Contacts of the helix formed by residues 383 - 401 (chain A) in PDB entry 4PK7
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 GLU 383 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLY* 4.0 25.7 + - - +
342A GLU 5.0 1.3 + - - -
344A ARG* 4.2 3.6 - - - +
381A ASP* 2.6 25.6 + - - +
382A LYS* 1.3 74.9 - - + +
384A TYR* 1.3 64.8 + - - +
385A ASP* 4.7 12.5 + - - +
386A VAL* 3.3 16.0 + - + +
387A ALA 3.2 15.6 + - - -
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Residues in contact with TYR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASP 5.1 7.2 - - - -
382A LYS 3.6 9.7 + - - -
383A GLU* 1.3 70.0 + - - +
385A ASP* 1.3 66.2 + - - +
387A ALA* 3.1 16.1 + - + +
388A VAL* 3.1 17.9 + - - +
419A SER* 4.7 6.7 - - - -
420A ALA* 5.2 7.9 - - + +
421A HIS* 3.7 50.0 - + + +
424A VAL* 3.9 20.0 - - + +
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Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.4 26.4 - - + +
383A GLU* 3.3 12.5 + - - +
384A TYR* 1.3 80.3 - - - +
386A VAL* 1.3 61.6 + - + +
388A VAL* 3.6 13.3 + - - +
389A GLN* 3.6 10.7 + - - +
421A HIS* 5.0 7.4 - - - -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLY* 3.3 31.2 - - - +
344A ARG* 4.2 11.7 - - + -
345A LEU* 3.6 19.3 - - + +
348A LEU* 3.5 19.9 - - + +
378A MET* 4.8 5.4 - - - +
381A ASP* 3.3 25.8 - - + +
383A GLU* 3.3 26.1 + - + +
384A TYR 3.1 0.4 - - - -
385A ASP* 1.3 79.7 - - + +
387A ALA* 1.3 62.5 + - - +
389A GLN* 3.6 1.2 + - - +
390A ALA* 3.1 18.7 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A MET 3.3 15.3 - - - +
379A THR* 3.5 23.3 - - - +
380A LEU* 4.7 0.2 - - - -
381A ASP 4.0 9.9 - - - +
383A GLU 3.2 9.6 + - - +
384A TYR* 3.1 15.1 + - + +
386A VAL* 1.3 78.4 - - - +
388A VAL* 1.3 66.5 + - - +
390A ALA* 3.5 2.8 + - - +
391A ILE* 3.3 25.1 + - - +
424A VAL* 4.6 10.1 - - + -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A TYR 3.1 14.6 + - - +
385A ASP* 3.9 9.2 - - - +
386A VAL 3.2 0.2 - - - -
387A ALA* 1.3 75.5 - - - +
389A GLN* 1.3 72.5 + - - +
391A ILE* 2.8 26.7 + - - +
392A LYS* 2.8 34.6 + - + +
421A HIS* 5.3 0.7 - - + +
423A PRO* 3.6 40.2 - - + +
424A VAL* 3.7 9.4 - - + +
427A ALA* 4.2 7.0 - - + -
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.3 32.3 - - + -
348A LEU* 3.9 15.2 - - + +
349A THR* 4.9 7.4 + - - +
352A GLN* 2.8 48.4 + - - +
385A ASP 3.6 3.3 + - - +
386A VAL 3.6 6.5 + - - +
387A ALA 3.5 0.2 - - - -
388A VAL* 1.3 92.8 - - - +
390A ALA* 1.3 58.1 + - - +
392A LYS* 4.1 12.3 - - - +
393A LEU* 3.0 15.8 + - - +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.5 21.3 - - + +
375A ILE* 3.9 11.4 - - + +
378A MET* 3.4 39.5 - - + +
379A THR* 4.0 2.0 - - - +
386A VAL 3.1 7.3 + - - +
387A ALA 3.8 2.2 - - - +
388A VAL 3.1 1.2 - - - -
389A GLN* 1.3 76.8 - - - +
391A ILE* 1.3 57.7 + - - +
393A LEU* 3.5 5.1 + - - +
394A LEU* 3.0 33.8 + - - +
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 3.9 18.8 - - + +
387A ALA 3.4 14.8 - - - +
388A VAL 2.8 6.4 + - - +
390A ALA* 1.3 73.7 - - - +
392A LYS* 1.3 62.3 + - - +
394A LEU* 3.0 8.2 + - + +
395A THR* 2.8 31.0 + - - -
413A VAL* 4.2 13.9 - - + -
416A LEU* 3.5 26.2 - - + -
424A VAL* 3.8 30.5 - - + +
427A ALA* 3.5 29.8 - - + +
428A ALA* 3.9 8.7 - - + +
431A PHE* 4.3 6.0 - - + -
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Residues in contact with LYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 3.6 17.5 - - - +
388A VAL* 2.8 38.5 + - + +
389A GLN* 4.1 12.2 - - - +
391A ILE* 1.3 75.9 - - - +
393A LEU* 1.3 61.6 + - - +
395A THR* 3.2 10.7 + - - -
396A LEU* 3.1 27.2 + - + +
427A ALA* 4.2 13.7 - - + -
430A GLU* 4.4 17.3 + - - +
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.0 15.0 - - + +
351A LEU* 3.8 23.6 - - + -
352A GLN* 3.6 40.9 - - + +
355A TYR* 4.0 19.3 - - + -
375A ILE* 3.6 34.8 - - + -
389A GLN 3.0 19.8 + - - +
390A ALA 3.7 3.4 - - - +
392A LYS* 1.3 78.3 - - - +
394A LEU* 1.3 57.5 + - - +
396A LEU* 3.3 4.7 + - + +
397A VAL* 3.0 31.5 + - + +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR* 6.4 0.7 - - + -
372A LYS* 5.3 3.6 - - + -
375A ILE* 3.6 22.2 - - + -
376A VAL* 3.8 23.3 - - + -
379A THR* 3.5 32.3 - - + -
390A ALA 3.0 16.7 + - - +
391A ILE* 3.0 7.8 + - + +
393A LEU* 1.3 76.3 - - - +
395A THR* 1.3 62.0 + - - +
397A VAL* 3.7 14.5 - - + +
398A LEU* 3.3 18.4 + - - +
405A LEU* 3.8 29.5 - - + +
413A VAL* 4.2 12.3 - - + -
431A PHE* 3.7 18.5 - - + -
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Residues in contact with THR 395 (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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391A ILE* 2.8 15.6 + - - +
392A LYS* 3.3 12.2 - - - -
393A LEU 3.1 0.2 - - - -
394A LEU* 1.3 76.2 - - - +
396A LEU* 1.3 65.4 + - + +
398A LEU* 2.9 22.3 + - + +
399A GLN* 3.3 7.7 + - - +
427A ALA 4.3 2.3 + - - -
430A GLU* 5.1 4.8 - - + +
431A PHE* 3.7 35.7 + - + +
434A LYS* 3.2 37.0 - - + +
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Residues in contact with LEU 396 (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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352A GLN* 3.8 49.8 - - + +
355A TYR* 3.8 23.4 - - + +
356A TYR* 3.9 30.7 - - + +
392A LYS* 3.1 16.4 + - + +
393A LEU* 3.3 6.2 + - + +
395A THR* 1.3 75.8 - - + +
397A VAL* 1.3 63.5 + - - +
399A GLN* 3.1 37.7 + - - +
400A SER* 3.5 10.4 + - - -
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 4.0 27.6 - - + +
368A THR* 4.1 14.8 - - + -
375A ILE* 6.0 0.7 - - + -
393A LEU* 3.0 31.1 + - + +
394A LEU* 3.7 14.8 - - + +
396A LEU* 1.3 75.2 - - - +
398A LEU* 1.3 63.1 + - - +
400A SER* 2.9 23.7 + - - +
401A SER* 3.0 13.4 + - - +
404A VAL* 3.5 31.9 - - + -
405A LEU* 4.4 11.9 - - + -
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Residues in contact with LEU 398 (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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394A LEU 3.3 5.6 + - - +
395A THR* 2.9 16.8 + - + +
397A VAL* 1.3 81.2 - - - +
399A GLN* 1.3 62.6 + - + +
401A SER* 3.3 18.1 + - - +
402A GLU* 3.9 21.8 + - + +
405A LEU* 3.6 27.1 - - + -
431A PHE* 3.6 34.3 - - + +
434A LYS* 4.4 13.0 - - + -
435A LYS* 3.9 41.1 - - + +
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Residues in contact with GLN 399 (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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356A TYR* 6.2 0.6 - - - -
357A ASN* 5.8 4.6 + - - +
395A THR* 3.6 7.0 - - - +
396A LEU* 3.1 32.7 + - - +
398A LEU* 1.3 78.8 - - - +
400A SER* 1.3 64.9 + - - +
401A SER* 3.0 1.9 + - - -
402A GLU* 5.0 2.3 - - - +
434A LYS* 2.4 40.0 + - - +
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Residues in contact with SER 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A TYR* 3.9 20.7 - - - -
359A GLU* 6.5 1.6 - - - -
360A LEU* 5.3 17.0 - - - +
365A GLU* 4.2 13.3 + - - +
396A LEU 3.5 6.0 + - - -
397A VAL* 2.9 22.9 + - - +
399A GLN* 1.3 76.9 - - - +
401A SER* 1.3 69.5 + - - +
403A GLU* 4.7 0.7 - - - +
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Residues in contact with SER 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU* 3.2 20.5 + - - +
397A VAL* 3.0 16.5 + - - +
398A LEU* 3.4 12.6 - - - +
399A GLN 3.0 4.4 + - - -
400A SER* 1.3 91.3 + - - +
402A GLU* 1.3 63.7 + - - +
403A GLU* 3.1 39.2 + - - +
404A VAL* 4.4 12.1 - - - +
405A LEU* 5.6 0.5 - - - +
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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
------------------------------------------------------------
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