Contacts of the helix formed by residues 390 - 406 (chain A) in PDB entry 4ASQ
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 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU 3.6 13.2 - - - +
208A TYR* 3.6 18.2 - - + -
213A PHE* 4.9 1.0 - - - -
388A GLY* 3.9 10.4 - - - -
389A ALA* 1.3 79.2 - - - +
391A PRO* 1.3 74.7 - - + +
392A GLY* 2.8 18.4 + - - -
393A PHE* 3.0 38.1 + - - +
394A HIS 3.6 2.9 + - - -
509A VAL* 4.1 8.2 - - - +
564A TRP* 3.2 38.4 - - + +
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Residues in contact with PRO 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.8 34.1 - - + +
208A TYR* 3.7 19.7 - - + +
388A GLY* 5.8 0.4 - - - -
390A ASN* 1.3 89.2 - - + +
392A GLY* 1.3 59.0 + - - +
394A HIS* 3.4 16.5 + - + +
395A GLU* 3.5 18.2 + - - +
503A GLU* 4.5 3.4 - - - +
506A ARG* 3.7 37.3 - - + +
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Residues in contact with GLY 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 4.2 1.6 - - - -
390A ASN* 2.8 16.4 + - - -
391A PRO* 1.3 71.0 - - - +
393A PHE* 1.3 63.2 + - - -
395A GLU 3.4 1.1 + - - -
396A ALA* 3.1 24.4 + - - +
506A ARG* 3.3 24.4 - - - +
509A VAL* 3.9 13.2 - - - -
510A SER* 3.6 6.4 - - - -
513A ILE* 3.8 6.7 - - - -
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Residues in contact with PHE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 3.8 19.3 - - + +
389A ALA* 3.8 11.9 - - + -
390A ASN* 3.0 42.6 + - - +
392A GLY* 1.3 76.3 - - - +
394A HIS* 1.3 61.9 + - - +
396A ALA* 3.2 11.5 + - - +
397A VAL* 3.3 18.2 + - - +
513A ILE* 3.6 23.3 - - + -
517A PHE* 3.7 14.4 - + - -
555A MET* 3.6 33.9 - - + -
564A TRP* 3.6 35.7 - + + -
567A ALA* 3.9 13.7 - - + -
568A LEU* 4.0 12.3 - - + -
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Residues in contact with HIS 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A HIS 5.4 0.3 - - - +
370A GLY 4.9 0.2 - - - -
371A HIS* 2.8 50.3 + - + +
374A TYR* 3.5 30.6 - + + -
375A PHE* 3.4 26.7 - + - -
378A TYR* 2.8 24.9 + - - -
387A THR* 4.6 4.0 + - - -
388A GLY* 3.4 30.1 - - - -
390A ASN 3.6 3.4 + - - +
391A PRO* 3.4 13.2 + - + +
392A GLY 3.3 0.4 - - - -
393A PHE* 1.3 79.4 - - - +
395A GLU* 1.3 62.3 + - - +
396A ALA 3.5 0.3 + - - -
397A VAL* 3.8 11.3 + - - +
398A GLY 4.9 0.7 + - - -
1624A FLC 3.9 15.3 + - - +
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A HIS* 3.0 26.7 + - + +
371A HIS* 3.2 11.9 - - - -
391A PRO 3.5 13.2 + - - +
392A GLY 3.4 2.6 + - - +
393A PHE 3.3 0.6 - - - -
394A HIS* 1.3 75.7 - - - +
396A ALA* 1.3 61.1 + - - +
397A VAL 3.5 0.4 + - - -
398A GLY 4.5 1.0 + - - -
399A ASP* 3.9 6.6 + - - -
506A ARG* 3.7 38.2 + - + +
507A TYR* 3.3 20.1 + - + -
510A SER* 3.4 24.7 + - - +
1615A ZN 2.0 37.2 - - - -
1624A FLC 4.3 4.9 + - - +
1P ARG 3.1 8.2 + - - +
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Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLY 3.1 16.8 + - - +
393A PHE 3.2 5.3 + - - +
395A GLU* 1.3 78.1 - - - +
397A VAL* 1.3 65.6 + - - +
398A GLY 3.4 0.4 - - - -
399A ASP* 3.2 4.5 + - - +
400A VAL* 3.1 25.0 + - - +
510A SER* 3.3 13.2 - - - +
513A ILE* 4.0 10.8 - - + -
514A GLN* 4.1 9.1 - - + +
517A PHE* 3.9 26.7 - - + -
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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
----------------------------------------------------------
307A PHE* 4.6 11.4 - - + -
312A LEU* 6.5 0.2 - - + -
370A GLY* 3.7 24.0 - - - +
374A TYR* 3.7 14.4 - - + -
393A PHE 3.3 16.8 - - - +
394A HIS 4.1 3.4 - - - +
395A GLU 3.5 1.4 - - - -
396A ALA* 1.3 77.6 - - - +
398A GLY* 1.3 64.0 + - - +
400A VAL* 3.3 16.2 + - - +
401A LEU* 3.8 9.6 + - + +
517A PHE* 5.7 1.6 - - + -
552A PHE* 4.1 20.0 - - + -
555A MET* 5.3 2.9 - - + -
556A LEU* 3.7 42.4 - - + -
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Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A HIS 3.2 26.1 - - - +
367A HIS* 3.7 9.9 + - - -
370A GLY* 3.6 12.1 - - - -
394A HIS 4.9 0.8 + - - -
395A GLU 4.5 2.6 + - - -
396A ALA 3.4 0.2 - - - -
397A VAL* 1.3 78.6 - - - +
399A ASP* 1.3 59.5 + - - +
401A LEU* 3.2 10.7 + - - +
402A SER* 3.0 26.9 + - - -
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Residues in contact with ASP 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A HIS* 2.8 37.1 + - - +
395A GLU 3.9 7.4 + - - +
396A ALA 3.2 7.6 + - - +
398A GLY* 1.3 74.8 - - - +
400A VAL* 1.3 59.7 + - - +
402A SER* 3.6 9.5 + - - -
403A LEU* 3.0 32.2 + - - +
438A LYS* 3.5 15.2 + - - +
510A SER* 4.2 0.3 + - - -
511A PHE* 3.7 13.3 - - - -
514A GLN* 3.1 36.6 + - - +
3P PRO* 5.5 2.1 - - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA 3.1 16.2 + - - +
397A VAL 3.5 7.4 - - - +
398A GLY 3.3 0.4 - - - -
399A ASP* 1.3 78.4 - - - +
401A LEU* 1.3 60.5 + - - +
403A LEU* 3.5 19.1 + - - +
404A SER* 3.6 6.4 + - - -
514A GLN* 3.7 14.8 - - + +
517A PHE* 3.6 28.7 - - + +
518A TYR* 3.6 32.0 - - + +
521A ALA* 4.9 0.7 - - + -
542A ILE* 4.2 12.3 - - + +
552A PHE* 3.7 24.9 - - + -
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.4 29.8 - - + -
307A PHE* 3.5 50.0 - - + -
310A MET* 3.8 24.5 - - + -
312A LEU* 5.9 0.7 - - + -
366A HIS* 4.3 11.2 - - + +
397A VAL* 3.8 11.2 + - + +
398A GLY 3.2 7.2 + - - +
400A VAL* 1.3 76.3 - - - +
402A SER* 1.3 60.6 + - - +
404A SER* 2.7 23.7 + - - -
405A VAL* 2.9 19.6 + - - +
542A ILE* 3.8 13.2 - - + -
552A PHE* 4.4 10.3 - - + -
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Residues in contact with SER 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PHE* 3.0 45.8 + - - -
366A HIS* 3.4 8.3 - - - +
367A HIS 4.1 0.2 + - - -
398A GLY 3.0 15.8 + - - -
399A ASP* 3.6 15.3 + - - -
400A VAL 3.3 0.2 - - - -
401A LEU* 1.3 74.9 - - - +
403A LEU* 1.3 59.7 + - - +
405A VAL* 3.7 10.2 - - - +
406A SER* 2.9 31.1 + - - -
438A LYS* 5.9 2.7 - - - -
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Residues in contact with LEU 403 (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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399A ASP 3.0 16.6 + - - +
400A VAL* 3.6 8.5 - - - +
401A LEU 3.2 0.2 - - - -
402A SER* 1.3 76.4 - - - +
404A SER* 1.3 59.1 + - - +
406A SER* 2.6 23.3 + - - +
407A THR* 3.4 11.3 - - - +
434A THR* 4.3 15.7 - - + -
438A LYS* 4.0 22.2 - - - -
514A GLN* 3.9 23.8 - - + +
515A PHE* 4.1 29.2 - - + -
518A TYR* 3.7 41.1 + - + -
585A TYR* 4.4 10.6 + - + +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.1 18.2 - - - -
400A VAL 3.6 2.0 + - - -
401A LEU* 2.7 21.5 + - - -
403A LEU* 1.3 75.4 - - - +
405A VAL* 1.3 62.2 + - - +
406A SER 3.2 0.2 - - - -
407A THR* 2.7 24.7 + - - -
410A HIS* 3.2 9.4 - - - +
518A TYR* 3.7 9.3 - - - -
540A CYS 3.4 22.7 - - - -
541A ASP* 3.7 4.4 - - - +
542A ILE* 3.7 25.9 - - - +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.6 22.4 - - + -
362A LEU* 3.9 26.7 - - + -
363A PHE* 3.9 16.8 - - + -
366A HIS* 3.6 28.0 - - + +
401A LEU 2.9 21.8 + - - +
402A SER* 3.4 8.3 + - - +
404A SER* 1.3 76.5 + - - +
406A SER* 1.3 57.3 - - - +
407A THR 3.4 1.6 + - - +
410A HIS* 3.7 19.6 - - + +
411A LEU* 3.2 25.9 - - + +
414A ILE* 5.4 0.9 - - + -
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL* 4.7 1.6 - - - +
359A GLN* 5.5 0.8 - - - +
363A PHE* 3.5 26.9 - - - -
402A SER 2.9 15.0 + - - -
403A LEU* 2.6 27.8 + - - +
405A VAL* 1.3 75.4 - - - +
407A THR* 1.3 63.4 + - - +
408A PRO* 3.7 0.9 - - - +
411A LEU* 3.4 13.9 - - - +
430A GLN* 3.3 25.5 + - - +
434A THR* 4.9 5.4 + - - +
585A TYR* 5.1 2.8 + - - -
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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