Contacts of the helix formed by residues 327 - 337 (chain F) in PDB entry 6MZL
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 327 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214F TYR* 5.0 1.9 - - - -
217F TYR* 5.1 6.0 - - - -
321F LEU* 3.4 39.8 + - - +
324F LYS* 3.5 39.8 - - + +
325F GLN* 4.1 1.8 - - - -
326F ASN* 1.3 72.1 - - - +
328F GLN* 1.3 62.9 + - - +
329F ILE* 3.1 24.9 + - - +
330F TRP* 3.5 23.3 - - + +
331F ASN* 3.2 24.8 + - - +
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Residues in contact with GLN 328 (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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214F TYR* 3.6 33.4 + - + -
246F HIS* 5.1 7.1 + - - -
247F MET* 4.6 7.9 - - - -
250F GLU* 3.3 38.9 + - - +
326F ASN 3.4 4.9 + - - -
327F ASN* 1.3 70.3 + - - +
329F ILE* 1.3 61.9 + - + +
331F ASN* 3.0 27.4 + - - +
332F ILE* 2.9 36.1 + - + +
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Residues in contact with ILE 329 (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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214F TYR* 5.3 4.0 - - + +
217F TYR* 4.4 19.1 - - + +
218F TYR* 4.5 7.0 - - + +
221F LEU* 3.8 28.3 - - + -
243F LEU* 4.1 22.9 - - + -
247F MET* 5.1 9.9 - - + -
317F LEU* 5.5 1.8 - - + -
321F LEU* 4.1 15.0 - - + -
324F LYS* 3.7 26.2 - - - +
327F ASN* 3.1 13.0 + - - +
328F GLN* 1.3 76.5 - - + +
330F TRP* 1.3 57.8 + - - +
332F ILE* 3.1 13.3 + - + +
333F VAL* 2.9 29.6 + - + +
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Residues in contact with TRP 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F TYR* 3.7 24.2 - + - -
317F LEU* 5.6 0.9 - - + -
318F LYS* 5.0 21.1 - - + -
321F LEU* 3.8 26.7 - - + +
327F ASN* 3.4 32.6 + - + +
328F GLN 3.2 0.4 - - - -
329F ILE* 1.3 79.9 - - - +
331F ASN* 1.3 57.5 + - - +
333F VAL* 3.3 26.5 + - + +
334F GLN* 2.9 62.5 + - + +
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Residues in contact with ASN 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F ASN 5.5 1.4 - - - -
327F ASN 3.2 19.6 + - - +
328F GLN* 3.0 37.3 + - - +
330F TRP* 1.3 74.3 - - - +
332F ILE* 1.3 60.7 + - - +
334F GLN* 3.2 23.2 + - - +
335F GLU* 2.9 40.1 + - - +
336F HIS* 4.2 1.7 - - - -
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Residues in contact with ILE 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F LEU* 3.8 30.1 - - + -
246F HIS* 3.6 34.8 - - + +
247F MET* 4.0 18.2 - - - -
305F PHE* 3.6 32.8 - - + -
328F GLN* 2.9 25.7 + - + +
329F ILE* 3.1 10.1 + - - +
331F ASN* 1.3 72.8 - - - +
333F VAL* 1.3 60.8 + - + +
336F HIS* 2.9 45.3 + - + +
337F LEU* 3.8 4.1 + - + +
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Residues in contact with VAL 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F TYR* 4.1 13.7 - - + +
317F LEU* 3.8 23.6 - - + -
321F LEU* 3.9 12.6 - - + -
329F ILE* 2.9 20.4 + - + +
330F TRP* 3.3 38.1 + - + +
332F ILE* 1.3 77.0 - - + +
334F GLN* 1.3 62.1 + - - +
337F LEU* 3.3 42.0 - - + +
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Residues in contact with GLN 334 (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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330F TRP* 2.9 50.4 + - + +
331F ASN* 3.2 25.3 + - - +
332F ILE 3.2 0.4 - - - -
333F VAL* 1.3 80.4 - - + +
335F GLU* 1.3 83.0 + - - +
336F HIS 3.7 0.2 + - - -
337F LEU* 4.8 1.2 + - - +
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Residues in contact with GLU 335 (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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303F SER* 3.7 12.0 - - - -
331F ASN* 2.9 36.1 + - - +
334F GLN* 1.3 94.5 - - - +
336F HIS* 1.3 73.3 + - + +
337F LEU 3.9 0.2 - - - -
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Residues in contact with HIS 336 (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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246F HIS* 3.4 27.8 + + - -
301F ARG 3.4 22.0 + - - -
302F THR* 4.6 2.2 - - - -
303F SER* 3.3 37.9 + - - -
305F PHE* 3.2 35.3 - + + +
331F ASN 4.2 3.8 - - - -
332F ILE* 2.9 39.3 + - + +
335F GLU* 1.3 89.7 + - + +
337F LEU* 1.3 66.5 + - - +
338F TYR 3.6 0.7 + - - -
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Residues in contact with LEU 337 (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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239F LEU* 5.4 6.3 - - + -
303F SER* 5.1 2.6 - - - -
305F PHE* 3.9 17.0 - - + -
307F LEU* 3.7 22.4 - - + -
309F ILE* 5.8 2.9 - - + -
314F TYR* 4.6 12.1 - - + -
317F LEU* 5.1 4.9 - - + -
332F ILE* 4.4 0.4 - - + +
333F VAL* 3.3 55.7 + - + +
334F GLN 4.8 1.8 + - - +
335F GLU 3.9 0.5 - - - -
336F HIS* 1.3 78.4 - - - +
338F TYR* 1.3 60.2 + - - +
339F ILE* 3.9 27.3 - - + +
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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