Contacts of the helix formed by residues 339 - 353 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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702A ASP 3.8 11.5 - - - +
703A THR 3.1 28.9 + - - +
705A MET* 3.9 6.9 - - - +
333F LEU* 4.1 0.7 - - - +
336F GLU* 3.2 38.9 + - + +
337F PRO 3.4 1.8 - - - -
338F SER* 1.4 74.7 + - - +
340F LYS* 1.3 62.0 + - - +
341F THR* 3.1 14.2 + - - -
342F ILE* 3.0 43.3 + - + +
343F HIS* 3.2 24.4 + - - -
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Residues in contact with LYS 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F SER 4.0 9.9 - - - +
339F ASN* 1.3 69.1 + - - +
341F THR* 1.3 59.8 + - - +
343F HIS* 3.4 11.4 + - + +
344F ALA* 3.0 30.9 + - - +
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Residues in contact with THR 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A THR 5.4 1.9 + - - -
705A MET* 4.0 20.6 + - + -
706A GLU* 4.8 6.5 - - - +
310F PHE* 3.7 23.3 - - + -
339F ASN* 3.1 11.5 + - - -
340F LYS* 1.3 78.6 - - - +
342F ILE* 1.3 56.1 + - - +
344F ALA* 3.5 7.1 + - - +
345F GLU* 3.1 28.3 + - - +
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Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A MET* 4.0 7.6 - - + -
306F ILE* 3.7 19.1 - - + -
310F PHE* 4.0 26.7 - - + -
329F LEU* 3.4 29.4 - - + +
332F ALA* 3.6 27.6 - - + +
333F LEU* 3.8 20.4 - - + +
336F GLU 4.2 3.8 - - - +
339F ASN* 3.0 31.2 + - + +
341F THR* 1.3 72.0 - - - +
343F HIS* 1.4 60.2 + - - +
345F GLU* 3.4 2.1 + - - +
346F LEU* 3.0 29.8 + - + +
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Residues in contact with HIS 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333F LEU* 3.7 25.0 - - + +
337F PRO 2.7 26.9 + - - -
338F SER* 4.3 4.8 - - - -
339F ASN 3.2 26.7 + - - -
340F LYS* 3.6 13.0 - - + +
341F THR 3.3 0.2 - - - -
342F ILE* 1.4 76.6 - - - +
344F ALA* 1.4 52.0 + - - +
346F LEU* 3.1 7.6 + - - +
347F SER* 2.8 41.5 + - - +
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Residues in contact with ALA 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F LYS 3.0 18.2 + - - +
341F THR* 3.7 7.9 - - - +
343F HIS* 1.4 74.7 - - - +
345F GLU* 1.3 57.8 + - - +
347F SER* 4.1 6.3 - - - -
348F LYS* 3.2 33.8 + - - +
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Residues in contact with GLU 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F PHE* 3.6 24.5 - - + -
314F LYS* 3.4 45.5 + - + +
317F ALA* 4.6 8.8 - - - +
318F GLN* 4.9 3.3 + - - +
329F LEU* 3.9 21.7 - - + +
341F THR* 3.1 19.0 + - - +
342F ILE* 3.7 4.3 - - - +
343F HIS 3.2 0.2 - - - -
344F ALA* 1.3 75.0 - - - +
346F LEU* 1.4 62.1 + - - +
348F LYS* 3.6 20.5 + - - +
349F LEU* 3.2 23.6 + - - +
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F ILE* 3.9 29.4 - - + -
329F LEU* 3.8 39.5 - - + +
330F ARG* 4.2 15.3 - - + +
333F LEU* 3.9 26.7 - - + -
342F ILE* 3.0 21.2 + - + +
343F HIS* 3.1 5.4 + - - +
345F GLU* 1.4 73.5 - - - +
347F SER* 1.3 55.8 + - - +
349F LEU* 3.2 12.8 + - + +
350F VAL* 2.9 42.7 + - + +
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Residues in contact with SER 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F HIS* 2.8 24.7 + - - +
344F ALA* 4.1 6.1 - - - -
346F LEU* 1.3 73.3 - - - +
348F LYS* 1.4 55.3 + - - +
350F VAL* 3.3 12.1 - - - +
351F LYS* 3.1 35.6 + - - +
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Residues in contact with LYS 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344F ALA* 3.2 23.0 + - - +
345F GLU* 3.7 22.3 + - - +
347F SER* 1.4 76.8 - - - +
349F LEU* 1.3 58.5 + - - +
351F LYS* 3.9 4.4 - - - +
352F LYS* 3.1 64.6 + - - +
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Residues in contact with LEU 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F ALA* 4.0 20.0 - - + -
322F TYR* 3.5 49.6 - - + +
325F ALA* 4.1 4.0 - - + -
326F ILE* 4.0 23.3 - - + +
329F LEU* 3.8 24.5 - - + -
345F GLU* 3.2 13.5 + - - +
346F LEU* 3.4 22.9 - - + +
348F LYS* 1.3 77.5 - - - +
350F VAL* 1.4 59.1 + - + +
352F LYS* 3.5 7.1 + - - +
353F HIS* 3.1 30.7 + - + +
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Residues in contact with VAL 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F ILE* 3.8 29.2 - - + -
330F ARG* 5.7 1.3 - - - +
346F LEU* 2.9 26.3 + - + +
347F SER* 3.3 20.9 - - - +
349F LEU* 1.4 75.0 - - + +
351F LYS* 1.4 63.9 + - + +
353F HIS* 3.3 27.4 + - + +
354F ALA* 4.9 1.2 - - - +
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Residues in contact with LYS 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347F SER* 3.1 22.4 + - - +
348F LYS* 3.9 5.6 - - - +
350F VAL* 1.4 77.8 - - + +
352F LYS* 1.4 61.3 + - + +
354F ALA* 3.4 20.4 - - - +
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Residues in contact with LYS 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322F TYR* 4.1 27.7 + - + +
348F LYS* 3.1 50.4 + - + +
349F LEU* 3.9 6.7 - - - +
351F LYS* 1.4 71.1 - - + +
353F HIS* 1.3 50.7 + - - +
354F ALA* 2.8 17.9 + - - -
355F ALA* 4.2 9.9 + - - +
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Residues in contact with HIS 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F TYR* 3.4 52.5 - + + +
323F SER* 4.4 7.0 + - - -
326F ILE* 6.0 6.9 - - + +
349F LEU* 3.1 16.2 + - + +
350F VAL* 3.3 21.0 - - + +
351F LYS 3.3 0.8 - - - -
352F LYS* 1.3 70.6 - - - +
354F ALA* 1.4 56.9 + - - +
355F ALA 3.9 2.0 - - - -
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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