Contacts of the helix formed by residues 339 - 355 (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 ASN 339 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704C GLU* 3.6 23.0 - - - +
705C MET* 3.7 8.1 - - - +
333E LEU* 4.1 0.7 - - - +
336E GLU* 3.2 40.8 + - + +
337E PRO 3.4 1.8 - - - -
338E SER* 1.4 74.8 + - - +
340E LYS* 1.3 62.6 + - - +
341E THR* 3.1 14.2 + - - -
342E ILE* 3.0 44.1 + - + +
343E HIS* 3.1 23.7 + - - -
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Residues in contact with LYS 340 (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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338E SER* 3.2 22.8 + - - +
339E ASN* 1.3 68.4 + - - +
341E THR* 1.3 61.4 + - - +
343E HIS* 3.4 10.7 + - + +
344E ALA* 3.0 30.6 + - - +
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Residues in contact with THR 341 (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* 6.1 0.7 + - - -
705C MET* 4.0 18.6 + - + -
706C GLU* 5.9 4.7 - - + +
310E PHE* 3.7 24.5 - - + -
314E LYS* 6.1 0.2 - - - +
339E ASN* 3.1 10.8 + - - -
340E LYS* 1.3 78.4 - - - +
342E ILE* 1.3 55.9 + - - +
344E ALA* 3.5 6.5 + - - +
345E GLU* 3.1 27.9 + - - +
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Residues in contact with ILE 342 (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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705C MET* 3.8 7.9 - - + -
306E ILE* 3.7 27.8 - - + -
310E PHE* 4.0 26.2 - - + -
329E LEU* 3.3 29.8 - - + +
332E ALA* 3.9 17.5 - - + +
333E LEU* 3.8 20.2 - - + +
336E GLU 4.2 4.0 - - - +
339E ASN* 3.0 30.1 + - + +
341E THR* 1.3 71.5 - - - +
343E HIS* 1.3 59.3 + - - +
345E GLU* 3.5 2.1 + - - +
346E LEU* 3.0 30.2 + - + +
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Residues in contact with HIS 343 (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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333E LEU* 3.7 23.0 - - + +
337E PRO 2.7 27.2 + - - -
338E SER* 4.3 5.0 - - - -
339E ASN 3.1 26.6 + - - -
340E LYS* 3.6 11.0 - - + +
341E THR 3.3 0.6 - - - -
342E ILE* 1.3 74.8 - - - +
344E ALA* 1.3 53.0 + - - +
346E LEU* 3.1 7.8 + - - +
347E SER* 2.8 37.2 + - - -
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Residues in contact with ALA 344 (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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340E LYS 3.0 16.8 + - - +
341E THR* 3.7 7.6 - - + +
343E HIS* 1.3 75.5 - - - +
345E GLU* 1.3 56.9 + - - +
347E SER* 4.1 5.8 - - - -
348E LYS* 3.2 34.6 + - - +
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Residues in contact with GLU 345 (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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310E PHE* 3.7 22.7 - - + -
314E LYS* 3.4 44.6 + - + +
317E ALA* 4.5 9.0 - - - +
318E GLN* 4.9 3.1 + - - +
329E LEU* 3.9 21.3 - - + -
341E THR* 3.1 18.4 + - - +
342E ILE 3.7 4.9 - - - +
343E HIS 3.2 0.2 - - - -
344E ALA* 1.3 75.8 - - - +
346E LEU* 1.4 62.5 + - - +
348E LYS* 3.7 20.8 + - - +
349E LEU* 3.2 23.7 + - - +
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Residues in contact with LEU 346 (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* 3.8 31.9 - - + -
329E LEU* 3.9 37.5 - - + +
330E ARG* 4.0 17.3 - - + +
333E LEU* 3.9 24.5 - - + -
342E ILE* 3.0 22.1 + - + +
343E HIS* 3.6 6.1 - - - +
345E GLU* 1.4 73.9 - - - +
347E SER* 1.3 60.1 + - - +
349E LEU* 3.2 12.7 + - + +
350E VAL* 2.9 38.0 + - + +
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Residues in contact with SER 347 (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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343E HIS 2.8 21.2 + - - -
344E ALA* 4.1 6.4 + - - -
346E LEU* 1.3 72.7 - - - +
348E LYS* 1.4 55.7 + - - +
350E VAL* 3.3 12.1 - - - +
351E LYS* 3.1 32.7 + - - +
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Residues in contact with LYS 348 (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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344E ALA* 3.2 23.9 + - - +
345E GLU* 3.7 22.1 + - - +
346E LEU 3.3 0.2 - - - -
347E SER* 1.4 78.2 + - - +
349E LEU* 1.3 56.5 + - - +
351E LYS* 3.7 4.9 + - - +
352E LYS* 3.1 65.3 + - + +
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Residues in contact with LEU 349 (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* 4.1 20.2 - - + -
322E TYR* 3.4 53.2 - - + +
325E ALA* 4.2 2.9 - - + -
326E ILE* 4.0 31.2 - - + +
329E LEU* 3.8 22.9 - - + -
345E GLU 3.2 13.7 + - - +
346E LEU* 3.2 15.5 + - + +
348E LYS* 1.3 77.3 - - - +
350E VAL* 1.4 60.2 + - + +
352E LYS* 3.5 6.8 + - - +
353E HIS* 3.0 30.4 + - + +
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Residues in contact with VAL 350 (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* 3.8 28.9 - - + -
330E ARG* 5.7 1.6 - - - +
346E LEU* 2.9 26.3 + - + +
347E SER* 3.3 21.8 - - - +
349E LEU* 1.4 73.8 - - + +
351E LYS* 1.4 58.8 + - + +
353E HIS* 3.5 7.6 + - - +
354E ALA* 3.1 30.7 + - - +
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Residues in contact with LYS 351 (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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347E SER* 3.1 19.7 + - - +
348E LYS* 3.9 5.6 - - - +
350E VAL* 1.4 77.3 - - + +
352E LYS* 1.4 61.6 + - + +
354E ALA* 3.5 18.7 - - + +
355E ALA* 3.7 5.0 + - - +
236G ASP* 5.1 4.9 + - - -
238G VAL* 3.9 40.8 - - + +
285G LEU* 5.1 3.8 - - + -
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Residues in contact with LYS 352 (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* 4.1 17.8 + - + +
348E LYS* 3.1 49.8 + - + +
349E LEU* 3.9 5.2 - - - +
351E LYS* 1.4 73.6 - - + +
353E HIS* 1.3 66.7 + - - +
355E ALA* 3.5 14.7 + - - +
284G LYS 3.8 18.7 + - - -
285G LEU* 3.6 35.5 - - + +
286G ASP* 2.9 37.3 + - + +
287G HIS* 6.0 1.0 - - - +
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Residues in contact with HIS 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E TYR* 3.3 43.6 - - + +
323E SER* 5.8 2.7 - - - -
349E LEU* 3.0 18.5 + - + +
350E VAL* 3.8 7.6 - - - +
352E LYS* 1.3 75.7 - - - +
354E ALA* 1.4 68.4 + - - +
355E ALA 3.1 12.8 - - - +
356E GLN* 4.2 6.6 - - - +
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Residues in contact with ALA 354 (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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350E VAL 3.1 18.7 + - - +
351E LYS* 3.5 11.9 - - + +
353E HIS* 1.4 80.7 - - - +
355E ALA* 1.4 59.1 + - - +
356E GLN* 3.4 6.2 + - - +
238G VAL* 6.4 0.2 - - + -
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Residues in contact with ALA 355 (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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351E LYS 3.7 3.1 + - - +
352E LYS 3.5 13.5 - - - +
353E HIS 3.1 10.7 + - - +
354E ALA* 1.4 75.1 - - - +
356E GLN* 1.3 58.2 + - - +
238G VAL* 4.3 29.8 - - + -
285G LEU* 4.5 15.5 - - + -
287G HIS* 4.5 14.0 + - + +
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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