Contacts of the helix formed by residues 325 - 336 (chain A) in PDB entry 4PJW
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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316A MSE 3.8 0.7 - - - +
321A ASP 5.0 2.3 - - - +
322A ALA 3.4 22.5 - - - +
323A PHE 3.0 6.0 + - - -
324A LEU* 1.3 75.9 + - - +
326A ASP* 1.3 67.4 + - - +
327A SER* 3.0 34.3 + - - +
328A TYR* 3.2 15.2 + - - -
329A LEU* 2.9 26.4 + - - +
363A LYS* 3.3 25.4 - - + +
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASN* 1.3 75.9 - - - +
327A SER* 1.3 57.8 + - - +
329A LEU* 3.6 10.8 - - - +
330A LYS* 2.9 52.9 + - - +
363A LYS* 3.5 24.0 - - + +
367A PHE* 4.7 8.5 - - + +
370A ARG* 6.0 3.0 - - - -
371A PHE* 5.9 1.0 - - - -
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Residues in contact with SER 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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289A PHE* 5.0 1.6 - - - -
325A ASN* 3.0 20.5 + - - +
326A ASP* 1.3 77.6 - - - +
328A TYR* 1.3 73.5 + - - +
330A LYS* 3.5 17.5 + - - +
331A TYR* 3.3 21.0 - - - -
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Residues in contact with TYR 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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227A MSE 5.2 1.2 - - - +
286A ASN* 5.7 2.4 + - - -
289A PHE* 3.6 45.1 - + - -
312A ILE* 3.3 31.9 - - + +
315A TRP* 4.9 0.9 - + - -
316A MSE 3.9 8.9 - - + +
322A ALA 4.2 8.7 - - - -
323A PHE* 3.3 63.3 - + - +
325A ASN* 3.2 14.8 + - - -
327A SER* 1.3 101.2 + - - +
329A LEU* 1.3 64.2 + - - +
330A LYS 3.2 2.0 + - - -
331A TYR* 3.6 12.0 + - - +
332A VAL* 4.2 2.4 + - - +
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Residues in contact with LEU 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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316A MSE 3.3 31.1 - - + +
324A LEU* 4.0 18.6 - - + -
325A ASN 2.9 19.7 + - - +
326A ASP* 4.0 6.7 - - - +
328A TYR* 1.3 77.1 - - - +
330A LYS* 1.3 63.8 + - - +
332A VAL* 3.1 9.3 + - + +
333A GLY 2.9 17.0 + - - -
351A LEU* 4.1 25.8 - - + -
354A LEU* 4.2 3.8 - - + -
363A LYS* 4.1 11.4 - - + +
364A LEU* 4.2 4.7 - - + -
367A PHE* 3.4 48.3 - - + -
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP* 2.9 36.1 + - - +
327A SER* 3.5 15.7 + - - +
329A LEU* 1.3 77.2 - - - +
331A TYR* 1.3 94.8 + - + +
333A GLY* 3.1 3.2 + - - +
334A TRP* 2.9 73.7 + - + +
367A PHE* 4.9 2.5 - - - -
371A PHE* 5.6 3.4 - - - -
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Residues in contact with TYR 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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289A PHE* 3.9 20.3 - + - -
293A PHE* 3.8 31.2 - + + -
294A VAL* 3.6 21.9 - - + +
297A TYR* 3.8 32.3 - + + -
309A ILE* 4.3 4.3 - - + -
312A ILE* 4.3 4.0 - - + -
327A SER 3.3 23.3 - - - -
328A TYR* 3.7 17.7 - - - +
329A LEU 3.2 0.2 - - - -
330A LYS* 1.3 99.0 + - + +
332A VAL* 1.3 52.8 + - - +
334A TRP* 3.4 20.6 + + - +
335A THR* 2.6 38.1 + - - -
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Residues in contact with VAL 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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309A ILE* 3.9 16.8 - - + -
312A ILE* 3.7 29.4 - - + -
313A GLY 5.3 0.2 - - - +
316A MSE 5.0 8.3 - - - -
328A TYR 4.7 4.7 - - - +
329A LEU* 3.1 11.6 + - + +
331A TYR* 1.3 74.5 - - - +
333A GLY* 1.3 65.0 + - - +
335A THR* 3.9 1.5 - - - -
336A MSE 3.2 23.6 + - + +
347A CYS* 3.8 31.4 - - + +
350A ALA* 4.8 9.9 - - + -
351A LEU* 4.0 25.1 - - + -
367A PHE* 4.7 1.1 - - + -
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Residues in contact with GLY 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 LEU 2.9 13.7 + - - -
330A LYS 3.1 4.9 + - - -
332A VAL* 1.3 76.9 - - - +
334A TRP* 1.3 63.9 + - - +
336A MSE 3.5 8.5 - - - +
337A HIS* 3.1 22.3 + - - -
367A PHE* 3.9 11.9 - - - -
371A PHE* 3.6 28.1 - - - -
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Residues in contact with TRP 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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297A TYR* 3.4 27.6 - - + +
330A LYS* 2.9 58.3 + - + +
331A TYR* 3.8 26.7 - + - +
333A GLY* 1.3 77.7 - - - +
335A THR* 1.3 60.1 + - - +
336A MSE 3.1 0.2 - - - -
337A HIS* 2.9 34.7 + + - +
338A ASP 4.1 0.2 + - - -
371A PHE* 4.9 9.9 - + - -
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Residues in contact with THR 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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297A TYR* 3.7 24.2 - - + +
305A ARG* 5.4 0.7 - - + +
309A ILE* 3.7 20.9 - - + +
331A TYR 2.6 22.7 + - - -
334A TRP* 1.3 71.3 - - - +
336A MSE 1.3 60.5 + - - +
337A HIS 3.0 5.8 - - - -
338A ASP* 3.0 24.9 + - + +
343A VAL* 3.1 31.4 - - + +
344A ARG* 4.2 2.4 - - - +
347A CYS* 3.4 19.5 - - - -
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Residues in contact with MSE 336 (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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332A VAL* 3.2 19.2 + - + +
333A GLY* 3.5 11.0 - - - +
334A TRP 3.0 0.2 + - - -
335A THR* 1.3 77.2 - - - +
337A HIS* 1.3 58.3 + - + +
338A ASP 3.3 0.7 - - - -
344A ARG* 3.3 14.6 - - - +
347A CYS* 3.8 19.7 - - + -
348A LEU* 4.8 4.9 - - + -
351A LEU* 4.2 17.9 - - + -
367A PHE* 4.9 1.3 - - - -
371A PHE* 3.4 42.4 - - + +
374A ARG* 3.1 45.8 + - + -
375A ILE* 4.2 13.2 - - - -
378A MSE 3.7 23.6 - - + +
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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