Contacts of the helix formed by residues 347 - 365 (chain A) in PDB entry 4WPN
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 ASP 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A GLN* 3.2 31.0 + - + +
345A GLN* 3.4 2.2 + - - +
346A ILE* 1.3 88.7 - - + +
348A LYS* 1.3 59.4 + - - +
349A GLU* 4.0 10.6 - - - +
350A GLN* 3.2 27.2 + - - +
351A TYR* 2.9 25.6 + - - +
380A TYR* 3.6 19.7 - - + +
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Residues in contact with LYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASP* 1.3 73.5 - - - +
349A GLU* 1.3 56.0 + - - +
351A TYR* 3.4 3.3 - - + +
352A ASP* 2.7 48.9 + - - +
380A TYR* 3.6 32.6 + - + +
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASP* 3.4 11.2 + - - +
348A LYS* 1.3 78.1 - - - +
350A GLN* 1.3 63.7 + - - +
352A ASP* 3.2 8.0 + - - +
353A LYS* 2.9 29.4 + - - +
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Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 3.9 17.0 + - + +
301A GLN* 5.1 2.0 - - - +
345A GLN* 4.9 3.8 - - + -
346A ILE* 3.6 21.5 - - + -
347A ASP* 3.2 21.9 + - - +
349A GLU* 1.3 81.0 - - + +
351A TYR* 1.3 65.6 + - - +
353A LYS* 3.4 16.4 + - - +
354A ILE* 3.0 37.1 + - + +
401A ILE 4.7 2.8 + - - -
402A PHE* 3.9 34.8 + - - +
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Residues in contact with TYR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLN* 4.6 3.3 - - + +
347A ASP 2.9 18.6 + - - +
348A LYS* 3.4 8.3 - - + +
350A GLN* 1.3 76.9 - - - +
352A ASP* 1.3 76.2 + - - +
354A ILE* 3.7 9.3 - - - +
355A LEU* 3.1 51.3 + - + +
374A PRO* 3.4 22.3 - - + +
379A GLY 4.9 1.6 - - - -
380A TYR* 3.8 41.7 - + + -
381A PHE 3.7 20.2 - - - -
382A VAL* 4.1 9.1 - - + +
602A CL 4.5 7.0 - - + -
604A CL 3.5 27.1 - - + +
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LYS* 2.7 36.7 + - - +
349A GLU* 3.2 7.5 + - - +
351A TYR* 1.3 83.2 - - - +
353A LYS* 1.3 60.9 + - - +
355A LEU* 3.3 6.1 + - - +
356A ASP* 2.8 31.7 + - - +
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Residues in contact with LYS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLU 2.9 16.8 + - - +
350A GLN* 3.7 18.1 - - - +
352A ASP* 1.3 76.0 - - - +
354A ILE* 1.3 56.0 + - + +
356A ASP* 3.4 8.0 - - + +
357A LEU* 2.9 42.7 + - + +
399A GLU* 5.5 4.0 - - - -
400A GLU* 2.5 31.7 + - - +
401A ILE 3.2 18.4 + - - +
402A PHE* 4.8 2.8 - - - +
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Residues in contact with ILE 354 (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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345A GLN* 3.4 41.1 - - + +
350A GLN* 3.0 28.7 + - + +
351A TYR* 3.7 4.9 - - - +
352A ASP 3.2 0.2 - - - -
353A LYS* 1.3 74.3 - - - +
355A LEU* 1.3 59.3 + - - +
357A LEU* 3.2 3.5 + - - +
358A ILE* 2.9 45.7 + - + +
382A VAL* 4.1 17.3 - - + -
401A ILE* 3.6 27.3 - - + +
402A PHE 3.6 10.5 - - - +
403A GLY* 3.7 7.9 - - - -
405A VAL* 4.2 13.5 - - + -
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Residues in contact with LEU 355 (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 TYR* 3.1 54.9 + - + +
352A ASP* 3.8 5.2 - - - +
354A ILE* 1.3 72.8 - - - +
356A ASP* 1.3 67.1 + - - +
358A ILE* 3.3 19.1 + - + +
359A GLU* 3.1 28.1 + - + +
372A GLY 5.5 0.7 - - - +
373A GLY* 4.5 4.3 - - - -
374A PRO* 4.4 25.6 - - + -
382A VAL* 4.1 22.7 - - + -
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ASP 2.8 17.9 + - - +
353A LYS* 3.4 9.8 - - + +
355A LEU* 1.3 75.9 - - - +
357A LEU* 1.3 61.6 + - - +
359A GLU* 3.1 18.5 + - - +
360A SER* 3.2 10.9 + - - -
395A ARG* 2.9 37.5 + - - -
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Residues in contact with LEU 357 (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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353A LYS* 2.9 52.5 + - + +
354A ILE* 3.2 5.1 + - - +
356A ASP* 1.3 73.7 - - - +
358A ILE* 1.3 64.4 + - - +
360A SER* 2.6 23.3 + - - +
361A GLY 3.2 0.5 + - - -
395A ARG* 3.9 45.3 - - + +
396A ILE* 3.1 18.8 - - + +
399A GLU* 3.6 27.6 - - + +
400A GLU 4.0 7.2 - - - +
401A ILE* 4.0 23.8 - - + -
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Residues in contact with ILE 358 (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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354A ILE* 2.9 24.1 + - + +
355A LEU* 3.3 15.7 + - + +
357A LEU* 1.3 74.8 - - + +
359A GLU* 1.3 66.1 + - - +
361A GLY 3.4 1.0 + - - -
362A LYS* 3.3 23.5 + - - +
372A GLY* 3.7 34.1 - - - +
382A VAL* 3.8 29.4 - - + -
385A THR* 4.0 9.9 - - + +
387A PHE* 3.6 18.7 - - + -
396A ILE* 5.0 0.7 - - - -
405A VAL* 3.8 32.8 - - + -
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LEU* 3.1 17.7 + - + +
356A ASP* 3.1 12.6 + - - +
358A ILE* 1.3 78.2 - - - +
360A SER* 1.3 59.6 + - - +
362A LYS* 3.3 35.2 + - - +
363A LYS* 2.9 39.8 + - + +
372A GLY 4.2 4.7 - - - +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP 3.2 3.6 + - - -
357A LEU* 2.6 24.3 + - - -
359A GLU* 1.3 78.2 - - - +
361A GLY* 1.3 53.8 + - - +
363A LYS* 4.3 11.4 - - - +
364A GLU* 2.6 46.4 + - - +
395A ARG* 3.5 51.6 - - - +
396A ILE* 3.8 2.8 + - - +
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Residues in contact with GLY 361 (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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357A LEU 3.2 4.6 + - - -
358A ILE 3.4 4.9 + - - -
359A GLU 3.2 0.8 - - - -
360A SER* 1.3 82.7 + - - +
362A LYS* 1.3 63.4 + - - +
364A GLU* 3.8 2.9 - - - +
365A GLY 3.0 6.6 + - - -
366A ALA* 3.0 25.0 + - - +
387A PHE* 4.1 7.4 - - - -
394A MET* 4.8 1.1 - - - +
396A ILE* 4.0 31.0 - - - -
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Residues in contact with LYS 362 (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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358A ILE* 3.3 14.4 + - - +
359A GLU* 3.3 33.5 + - - +
361A GLY* 1.3 74.4 - - - +
363A LYS* 1.3 62.0 + - - +
365A GLY* 3.2 12.3 + - - -
366A ALA 4.3 6.0 + - - +
368A LEU* 3.7 29.8 - - + +
372A GLY* 2.8 34.2 + - - -
387A PHE* 3.9 15.2 - - + -
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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
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359A GLU* 2.9 23.2 + - - +
360A SER* 3.8 9.3 - - - +
362A LYS* 1.3 74.7 - - - +
364A GLU* 1.3 63.1 + - + +
365A GLY* 3.0 10.2 + - - -
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Residues in contact with GLU 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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360A SER* 2.6 30.4 + - - +
361A GLY 3.8 1.6 - - - +
363A LYS* 1.3 75.9 - - + +
365A GLY* 1.3 57.6 + - - +
366A ALA 3.8 0.2 - - - -
393A GLU 5.0 1.9 - - - +
394A MET* 3.3 30.9 - - + +
395A ARG* 2.8 49.6 + - - +
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Residues in contact with GLY 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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361A GLY 3.0 2.8 + - - -
362A LYS 3.6 9.0 - - - -
363A LYS 3.0 5.4 - - - -
364A GLU* 1.3 79.9 - - - +
366A ALA* 1.3 64.4 + - - +
367A LYS 4.1 0.3 + - - -
389A ASN* 4.6 4.0 - - - +
394A MET* 3.4 9.5 - - - +
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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