
335H VAL* 3.6 22.7 - - + -
361H PHE 3.0 14.2 + - - +
362H TRP* 3.8 11.4 - - + +
364H ALA* 1.3 74.9 - - - +
366H VAL* 1.3 56.9 + - + +
368H MET* 4.1 2.6 - - - -
369H THR* 2.8 49.1 + - + +
500H PGW 3.6 35.7 - - + -
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Residues in contact with VAL 366 (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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362H TRP* 3.0 45.1 + - + +
363H TRP* 3.7 8.5 - - + +
365H VAL* 1.3 77.7 - - + +
367H SER* 1.3 59.4 + - - +
369H THR* 3.9 4.3 - - - -
371H VAL* 2.9 31.8 + - + -
372H GLY* 2.9 28.3 + - - +
373H TYR* 3.4 44.4 - - + +
374H GLY 5.1 1.3 - - - +
375H ASP* 5.2 2.2 - - - +
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Residues in contact with SER 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H TRP* 2.7 46.1 + - - -
364H ALA 3.7 2.9 - - - -
365H VAL 3.2 0.2 - - - -
366H VAL* 1.3 77.6 - - - +
368H MET* 1.3 61.3 + - - +
369H THR 3.2 1.6 - - - -
370H THR* 2.8 26.0 + - - +
372H GLY* 4.9 3.0 - - - +
387H GLY 5.4 1.6 - - - -
390H CYS* 3.9 18.8 - - - -
391H ALA* 4.2 15.9 - - - +
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Residues in contact with MET 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H LEU* 4.2 22.9 - - + +
334H GLY* 4.0 20.6 - - - +
335H VAL* 3.9 29.8 - - - -
338H PHE* 4.5 7.2 - - + -
364H ALA 2.9 20.4 + - - +
365H VAL* 4.2 2.9 - - - +
367H SER* 1.3 75.8 - - - +
369H THR* 1.3 60.2 + - - +
370H THR* 3.1 4.6 + - - +
390H CYS* 3.5 27.1 - - - +
391H ALA 4.9 0.4 - - - -
393H ALA* 4.1 2.7 - - + +
394H GLY* 3.3 45.6 - - - +
395H VAL* 3.9 1.2 + - - -
397H THR* 3.9 17.9 - - + +
398H ILE* 3.8 6.0 - - - +
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Residues in contact with THR 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H LEU* 4.8 12.6 - - + -
365H VAL* 2.8 32.9 + - + +
366H VAL* 3.5 4.2 + - - -
368H MET* 1.3 78.3 - - + +
370H THR* 1.3 73.5 + - - +
371H VAL* 3.3 25.5 + - - +
398H ILE* 3.9 22.6 - - + +
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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