Contacts of the helix formed by residues 332 - 344 (chain J) in PDB entry 6NIL
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 GLY 332 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330J ILE 3.7 1.6 + - - -
331J MET* 1.3 75.3 - - - +
333J TYR* 1.3 55.1 - - - -
334J LYS* 3.2 3.6 - - - -
335J ASP* 2.7 11.8 + - - +
336J PHE* 2.6 45.6 + - - -
357J LEU* 5.6 0.4 - - - -
361J PHE* 4.4 15.0 - - - -
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Residues in contact with TYR 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332J GLY* 1.3 72.5 - - - -
334J LYS* 1.3 60.8 + - - +
335J ASP 3.5 0.2 + - - -
336J PHE* 4.2 2.6 - - - +
337J LYS* 3.3 37.9 + - + +
351J PHE* 3.7 36.5 - + - -
353J PRO* 4.3 14.0 - - + +
357J LEU* 4.3 23.9 - - + +
358J ASP* 4.3 18.7 + - - +
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Residues in contact with LYS 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332J GLY 3.2 1.0 - - - -
333J TYR* 1.3 79.4 - - - +
335J ASP* 1.3 76.7 + - - +
337J LYS* 3.8 9.2 - - - +
338J TYR* 3.4 28.1 + - - +
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Residues in contact with ASP 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J TYR* 4.1 15.8 + - + -
302J LYS* 3.4 32.5 + - - +
329J GLU* 5.4 0.9 - - - +
330J ILE 5.1 0.7 - - - +
331J MET* 3.4 35.2 - - + +
332J GLY 2.7 17.4 + - - +
334J LYS* 1.3 94.5 - - - +
336J PHE* 1.3 59.2 + - - +
337J LYS 3.3 1.1 - - - -
338J TYR* 3.5 9.3 - - - +
339J CYS* 2.8 23.4 + - - +
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Residues in contact with PHE 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J PHE* 4.1 16.9 - + - -
204J PHE* 3.6 24.9 - - + -
206J ASN* 4.4 20.0 - - - -
304J ALA* 4.0 16.2 - - + -
331J MET* 3.3 49.8 - - + -
332J GLY* 2.6 35.8 + - - +
333J TYR* 4.7 3.4 - - - -
335J ASP* 1.3 71.0 - - - +
337J LYS* 1.3 58.5 + - - +
339J CYS* 3.3 4.2 + - - +
340J TRP* 2.9 25.5 + - - +
351J PHE* 4.2 19.4 - - + -
354J TRP* 4.2 13.7 - + - -
357J LEU* 3.8 22.0 - - + -
361J PHE* 6.2 0.2 - + - -
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Residues in contact with LYS 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333J TYR* 3.3 41.9 + - + +
334J LYS* 3.8 10.1 - - - +
336J PHE* 1.3 76.3 - - - +
338J TYR* 1.3 62.7 + - - +
340J TRP* 3.5 9.4 - - - +
341J GLU* 3.0 56.4 + - - +
351J PHE* 4.1 29.5 - - + -
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Residues in contact with TYR 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221J THR* 3.8 30.7 - - + +
233J TRP* 5.7 1.6 - - - -
235J ARG* 4.9 7.4 + - - -
274J TYR* 3.4 35.4 - + - -
334J LYS* 3.4 25.8 - - - +
335J ASP* 3.2 11.7 + - - +
336J PHE 3.2 0.6 - - - -
337J LYS* 1.3 80.6 - - - +
339J CYS* 1.3 63.2 + - - +
341J GLU* 4.2 13.7 - - - -
342J ASN* 3.0 58.9 + - - +
343J PHE* 4.8 4.0 - + - -
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Residues in contact with CYS 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195J MET* 5.5 0.2 - - - -
200J PHE* 3.6 24.7 - - + -
204J PHE* 4.0 8.1 - - - -
219J CYS* 3.8 30.3 - - - -
274J TYR* 5.2 6.1 - - + -
331J MET* 4.1 13.5 - - + -
335J ASP 2.8 16.3 + - - +
336J PHE* 3.3 6.0 + - - +
338J TYR* 1.3 76.1 - - - +
340J TRP* 1.3 58.7 + - - +
343J PHE* 3.1 39.8 + - + +
344J VAL* 3.4 4.7 - - - +
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Residues in contact with TRP 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197J PRO* 3.7 22.7 - - + -
200J PHE* 3.5 37.9 - + - -
201J TYR* 3.5 22.9 - + - -
336J PHE 2.9 15.9 + - - +
337J LYS* 3.5 6.5 - - - +
338J TYR 3.2 0.6 - - - -
339J CYS* 1.3 79.1 - - - +
341J GLU* 1.3 61.2 + - + +
342J ASN 3.3 1.3 + - - -
344J VAL* 3.4 36.5 + - + +
346J ASN* 3.2 47.2 + - + +
349J GLU* 3.5 27.1 + - - -
350J PRO* 4.6 2.0 - - + -
351J PHE* 3.4 42.8 - + + +
352J LYS* 4.7 2.9 - - + -
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Residues in contact with GLU 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337J LYS* 3.0 41.5 + - - +
338J TYR* 4.1 11.6 - - - +
340J TRP* 1.3 79.3 - - + +
342J ASN* 1.3 78.6 + - - +
344J VAL 5.3 0.9 - - - -
346J ASN* 3.7 15.0 + - - +
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Residues in contact with ASN 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J GLU* 4.9 3.5 - - - +
194J ALA* 5.6 0.7 - - - +
235J ARG* 3.6 36.4 - - - +
338J TYR* 3.0 53.1 + - + +
340J TRP 3.3 0.2 - - - -
341J GLU* 1.3 94.0 + - - +
343J PHE* 1.3 80.8 + - + +
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Residues in contact with PHE 343 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193J GLU 4.5 3.6 - - - -
194J ALA* 3.3 13.1 - - - -
195J MET* 3.0 30.5 + - + +
219J CYS* 3.7 17.7 - - + -
220J PHE 3.2 27.4 - - - -
221J THR* 3.5 14.1 - - - -
235J ARG* 3.6 20.6 - - + -
236J GLY 3.5 13.9 - - - -
237J VAL* 3.6 26.2 - - + -
274J TYR* 4.6 9.6 - + - -
338J TYR* 4.4 4.5 - + - -
339J CYS* 3.1 42.7 + - - +
342J ASN* 1.3 89.3 - - + +
344J VAL* 1.3 62.5 + - + +
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Residues in contact with VAL 344 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194J ALA* 5.0 1.6 - - - -
195J MET* 3.3 13.0 - - + +
197J PRO* 3.8 20.0 - - + -
200J PHE* 3.7 27.1 - - + -
339J CYS 3.4 18.2 - - - +
340J TRP* 3.4 46.5 + - + +
341J GLU* 5.5 0.7 - - - -
342J ASN 3.9 0.4 + - - -
343J PHE* 1.3 83.7 - - + +
345J TYR* 1.3 67.7 + - - +
346J ASN* 2.8 20.2 + - - +
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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