Contacts of the helix formed by residues 404 - 420 (chain Y) in PDB entry 5MG3
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 THR 404 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66Y MET* 3.5 7.3 - - - +
67Y PHE* 6.6 0.2 - - - -
278Y ILE* 4.3 27.6 - - + -
281Y SER* 2.7 34.5 + - - +
285Y LEU* 4.4 2.8 - - - +
321Y TYR* 3.8 10.7 - - - +
389Y GLU* 2.8 29.8 + - - +
403Y GLY* 1.3 67.3 - - - -
405Y SER* 1.3 56.6 + - - +
406Y LEU 3.1 1.3 - - - -
407Y LEU* 2.8 26.6 + - + -
408Y ILE* 3.1 16.5 + - + +
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Residues in contact with SER 405 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Y MET* 2.8 45.4 + - - +
67Y PHE* 4.0 4.6 - - - -
82Y ILE* 3.8 14.2 - - - +
195Y ILE* 3.2 25.4 - - - +
278Y ILE* 5.7 0.2 - - - +
401Y PHE* 4.1 14.6 - - - -
403Y GLY 4.2 0.7 - - - -
404Y THR* 1.3 74.1 - - - +
406Y LEU* 1.4 59.4 + - - +
407Y LEU 3.2 0.2 - - - -
408Y ILE* 3.8 11.0 - - - +
409Y VAL* 3.5 18.7 + - - +
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Residues in contact with LEU 406 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Y ILE* 4.7 5.2 - - + -
199Y LEU* 6.0 1.6 - - + -
234Y VAL* 5.5 3.4 - - + +
237Y VAL* 5.0 6.4 - - - +
392Y ARG* 3.2 27.1 + - - +
397Y VAL* 4.1 11.0 - - + -
399Y PHE* 3.9 37.0 - - + -
401Y PHE* 3.1 54.1 - - + +
402Y GLY* 4.3 2.7 - - - +
403Y GLY 2.8 12.1 + - - +
405Y SER* 1.4 78.2 - - - +
407Y LEU* 1.4 58.1 + - - +
409Y VAL* 4.8 9.6 - - + -
410Y VAL* 4.4 15.5 - - + +
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Residues in contact with LEU 407 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237Y VAL* 4.1 25.6 - - + -
274Y VAL* 4.2 22.7 - - + -
277Y ALA* 4.7 7.9 - - + -
278Y ILE 5.8 0.2 - - - +
321Y TYR* 4.6 4.0 - - - +
385Y CYS* 4.3 27.6 - - + +
388Y PRO* 4.7 5.6 - - + -
389Y GLU* 3.4 29.6 - - + +
392Y ARG* 3.6 3.7 - - - +
404Y THR* 2.8 21.4 + - + +
406Y LEU* 1.4 79.8 - - - +
408Y ILE* 1.4 62.9 + - + +
409Y VAL 3.5 0.7 - - - -
410Y VAL* 3.3 14.5 + - - +
411Y VAL* 3.4 27.7 + - + +
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Residues in contact with ILE 408 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67Y PHE* 5.9 1.1 - - + -
82Y ILE* 4.3 7.0 - - + -
86Y ILE* 5.3 2.7 - - + -
191Y ILE* 4.2 27.6 - - + -
195Y ILE* 3.6 19.1 - - + -
274Y VAL* 4.3 15.7 - - + -
278Y ILE* 3.9 45.5 - - + -
404Y THR* 3.1 15.8 + - + +
405Y SER* 3.6 13.2 - - - +
407Y LEU* 1.4 72.6 - - + +
409Y VAL* 1.4 65.8 + - - +
411Y VAL* 3.6 7.8 + - - +
412Y VAL* 3.3 25.0 + - + +
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Residues in contact with VAL 409 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Y ILE* 4.0 20.2 - - + +
192Y PHE* 4.3 11.4 - - + +
195Y ILE* 3.9 35.0 - - + +
196Y VAL* 4.8 4.9 - - + +
199Y LEU* 5.5 9.2 - - + -
399Y PHE* 6.2 0.7 - - + -
405Y SER 3.5 15.7 + - - +
406Y LEU* 4.8 10.3 - - + -
408Y ILE* 1.4 78.0 - - - +
410Y VAL* 1.3 71.3 + - + +
412Y VAL* 3.2 16.4 - - + +
413Y ILE* 3.1 34.9 + - + +
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Residues in contact with VAL 410 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Y LEU* 5.6 3.8 - - + -
234Y VAL* 3.8 42.0 - - + +
237Y VAL* 4.1 24.2 - - + -
238Y GLU* 5.2 2.2 - - + +
406Y LEU* 4.4 13.9 - - + +
407Y LEU* 3.3 10.9 + - - +
408Y ILE 3.3 0.4 - - - -
409Y VAL* 1.3 85.4 - - + +
411Y VAL* 1.3 60.1 + - - +
413Y ILE* 3.5 15.5 + - + +
414Y MET* 3.4 37.9 + - + +
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Residues in contact with VAL 411 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237Y VAL* 5.4 3.1 - - + -
241Y GLN* 6.0 0.9 - - - +
271Y MET* 3.8 28.1 - - + +
274Y VAL* 3.7 42.0 - - + -
407Y LEU* 3.4 22.4 + - + +
408Y ILE 3.8 7.9 - - - +
409Y VAL 3.4 0.2 - - - -
410Y VAL* 1.3 74.4 - - + +
412Y VAL* 1.4 66.7 + - + +
414Y MET* 3.4 20.1 - - + +
415Y ASP* 3.3 20.3 + - + +
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Residues in contact with VAL 412 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Y SER* 3.9 35.4 - - - +
191Y ILE* 4.4 5.8 - - + -
192Y PHE* 3.9 30.4 - - + +
408Y ILE 3.3 9.8 + - - +
409Y VAL* 3.2 27.6 - - + +
411Y VAL* 1.4 76.6 - - + +
413Y ILE* 1.3 57.6 + - - +
414Y MET 3.5 0.2 - - - -
415Y ASP* 3.7 10.1 - - + +
416Y PHE* 3.1 40.6 + - + +
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Residues in contact with ILE 413 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481E VAL* 5.9 4.0 - - + -
482E THR* 5.7 8.3 - - + +
485E MET* 3.9 46.4 - - + +
489E LEU* 6.0 1.6 - - + -
192Y PHE* 4.4 11.0 - - + -
196Y VAL* 6.4 1.8 - - + -
199Y LEU* 4.2 25.1 - - + -
234Y VAL* 6.4 0.9 - - + -
238Y GLU* 5.7 2.7 - - - +
409Y VAL* 3.1 26.0 + - + +
410Y VAL* 3.6 16.2 - - + +
412Y VAL* 1.3 72.8 - - - +
414Y MET* 1.3 63.9 + - + +
416Y PHE* 4.3 0.7 - - - +
417Y MET* 3.1 28.1 + - + +
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Residues in contact with MET 414 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237Y VAL* 4.6 5.6 - - + -
238Y GLU* 3.4 46.4 - - + +
241Y GLN* 3.5 28.9 - - - +
268Y LYS* 3.7 33.3 - - + +
271Y MET* 3.8 17.0 - - + +
346Y LEU* 4.5 3.6 - - - +
410Y VAL* 3.4 29.8 + - + +
411Y VAL* 3.4 11.9 - - + +
413Y ILE* 1.3 75.1 - - + +
415Y ASP* 1.4 61.6 + - - +
417Y MET* 3.3 5.5 + - - +
418Y ALA* 3.1 22.3 + - - +
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Residues in contact with ASP 415 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Y SER* 4.2 17.5 + - - -
271Y MET* 4.5 7.0 - - + -
346Y LEU* 4.1 12.7 - - - +
411Y VAL* 3.3 14.0 + - + +
412Y VAL* 3.6 14.3 - - + +
413Y ILE 3.3 0.2 - - - -
414Y MET* 1.4 77.1 - - - +
416Y PHE* 1.4 62.7 + - + +
418Y ALA* 3.3 5.0 + - - +
419Y GLN* 3.1 32.7 + - - +
435Y LYS* 2.8 43.9 + - - +
438Y LEU* 4.8 2.1 - - - +
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Residues in contact with PHE 416 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485E MET* 6.3 0.2 - - + -
26Y VAL* 4.2 19.1 - - + -
183Y ILE* 3.8 23.3 - - + -
184Y GLY* 4.0 15.9 - - - -
188Y SER* 4.2 24.0 - - - -
189Y ILE* 4.0 23.1 - - + -
192Y PHE* 3.7 41.5 - + + -
412Y VAL* 3.1 28.1 + - + +
413Y ILE 4.7 0.7 - - - +
415Y ASP* 1.4 77.0 - - + +
417Y MET* 1.3 60.5 + - - +
419Y GLN* 2.9 33.6 + - + +
420Y VAL* 2.9 26.5 + - + +
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Residues in contact with MET 417 (chain Y).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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481E VAL* 3.8 24.2 - - + +
485E MET* 4.6 28.5 - - + -
265Y LEU* 3.2 27.8 - - + +
413Y ILE* 3.1 23.0 + - + +
414Y MET* 3.3 7.2 + - - +
416Y PHE* 1.3 78.7 - - - +
418Y ALA* 1.4 55.7 + - - +
420Y VAL* 3.9 10.9 - - + +
421Y GLN* 3.1 47.0 + - - +
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Residues in contact with ALA 418 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265Y LEU* 3.9 12.2 - - + +
345Y ASN 4.7 2.7 - - - +
346Y LEU* 3.1 41.3 - - + +
348Y LYS* 3.3 30.1 - - + +
414Y MET 3.1 12.3 + - - +
415Y ASP 3.7 7.6 - - - +
417Y MET* 1.4 75.8 - - - +
419Y GLN* 1.3 65.1 + - - +
420Y VAL 3.2 1.0 + - - -
421Y GLN* 3.4 7.4 + - - +
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Residues in contact with GLN 419 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183Y ILE* 4.1 33.8 - - + +
345Y ASN* 3.4 38.3 + - - +
346Y LEU* 5.2 0.8 - - - +
348Y LYS* 4.9 4.0 - - - +
415Y ASP* 3.1 25.6 + - - +
416Y PHE* 2.9 29.4 + - + +
418Y ALA* 1.3 73.9 - - - +
420Y VAL* 1.3 58.3 + - - +
421Y GLN 3.4 0.7 + - - -
422Y THR* 3.9 6.8 + - - -
423Y LEU* 3.8 18.2 + - - +
435Y LYS* 3.9 29.1 + - + +
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Residues in contact with VAL 420 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y LEU* 4.0 32.9 - - + +
26Y VAL* 4.9 11.4 - - + -
183Y ILE* 5.3 0.2 - - + -
192Y PHE* 6.4 0.2 - - + -
416Y PHE* 2.9 32.5 + - + +
417Y MET* 3.9 15.3 - - + +
418Y ALA 3.2 0.2 + - - -
419Y GLN* 1.3 74.3 - - + +
421Y GLN* 1.3 79.7 + - - +
422Y THR 3.5 0.7 + - - -
423Y LEU* 3.6 20.3 + - + +
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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