Contacts of the helix formed by residues 325 - 335 (chain A) in PDB entry 1F9O
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 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ASP 5.0 0.8 + - - -
233A ALA* 3.6 43.2 + - + +
234A ARG* 3.8 3.0 - - - +
237A GLN* 3.2 21.4 + - - +
296A LEU* 3.5 6.7 - - + +
323A TYR 4.5 1.3 - - - +
324A GLN* 1.3 75.0 - - - +
326A PRO* 1.3 63.5 - - - +
327A PHE* 3.2 9.5 + - - +
328A ALA* 3.2 26.0 + - + +
329A ALA 3.3 8.5 + - - -
349A TRP* 5.1 0.5 - - - -
356A GLN* 2.8 14.7 + - - +
421A ARG* 3.5 26.9 - - - +
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Residues in contact with PRO 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ASN* 1.3 86.9 - - - +
327A PHE* 1.3 57.7 + - - +
329A ALA* 3.5 1.6 + - + -
330A TRP* 3.0 23.2 + - - +
353A LEU* 3.3 22.9 - - + +
356A GLN* 3.2 13.4 - - + +
357A LEU* 4.4 10.5 - - + -
360A TYR* 3.4 40.4 - - + +
421A ARG* 3.9 12.1 - - + +
422A VAL* 4.1 9.6 - - + -
425A LEU* 3.9 24.6 - - + +
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Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 3.6 24.9 - - + -
240A TYR* 3.6 28.7 - + - -
241A TRP* 3.5 39.7 - + - -
325A ASN* 3.1 9.7 + - - +
326A PRO* 1.3 76.8 - - - +
328A ALA* 1.3 65.8 + - - +
329A ALA 3.1 1.3 - - - -
330A TRP* 3.0 27.3 + + - +
331A VAL* 2.9 35.7 + - + +
421A ARG* 3.9 15.5 + - + +
424A GLU* 3.6 38.6 - - + +
425A LEU* 3.8 8.3 - - - +
428A LYS* 4.2 5.8 - - + -
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA* 3.7 30.7 - - + +
236A VAL* 4.4 11.9 - - + -
237A GLN* 4.7 2.5 - - + +
325A ASN* 3.2 22.4 + - + +
327A PHE* 1.3 81.1 - - - +
329A ALA* 1.3 57.5 + - - +
331A VAL* 3.4 8.0 + - - +
332A LEU* 3.0 38.9 + - + +
349A TRP* 4.8 5.2 - - + -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A ASN 3.3 2.6 + - - +
326A PRO 3.7 9.0 - - - +
327A PHE 3.1 0.6 - - - -
328A ALA* 1.3 78.5 - - - +
330A TRP* 1.3 63.0 + - - +
332A LEU 4.1 0.3 - - - -
333A SER* 2.7 30.2 + - - -
349A TRP* 3.5 43.0 - - + +
353A LEU* 4.0 13.0 - - + -
356A GLN* 3.9 19.5 - - - +
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Residues in contact with TRP 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A TYR* 3.8 35.4 - + - -
326A PRO 3.0 13.8 + - - +
327A PHE* 3.0 27.5 + + - +
329A ALA* 1.3 77.1 - - - +
331A VAL* 1.3 83.9 + - + +
333A SER* 3.9 3.4 - - - -
334A THR* 2.8 59.9 + - + +
335A ASP* 5.5 4.0 - - + -
353A LEU* 4.2 16.6 - - + +
425A LEU* 3.8 16.4 - - + -
428A LYS* 4.4 17.5 - - + -
429A THR* 3.5 29.9 - - + +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 4.4 7.9 - - + -
237A GLN* 5.6 0.4 - - - -
240A TYR* 3.8 24.7 - - + -
327A PHE* 2.9 44.7 + - + +
328A ALA* 3.5 9.6 - - - +
330A TRP* 1.3 88.4 - - + +
332A LEU* 1.3 59.7 + - - +
335A ASP* 3.0 38.9 + - + +
338A PHE* 3.6 37.1 - - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 3.9 25.4 - - + -
261A THR* 4.4 15.9 - - - -
264A GLY* 3.8 17.9 - - - -
267A LEU* 5.6 0.4 - - + -
328A ALA* 3.0 20.5 + - + +
331A VAL* 1.3 78.9 - - - +
333A SER* 1.3 58.6 + - - +
335A ASP 4.9 0.2 - - - -
338A PHE* 3.4 32.1 - - + +
339A LYS* 4.3 3.0 - - - -
340A PRO* 3.4 30.4 - - + +
346A ALA* 3.7 7.4 - - - +
349A TRP* 3.7 46.7 - - + +
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A ALA 2.7 23.1 + - - -
330A TRP* 3.5 5.4 + - - -
331A VAL 3.1 0.4 - - - -
332A LEU* 1.3 78.3 - - - +
334A THR* 1.3 71.9 + - - +
335A ASP 3.9 0.4 - - - -
346A ALA* 3.1 32.4 - - - +
349A TRP 3.9 1.3 - - - -
350A ALA* 3.7 25.3 - - - +
353A LEU* 4.7 4.2 - - - +
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Residues in contact with THR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A TRP* 2.8 56.6 + - + +
333A SER* 1.3 90.3 - - - +
335A ASP* 1.3 65.7 + - - +
336A ALA 3.6 2.8 + - - -
353A LEU* 5.6 2.7 - - + -
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Residues in contact with ASP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A TYR* 3.6 21.8 + - + -
243A ASP* 5.4 0.9 - - - +
244A GLN* 4.8 4.7 + - - -
330A TRP* 5.5 4.3 - - + -
331A VAL* 3.0 23.3 + - + +
332A LEU 5.1 0.7 - - - +
333A SER 3.9 0.2 - - - -
334A THR* 1.3 79.5 + - - +
336A ALA* 1.3 66.8 + - - +
337A ASN* 2.9 45.9 + - - +
338A PHE* 2.9 29.1 + - + +
339A LYS* 3.1 11.0 + - - -
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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