Contacts of the helix formed by residues 329 - 337 in PDB entry 2IIL
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 ARG 329
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321 GLY 3.2 19.5 + - - +
322 PHE* 3.0 46.7 + - - +
324 ASN 3.5 4.2 + - - +
325 LYS* 3.1 47.7 - - + +
327 PHE 3.2 0.8 - - - -
328 GLN* 1.3 77.3 - - - +
330 ASP* 1.3 67.0 + - - +
333 PHE* 2.9 36.5 - - + +
345 ASP* 5.0 9.3 + - - -
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Residues in contact with ASP 330
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325 LYS* 2.7 31.9 + - - +
326 ASN 3.6 4.3 - - - +
329 ARG* 1.3 76.3 - - - +
331 LEU* 1.3 67.3 + - + +
333 PHE* 3.4 3.7 + - - +
334 PHE 3.0 23.4 + - - -
342 SER* 3.6 15.6 + - - +
344 ASP* 5.2 2.4 - - - +
345 ASP* 3.0 21.7 - - - +
346 ASP* 3.3 16.7 - - - +
347 TYR* 2.8 37.1 + - + +
358 ASP* 5.0 3.4 - - + +
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Residues in contact with LEU 331
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64 ILE* 4.0 2.0 - - - -
68 GLN* 3.5 31.3 + - + +
71 MET* 3.2 30.5 - - + -
326 ASN* 3.1 27.8 + - - +
327 PHE* 2.8 17.1 + - - +
330 ASP* 1.3 70.1 - - - +
332 GLN* 1.3 58.0 + - - +
334 PHE* 3.4 7.5 - - + +
335 PHE* 3.1 23.9 + - - +
358 ASP* 3.5 20.2 - - + +
359 VAL* 2.8 43.3 - - + +
360 SER* 4.8 1.9 + - - +
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Residues in contact with GLN 332
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60 ALA* 5.2 7.0 - - + +
64 ILE* 3.0 41.5 - - + +
327 PHE 3.1 7.5 + - - -
328 GLN* 3.0 33.4 + - + +
330 ASP 3.5 0.2 - - - -
331 LEU* 1.3 72.5 - - - +
333 PHE* 1.3 73.3 + - - +
335 PHE* 2.9 19.1 + - - +
336 ASN* 2.7 56.1 + - - +
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Residues in contact with PHE 333
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328 GLN* 3.6 9.0 - - + -
329 ARG* 2.9 32.9 + - + +
330 ASP* 3.4 3.6 + - - +
332 GLN* 1.3 89.8 - - - +
334 PHE* 1.3 65.1 + - - +
336 ASN* 3.2 11.6 + - - -
337 PHE* 3.0 59.7 + + + -
342 SER* 5.1 8.5 - - - +
344 ASP* 5.3 8.3 - - - +
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Residues in contact with PHE 334
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330 ASP 3.0 9.8 + - - +
331 LEU* 3.4 14.4 - - + +
333 PHE* 1.3 75.5 - - - +
335 PHE* 1.3 57.2 + - + +
337 PHE 2.7 26.2 - - - +
339 ASP* 3.8 23.7 + - + -
340 PHE 2.9 32.8 - - - -
341 ARG* 4.5 0.9 - - - -
342 SER* 3.1 25.8 + - - +
360 SER* 2.8 33.7 - - - +
361 LYS* 3.5 24.0 - - - -
363 SER* 3.7 31.4 - - - -
364 LEU* 4.6 10.3 - - + -
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Residues in contact with PHE 335
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60 ALA* 5.6 6.1 - - + -
63 ILE* 3.3 35.9 - - + -
64 ILE* 4.2 17.9 - - + -
67 LYS* 3.3 44.2 - - + -
68 GLN* 5.3 1.8 - - - +
331 LEU 3.1 10.8 + - - +
332 GLN* 2.9 29.7 + - - +
334 PHE* 1.3 81.0 - - - +
336 ASN* 1.3 67.0 + - - +
338 CYS* 3.7 16.7 + - - -
361 LYS* 4.4 13.9 + - - +
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Residues in contact with ASN 336
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332 GLN* 2.7 39.9 + - - +
333 PHE* 3.2 16.3 + - + +
335 PHE* 1.3 76.3 - - - +
337 PHE* 1.3 71.8 + - + +
338 CYS* 3.0 16.6 + - - -
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Residues in contact with PHE 337
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333 PHE* 3.0 53.8 + + + +
334 PHE 2.7 19.3 - - - +
336 ASN* 1.3 81.0 - - - +
338 CYS* 1.3 53.4 + - - +
340 PHE* 2.8 41.2 + - + +
341 ARG 4.2 13.9 - - - -
342 SER* 5.6 0.9 - - - -
343 ARG 5.9 2.5 - - - -
344 ASP* 6.1 1.1 - - - -
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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
------------------------------------------------------------
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