Contacts of the helix formed by residues 321 - 336 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316E LEU* 2.9 30.9 + - + +
319E GLN* 4.7 13.7 - - + +
320E GLY* 1.4 74.9 - - - +
322E TYR* 1.3 57.8 + - - +
323E SER* 3.3 12.0 + - - +
324E GLU* 3.4 30.7 + - + +
325E ALA* 3.0 28.6 + - - +
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Residues in contact with TYR 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E ALA* 3.4 25.5 + - + -
320E GLY* 3.1 23.0 + - - +
321E GLU* 1.3 71.5 - - - +
323E SER* 1.3 64.4 + - - +
325E ALA* 3.9 0.8 - - - +
326E ILE* 3.2 30.0 + - - +
349E LEU* 3.4 35.1 - - + +
352E LYS* 4.1 20.1 + - + +
353E HIS* 3.3 51.6 - - + +
285G LEU 4.3 1.9 + - - -
286G ASP* 4.0 28.8 + - - +
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Residues in contact with SER 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321E GLU* 4.4 13.0 + - - -
322E TYR* 1.3 77.6 - - - +
324E GLU* 1.3 64.4 + - - +
326E ILE* 4.0 5.8 - - - +
327E PRO* 3.4 19.2 - - - +
353E HIS* 5.7 3.4 + - - -
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Residues in contact with GLU 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E LEU* 4.0 23.6 - - + +
321E GLU* 3.4 35.1 + - + +
323E SER* 1.3 85.0 + - - +
325E ALA* 1.3 63.3 + - - +
326E ILE 3.6 0.2 - - - -
327E PRO* 3.5 13.0 - - - +
328E ILE* 3.4 22.3 - - + +
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Residues in contact with ALA 325 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E GLY* 3.6 23.0 - - - +
316E LEU* 3.7 14.8 - - + +
317E ALA* 3.7 12.6 - - + +
321E GLU 3.0 16.6 + - - +
322E TYR 3.4 4.4 + - - +
324E GLU* 1.3 76.5 - - - +
326E ILE* 1.4 59.5 + - - +
328E ILE* 3.4 2.8 + - - +
329E LEU* 2.9 34.7 + - + +
349E LEU* 4.2 10.5 - - + -
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Residues in contact with ILE 326 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322E TYR 3.2 15.9 + - - +
323E SER* 4.0 7.2 - - - +
325E ALA* 1.4 74.2 - - - +
327E PRO* 1.4 75.7 - - + +
329E LEU* 3.4 1.2 + - - +
330E ARG* 2.9 73.2 + - - +
346E LEU* 3.8 11.9 - - + -
349E LEU* 4.0 13.0 - - + -
350E VAL* 3.8 27.8 - - + -
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Residues in contact with PRO 327 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323E SER 3.4 15.3 - - - +
324E GLU* 3.5 13.0 - - - +
326E ILE* 1.4 101.5 - - + +
328E ILE* 1.3 54.6 + - + +
330E ARG* 3.3 9.6 + - + +
331E ALA* 2.8 34.7 + - - +
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Residues in contact with ILE 328 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E LEU* 3.2 44.1 - - + +
312E LYS* 4.1 22.0 - - + +
313E GLY* 3.8 12.1 - - - +
316E LEU* 3.4 27.6 - - + -
324E GLU* 3.4 11.4 - - + +
325E ALA 3.4 6.5 + - - +
326E ILE 3.3 0.8 - - - -
327E PRO* 1.3 75.3 - - + +
329E LEU* 1.3 66.3 + - - +
331E ALA* 3.2 9.4 + - - +
332E ALA* 3.1 21.8 + - - +
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Residues in contact with LEU 329 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E LEU 5.4 0.2 - - - -
310E PHE* 3.8 45.3 - - + +
313E GLY* 3.9 19.3 - - - +
317E ALA* 4.9 2.7 - - + -
325E ALA* 2.9 19.8 + - + +
326E ILE 4.0 2.0 - - - +
328E ILE* 1.3 75.5 - - - +
330E ARG* 1.4 57.5 + - - +
332E ALA* 3.7 3.5 - - - +
333E LEU* 3.2 19.4 + - - +
342E ILE* 3.3 16.8 - - + +
345E GLU* 3.9 32.8 - - + +
346E LEU* 3.9 16.3 - - + +
349E LEU* 3.8 26.7 - - + -
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Residues in contact with ARG 330 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326E ILE* 2.9 55.7 + - - +
327E PRO* 3.6 8.0 - - + +
329E LEU* 1.4 75.2 - - - +
331E ALA* 1.3 53.6 + - - +
332E ALA 3.2 0.4 - - - -
333E LEU* 3.0 11.2 + - + +
334E LYS* 2.8 35.1 + - - +
346E LEU* 4.0 17.8 - - + +
350E VAL* 5.7 1.2 - - - +
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Residues in contact with ALA 331 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E LEU* 4.5 16.1 - - + +
327E PRO 2.8 20.7 + - - +
328E ILE* 3.4 10.1 - - - +
330E ARG* 1.3 71.3 - - - +
332E ALA* 1.3 59.0 + - - +
334E LYS* 3.5 21.9 + - - +
335E LEU* 3.6 14.9 - - - +
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Residues in contact with ALA 332 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ILE* 3.6 24.8 - - + +
309E LEU* 4.0 23.0 - - + +
310E PHE* 4.3 11.2 - - - +
328E ILE 3.1 12.1 + - - +
329E LEU* 3.7 11.4 - - - +
330E ARG 3.2 0.2 - - - -
331E ALA* 1.3 72.7 - - - +
333E LEU* 1.4 64.8 + - - +
335E LEU* 3.1 16.0 + - - +
336E GLU 3.4 8.0 + - - -
342E ILE* 4.1 13.2 - - + -
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Residues in contact with LEU 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E LEU 3.2 10.5 + - - +
330E ARG* 3.0 13.8 + - + +
332E ALA* 1.4 75.1 - - - +
334E LYS* 1.3 58.9 + - - +
336E GLU 3.0 19.5 - - - +
337E PRO* 3.0 51.8 - - + +
339E ASN 4.1 1.1 - - - +
342E ILE* 3.8 22.2 - - + +
343E HIS* 3.7 33.7 - - + +
346E LEU* 3.9 18.6 - - + -
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Residues in contact with LYS 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E ARG 2.8 11.7 + - - +
331E ALA* 3.5 16.4 - - - +
332E ALA 3.2 0.4 - - - -
333E LEU* 1.3 78.0 - - - +
335E LEU* 1.4 61.2 + - + +
337E PRO* 4.3 10.5 - - - +
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Residues in contact with LEU 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E ASP* 3.6 42.6 - - + +
306E ILE* 4.3 16.2 - - + -
309E LEU* 3.8 24.7 - - + -
331E ALA 3.6 11.4 - - - +
332E ALA 3.1 8.4 + - - +
334E LYS* 1.4 78.4 - - + +
336E GLU* 1.3 66.7 + - + +
337E PRO* 4.0 4.3 - - - +
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Residues in contact with GLU 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704C GLU* 2.9 33.3 - - - +
306E ILE* 3.6 28.0 - - + +
332E ALA 3.4 2.4 + - - -
333E LEU* 3.0 18.4 + - - +
335E LEU* 1.3 82.8 - - - +
337E PRO* 1.4 68.7 - - - +
338E SER* 3.3 6.5 + - - +
339E ASN* 3.2 34.6 + - + +
342E 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