Contacts of the helix formed by residues 361 - 378 (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 361 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A SER* 5.1 6.3 + - - -
324A LEU* 3.7 33.0 + - + +
360A LEU* 1.3 81.2 + - - +
362A SER* 1.3 62.8 + - - +
363A LYS* 2.7 37.2 + - - +
364A LEU* 3.0 25.9 + - + +
365A GLU* 3.2 25.3 + - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.3 3.8 + - - +
361A ASN* 1.3 74.2 + - - +
363A LYS* 1.3 65.6 + - - +
365A GLU* 3.5 9.1 + - - +
366A LEU* 3.3 21.8 + - - +
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Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 4.0 16.4 - - + +
325A ASN* 3.3 26.3 - - + +
326A ASP* 3.5 28.3 - - + +
329A LEU* 4.1 4.4 - - - +
361A ASN* 2.7 18.9 + - - +
362A SER* 1.3 75.0 + - - +
364A LEU* 1.3 60.9 + - - +
366A LEU* 3.6 19.6 + - + +
367A PHE* 3.4 20.3 + - - +
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Residues in contact with LEU 364 (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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324A LEU* 4.0 13.6 - - + +
329A LEU* 4.2 15.0 - - + -
351A LEU* 4.7 6.1 - - + -
354A LEU* 3.2 55.2 - - + +
355A TYR* 3.5 35.9 - - + +
359A GLU* 6.4 0.2 - - + -
361A ASN* 3.0 30.1 + - + +
362A SER 3.3 0.4 - - - -
363A LYS* 1.3 78.4 - - - +
365A GLU* 1.3 58.3 + - + +
367A PHE* 3.4 4.2 + - + +
368A THR* 3.0 34.2 + - - +
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Residues in contact with GLU 365 (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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355A TYR* 5.2 7.4 - - + +
360A LEU* 3.3 29.1 - - + +
361A ASN 3.2 12.2 + - - +
362A SER* 4.0 8.3 - - - +
364A LEU* 1.3 76.6 - - + +
366A LEU* 1.3 61.1 + - - +
368A THR* 4.0 6.1 - - - -
369A SER* 3.0 29.5 + - - -
400A SER* 3.8 16.7 - - - +
401A SER* 2.9 27.4 + - - +
403A GLU* 4.5 10.3 - - - +
404A VAL* 4.8 10.5 - - + +
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Residues in contact with LEU 366 (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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362A SER 3.3 16.0 + - - +
363A LYS* 3.8 22.9 - - + +
364A LEU 3.2 0.4 - - - -
365A GLU* 1.3 76.4 - - - +
367A PHE* 1.3 63.2 + - - +
369A SER* 2.7 24.0 + - - +
370A ARG* 3.0 17.0 + - + +
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Residues in contact with PHE 367 (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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326A ASP* 4.7 8.5 - - + +
329A LEU* 3.4 63.0 - - + -
330A LYS* 4.9 0.2 - - - -
332A VAL* 4.7 1.8 - - + -
333A GLY* 3.9 14.6 - - - -
336A MSE 4.9 1.8 - - - -
351A LEU* 3.7 39.9 - - + -
363A LYS 3.4 4.1 + - - +
364A LEU* 3.4 6.5 + - + +
366A LEU* 1.3 80.6 - - - +
368A THR* 1.3 67.9 + - - +
370A ARG* 3.0 11.8 + - - +
371A PHE* 2.9 66.7 + + + -
375A ILE* 5.7 1.1 - - + -
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Residues in contact with THR 368 (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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351A LEU* 5.8 2.6 - - - +
355A TYR* 2.5 32.3 + - - +
364A LEU* 3.0 15.2 + - - +
365A GLU* 4.0 6.3 - - - -
367A PHE* 1.3 84.9 - - - +
369A SER* 1.3 56.8 + - - +
371A PHE* 3.4 2.2 - - - +
372A LYS* 2.7 36.2 + - + +
375A ILE* 4.7 13.7 - - + -
393A LEU* 6.1 0.2 - - + -
397A VAL* 4.0 27.8 - - + -
404A VAL* 4.9 9.2 - - + -
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Residues in contact with SER 369 (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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365A GLU 3.0 17.3 + - - -
366A LEU* 2.7 27.9 + - - +
368A THR* 1.3 77.1 - - - +
370A ARG* 1.3 58.8 + - - +
371A PHE 3.7 0.3 + - - -
372A LYS* 4.0 9.0 + - - +
373A ASP 5.4 0.2 + - - -
404A VAL* 3.8 27.7 - - - +
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Residues in contact with ARG 370 (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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326A ASP* 6.0 2.7 - - - -
366A LEU* 3.0 20.5 + - - +
367A PHE* 3.3 11.9 - - - +
368A THR 3.0 0.8 - - - -
369A SER* 1.3 80.6 - - - +
371A PHE* 1.3 77.4 + - + +
372A LYS 3.6 0.4 - - - -
373A ASP* 5.5 0.3 + - - +
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Residues in contact with PHE 371 (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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326A ASP* 5.9 1.1 - - - -
330A LYS* 5.3 3.8 - - - -
333A GLY* 3.6 27.1 - - - -
334A TRP* 4.7 10.1 - + - -
336A MSE 3.4 28.7 - - + -
337A HIS* 4.0 13.5 - + - -
367A PHE* 2.9 60.2 + + + +
368A THR 3.4 2.9 - - - +
370A ARG* 1.3 95.7 - - + +
372A LYS* 1.3 65.1 + - - +
373A ASP* 3.4 3.1 - - - +
374A ARG* 3.5 9.0 + - + +
375A ILE* 3.1 26.7 + - + +
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Residues in contact with LYS 372 (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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368A THR* 2.7 22.2 + - + +
369A SER 4.0 8.2 + - - +
370A ARG 3.6 1.6 - - - -
371A PHE* 1.3 73.6 - - - +
373A ASP* 1.3 97.2 + - - +
375A ILE* 3.0 17.9 + - - +
376A VAL* 3.0 27.4 + - + +
394A LEU* 5.4 2.7 - - + -
404A VAL* 3.4 39.6 + - + +
405A LEU* 4.3 9.9 - - + -
406A THR* 4.2 11.9 - - - +
409A ASP* 2.9 32.7 + - - +
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Residues in contact with ASP 373 (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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370A ARG 5.5 0.6 + - - +
371A PHE 3.4 0.8 - - - -
372A LYS* 1.3 105.0 + - - +
374A ARG* 1.3 63.4 + - - +
376A VAL* 3.5 10.2 + - - +
377A SER* 3.3 21.8 + - - -
409A ASP* 4.5 2.8 - - - +
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Residues in contact with ARG 374 (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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336A MSE 3.1 45.9 + - + -
337A HIS* 3.4 40.6 - - + +
338A ASP 5.2 0.2 + - - -
344A ARG* 3.6 19.2 - - - +
371A PHE* 3.5 12.6 + - + +
372A LYS 3.3 0.4 - - - -
373A ASP* 1.3 80.1 - - - +
375A ILE* 1.3 59.4 + - - +
377A SER* 2.7 40.1 + - - -
378A MSE 3.3 32.2 + - + +
381A ASP* 4.5 2.6 + - - +
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Residues in contact with ILE 375 (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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336A MSE 4.2 22.7 - - - -
348A LEU* 4.8 3.4 - - + -
351A LEU* 4.6 6.1 - - + -
367A PHE* 5.7 0.7 - - + -
368A THR* 4.7 17.7 - - + +
371A PHE* 3.1 25.0 + - + +
372A LYS* 3.0 12.3 + - - +
374A ARG* 1.3 74.7 - - - +
376A VAL* 1.3 60.5 + - - +
377A SER 3.1 1.3 - - - -
378A MSE 2.9 29.5 + - + +
379A THR* 3.6 4.2 + - - +
390A ALA* 4.0 13.2 - - + +
393A LEU* 3.6 29.2 - - + -
394A LEU* 3.5 33.4 - - + -
397A VAL* 5.7 0.7 - - + -
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Residues in contact with VAL 376 (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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372A LYS* 3.0 20.5 + - + +
373A ASP* 3.6 12.3 - - - +
375A ILE* 1.3 76.3 - - - +
377A SER* 1.3 61.4 + - - +
379A THR* 2.5 37.6 + - + -
394A LEU* 4.0 22.7 - - + -
405A LEU* 5.0 1.1 - - + -
409A ASP* 4.1 41.5 - - + +
412A ASN* 4.8 18.3 - - + +
413A VAL* 5.4 1.8 - - + -
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP 3.3 10.4 + - - -
374A ARG* 2.7 44.3 + - - -
376A VAL* 1.3 84.6 - - - +
378A MSE 1.3 55.9 + - - +
379A THR 3.1 0.9 - - - -
380A LEU* 3.2 25.8 + - - +
381A ASP* 3.9 0.5 + - - -
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Residues in contact with MSE 378 (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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336A MSE 3.7 37.9 - - + +
344A ARG* 4.8 4.7 - - - +
348A LEU* 4.0 27.8 - - + -
374A ARG* 3.3 65.7 - - + +
375A ILE* 2.9 16.2 + - - +
377A SER* 1.3 78.4 + - - +
379A THR* 1.3 54.7 + - - +
380A LEU 2.9 5.8 - - - -
381A ASP* 3.0 34.2 + - + +
386A VAL* 4.2 7.4 - - + +
387A ALA* 3.3 12.0 - - - -
390A ALA* 3.6 11.8 - - + +
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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