Contacts of the helix formed by residues 339 - 354 (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 ASN 339 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704D GLU* 4.7 8.1 - - - +
705D MET* 3.5 25.3 - - - +
306H ILE* 5.1 0.2 - - - +
333H LEU* 4.1 0.9 - - - +
336H GLU* 3.4 26.3 + - + +
337H PRO 3.4 1.8 - - - -
338H SER* 1.4 74.9 + - - +
340H LYS* 1.3 62.1 + - - +
341H THR* 3.1 13.9 + - - -
342H ILE* 3.0 43.6 + - + +
343H HIS* 3.2 24.2 + - - -
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Residues in contact with LYS 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H SER 3.1 8.5 + - - +
339H ASN* 1.3 68.1 + - - +
341H THR* 1.3 60.8 + - - +
343H HIS* 3.4 9.0 + - - +
344H ALA* 3.0 30.1 + - - +
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Residues in contact with THR 341 (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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704D GLU 5.1 3.0 + - - +
705D MET* 3.8 23.0 - - + +
706D GLU* 6.0 2.7 - - + +
310H PHE* 3.7 23.6 - - + -
339H ASN* 3.1 10.5 + - - -
340H LYS* 1.3 77.2 - - - +
342H ILE* 1.4 58.4 + - - +
344H ALA* 3.5 6.5 + - + +
345H GLU* 3.0 27.7 + - - +
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Residues in contact with ILE 342 (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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705D MET* 4.5 12.8 - - + -
306H ILE* 3.7 29.6 - - + -
310H PHE* 4.5 10.1 - - + -
329H LEU* 3.3 34.3 - - + +
332H ALA* 3.8 16.6 - - + +
333H LEU* 3.8 20.6 - - + +
336H GLU 4.2 4.7 - - - +
339H ASN* 3.0 30.9 + - + +
341H THR* 1.4 72.2 - - - +
343H HIS* 1.4 60.4 + - - +
345H GLU* 3.4 6.7 + - - +
346H LEU* 3.0 30.4 + - + +
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Residues in contact with HIS 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H LEU* 3.7 25.4 - - + +
337H PRO 2.7 27.1 + - - -
338H SER* 4.3 5.3 - - - -
339H ASN 3.2 26.7 + - - -
340H LYS* 3.6 10.1 - - - +
342H ILE* 1.4 74.4 - - - +
344H ALA* 1.4 52.8 + - - +
346H LEU* 3.1 8.4 + - - +
347H SER* 2.8 41.3 + - - +
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Residues in contact with ALA 344 (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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340H LYS 3.0 17.2 + - - +
341H THR* 3.7 7.4 - - - +
343H HIS* 1.4 74.5 - - - +
345H GLU* 1.3 56.8 + - - +
347H SER* 4.1 5.6 - - - -
348H LYS* 3.2 34.5 + - - +
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Residues in contact with GLU 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H PHE* 3.5 25.6 - - + -
314H LYS* 3.4 44.4 + - + +
317H ALA* 4.6 9.4 - - - +
318H GLN* 5.0 2.6 + - - +
329H LEU* 3.9 19.3 - - + -
341H THR* 3.0 17.9 + - - +
342H ILE* 3.7 4.7 - - - +
344H ALA* 1.3 75.2 - - - +
346H LEU* 1.4 63.4 + - - +
348H LYS* 3.6 20.7 + - - +
349H LEU* 3.2 23.7 + - - +
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Residues in contact with LEU 346 (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* 3.8 32.5 - - + +
329H LEU* 3.8 39.0 - - + +
330H ARG* 4.5 5.8 - - + +
333H LEU* 3.9 27.8 - - + -
342H ILE* 3.0 22.0 + - + +
343H HIS* 3.6 6.1 - - - +
345H GLU* 1.4 74.0 - - - +
347H SER* 1.4 55.5 + - - +
349H LEU* 3.2 13.3 + - + +
350H VAL* 2.9 42.3 + - + +
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Residues in contact with SER 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343H HIS* 2.8 24.8 + - - +
344H ALA* 4.1 6.7 - - - -
346H LEU* 1.4 72.6 - - - +
348H LYS* 1.4 54.8 + - - +
350H VAL* 3.3 12.1 - - - +
351H LYS* 3.0 31.8 + - - +
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Residues in contact with LYS 348 (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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344H ALA* 3.2 23.4 + - - +
345H GLU* 3.7 21.8 + - - +
346H LEU 3.3 0.2 - - - -
347H SER* 1.4 77.3 - - - +
349H LEU* 1.3 56.1 + - - +
351H LYS* 3.7 4.3 + - - +
352H LYS* 3.1 65.5 + - + +
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Residues in contact with LEU 349 (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* 4.0 25.4 - - + +
322H TYR* 3.8 35.9 - - + +
325H ALA* 4.2 2.9 - - + -
326H ILE* 4.0 21.5 - - + +
329H LEU* 3.8 24.2 - - + -
345H GLU* 3.2 13.5 + - - +
346H LEU* 3.4 22.2 - - + +
348H LYS* 1.3 76.2 - - - +
350H VAL* 1.4 61.3 + - + +
352H LYS* 3.5 6.3 + - - +
353H HIS* 3.0 30.5 + - + +
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Residues in contact with VAL 350 (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* 3.8 29.2 - - + -
346H LEU* 2.9 26.4 + - + +
347H SER* 3.3 19.1 - - - +
349H LEU* 1.4 72.4 - - + +
351H LYS* 1.4 66.1 + - + +
353H HIS* 3.3 10.7 + - + +
354H ALA* 3.2 21.8 + - - +
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Residues in contact with LYS 351 (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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347H SER 3.0 18.6 + - - +
348H LYS* 3.9 5.4 - - - +
350H VAL* 1.4 77.3 - - + +
352H LYS* 1.4 62.1 + - + +
354H ALA* 3.3 25.1 + - - +
355H ALA* 5.2 0.5 - - - +
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Residues in contact with LYS 352 (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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348H LYS* 3.1 51.4 + - + +
349H LEU* 3.9 6.5 - - - +
351H LYS* 1.4 73.2 - - + +
353H HIS* 1.4 63.4 + - - +
354H ALA 3.4 0.5 + - - -
355H ALA* 3.4 20.5 - - - +
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Residues in contact with HIS 353 (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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322H TYR* 3.6 30.7 - - + +
323H SER* 5.2 7.0 + - - -
349H LEU* 3.0 18.7 + - + +
350H VAL* 3.5 11.2 - - + +
351H LYS 3.3 0.4 - - - -
352H LYS* 1.4 75.4 - - - +
354H ALA* 1.3 56.4 + - - +
355H ALA 3.0 12.2 + - - +
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Residues in contact with ALA 354 (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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350H VAL 3.2 12.2 + - - +
351H LYS* 3.5 17.8 - - - +
352H LYS 3.2 0.8 - - - -
353H HIS* 1.3 72.1 - - - +
355H ALA* 1.4 59.3 + - - +
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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