Contacts of the helix formed by residues 321 - 336 (chain H) in PDB entry 5MGX
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 GLU 321 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316H LEU* 2.8 34.6 + - + +
319H GLN* 4.7 11.0 - - + +
320H GLY* 1.3 74.7 - - - +
322H TYR* 1.4 58.1 + - - +
323H SER* 3.3 5.8 - - - +
324H GLU* 3.3 31.4 + - + +
325H ALA* 3.0 28.6 + - - +
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Residues in contact with TYR 322 (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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317H ALA* 5.3 1.3 - - - +
320H GLY* 3.1 9.3 + - - +
321H GLU* 1.4 71.9 - - - +
323H SER* 1.4 65.1 + - - +
325H ALA* 3.9 0.8 - - - +
326H ILE* 3.2 28.2 + - - +
349H LEU* 3.8 28.7 - - + +
353H HIS* 3.6 36.3 - - + +
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Residues in contact with SER 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H GLU* 3.3 3.8 - - - -
322H TYR* 1.4 77.4 - - - +
324H GLU* 1.3 60.4 + - - +
326H ILE* 5.1 1.0 - - - +
327H PRO* 3.4 19.1 - - - +
353H HIS* 5.2 5.0 - - - -
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Residues in contact with GLU 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H LEU* 4.4 20.8 - - + +
321H GLU* 3.3 39.3 + - + +
322H TYR 3.3 0.2 - - - -
323H SER* 1.3 79.1 - - - +
325H ALA* 1.3 63.3 + - - +
326H ILE 3.6 0.4 - - - -
327H PRO* 3.5 13.5 - - - +
328H ILE* 3.4 22.3 - - + +
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Residues in contact with ALA 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H GLY* 3.4 27.8 - - - +
316H LEU* 4.1 5.6 - - + -
317H ALA* 3.8 18.2 - - + +
321H GLU 3.0 17.8 + - - +
322H TYR 3.4 4.4 + - - +
324H GLU* 1.3 75.1 - - - +
326H ILE* 1.4 60.2 + - - +
328H ILE* 3.4 3.7 + - - +
329H LEU* 2.9 34.6 + - + +
349H LEU* 4.2 7.9 - - + -
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Residues in contact with ILE 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H TYR 3.2 15.9 + - - +
323H SER* 5.1 0.7 - - - +
325H ALA* 1.4 71.5 - - - +
327H PRO* 1.4 64.5 - - + +
329H LEU* 3.4 1.4 + - - +
330H ARG* 2.9 34.2 + - + +
346H LEU* 3.8 15.7 - - + +
349H LEU* 4.0 12.9 - - + +
350H VAL* 3.8 28.9 - - + -
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Residues in contact with PRO 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H SER 3.4 21.3 - - - +
324H GLU* 3.5 13.5 - - - +
326H ILE* 1.4 90.7 - - + +
328H ILE* 1.4 53.1 + - + +
330H ARG* 3.3 7.5 + - + +
331H ALA* 2.8 34.4 + - - +
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Residues in contact with ILE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H LEU* 3.2 44.5 - - + +
312H LYS* 4.2 20.6 - - + +
313H GLY* 3.8 12.1 - - - +
316H LEU* 3.9 22.2 - - + -
324H GLU* 3.4 18.8 - - + +
325H ALA 3.4 6.9 + - - +
326H ILE 3.3 0.4 - - - -
327H PRO* 1.4 79.4 - - + +
329H LEU* 1.4 61.9 + - - +
331H ALA* 3.2 9.4 + - - +
332H ALA* 3.1 22.0 + - - +
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Residues in contact with LEU 329 (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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309H LEU 5.4 0.2 - - - -
310H PHE* 3.6 46.4 - - + +
313H GLY* 3.9 20.0 - - - +
317H ALA* 5.0 2.7 - - + -
325H ALA* 2.9 21.4 + - + +
328H ILE* 1.4 72.5 - - - +
330H ARG* 1.4 56.9 + - - +
332H ALA* 3.6 3.1 + - - +
333H LEU* 3.2 19.8 + - - +
342H ILE* 3.3 18.0 - - + +
345H GLU* 3.9 27.8 - - + +
346H LEU* 3.8 20.8 - - + +
349H LEU* 3.8 27.4 - - + -
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Residues in contact with ARG 330 (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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326H ILE* 2.9 21.3 + - + +
327H PRO* 3.6 7.4 - - + +
329H LEU* 1.4 74.6 - - - +
331H ALA* 1.4 53.4 + - - +
333H LEU* 3.0 10.4 + - + +
334H LYS* 2.8 34.8 + - - +
346H LEU* 4.5 9.4 - - + +
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Residues in contact with ALA 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H LEU* 4.6 16.1 - - + +
327H PRO 2.8 20.8 + - - +
328H ILE* 3.4 9.9 - - - +
330H ARG* 1.4 71.1 - - - +
332H ALA* 1.4 60.5 + - - +
334H LYS* 3.5 20.0 - - - +
335H LEU* 3.6 14.7 - - - +
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Residues in contact with ALA 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ILE* 3.5 29.3 - - + +
309H LEU* 4.0 19.5 - - + +
310H PHE* 4.3 10.5 - - + +
328H ILE 3.1 11.1 + - - +
329H LEU* 3.7 11.9 - - - +
330H ARG 3.2 0.2 - - - -
331H ALA* 1.4 74.4 - - - +
333H LEU* 1.4 62.7 + - - +
335H LEU* 3.2 16.1 + - - +
336H GLU 3.4 8.1 + - - -
342H ILE* 3.8 12.4 - - + +
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Residues in contact with LEU 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H LEU 3.2 12.0 + - - +
330H ARG* 3.0 11.3 + - + +
332H ALA* 1.4 75.4 - - - +
334H LYS* 1.3 59.8 + - - +
336H GLU 3.0 19.5 - - - +
337H PRO* 2.9 53.1 - - + +
339H ASN 4.1 1.6 - - - +
342H ILE* 3.8 21.9 - - + +
343H HIS* 3.7 33.7 - - + +
346H LEU* 3.9 19.3 - - + -
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Residues in contact with LYS 334 (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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330H ARG 2.8 12.1 + - - +
331H ALA* 3.5 16.6 - - - +
332H ALA 3.3 0.2 - - - -
333H LEU* 1.3 76.8 - - - +
335H LEU* 1.4 60.1 + - + +
337H PRO* 4.2 11.9 - - - +
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Residues in contact with LEU 335 (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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304H ASP* 3.6 45.5 - - + +
306H ILE* 4.3 18.4 - - + -
309H LEU* 3.9 20.2 - - + -
331H ALA 3.6 17.3 - - - +
332H ALA* 3.2 7.2 + - - +
333H LEU 3.2 0.8 - - - -
334H LYS* 1.4 80.6 - - + +
336H GLU* 1.4 57.3 + - - +
337H PRO* 4.0 3.8 - - - +
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Residues in contact with GLU 336 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ILE* 3.7 22.9 - - + -
332H ALA 3.4 2.4 + - - -
333H LEU* 3.0 16.0 + - - +
335H LEU* 1.4 79.3 - - - +
337H PRO* 1.4 66.5 - - - +
338H SER* 3.3 5.9 + - - +
339H ASN* 3.4 27.7 + - + +
342H ILE* 4.2 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
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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