Contacts of the helix formed by residues 391 - 410 (chain A) in PDB entry 3QJS
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 SER 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A GLY* 4.2 8.3 + - - -
355A GLY* 4.8 4.9 - - - -
386A HIS 3.0 16.1 + - - -
387A LEU* 3.5 15.4 + - - +
388A GLN 4.1 0.2 + - - -
390A ALA* 1.3 78.6 - - - +
392A LEU* 1.3 62.8 + - - +
394A THR 3.6 0.2 + - - -
395A LEU* 2.7 53.0 + - - +
428A TRP* 4.5 1.6 - - - +
429A PHE* 4.7 7.8 - - - -
432A MET* 4.2 19.7 - - - +
433A MET* 5.9 0.3 - - - -
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Residues in contact with LEU 392 (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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240A LEU* 3.5 31.2 - - + -
243A ALA* 4.8 1.8 - - + -
244A TYR* 4.2 11.2 - - + -
247A ILE* 4.2 12.6 - - + -
349A PRO 3.8 5.2 - - - +
352A GLY* 3.2 39.9 - - - +
353A LEU* 3.3 23.8 - - + +
356A PHE* 3.6 23.8 - - + -
387A LEU 3.7 1.6 + - - +
388A GLN 3.2 11.2 + - - +
391A SER* 1.3 78.0 + - - +
393A VAL* 1.3 64.2 + - - +
395A LEU* 4.1 0.2 - - - +
396A THR* 2.9 33.1 + - - +
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Residues in contact with VAL 393 (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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80A PHE* 4.8 5.4 - - + -
81A THR* 4.3 23.1 - - + -
84A PHE* 4.8 13.1 - - + -
239A TRP* 3.5 30.5 - - - +
240A LEU* 3.8 23.1 - - + -
243A ALA* 4.4 9.8 - - + +
388A GLN 3.0 16.2 + - - +
389A VAL* 3.4 16.6 - - + +
391A SER 3.5 0.2 - - - -
392A LEU* 1.3 73.8 - - - +
394A THR* 1.3 65.2 + - - +
396A THR* 3.4 3.5 + - - -
397A ALA* 3.1 17.5 + - - +
801A HAS 4.1 8.7 - - + -
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Residues in contact with THR 394 (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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32A LEU* 3.9 34.1 - - + -
80A PHE* 3.8 11.9 - - + -
389A VAL 2.8 18.4 + - - -
390A ALA* 3.3 25.6 - - - +
391A SER 3.6 0.2 + - - -
392A LEU 3.4 0.2 - - - -
393A VAL* 1.3 73.1 - - - +
395A LEU* 1.3 49.4 + - - +
397A ALA* 2.7 7.6 + - - +
398A MET* 2.7 50.4 + - + -
428A TRP* 4.2 5.6 - - + -
800A HEM 3.5 14.9 - - - +
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Residues in contact with LEU 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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348A ALA* 3.1 34.6 - - + +
351A LEU* 4.4 2.2 - - + -
352A GLY 3.8 14.1 - - - +
391A SER* 2.7 37.2 + - - +
392A LEU 4.1 1.3 - - - +
394A THR* 1.3 72.0 - - - +
396A THR* 1.3 57.2 + - - +
398A MET* 3.9 17.9 - - - +
399A GLY 2.9 26.0 + - - -
425A VAL* 4.0 25.8 - - + +
428A TRP* 3.9 32.1 - - + -
429A PHE* 4.3 18.6 - - + +
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Residues in contact with THR 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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84A PHE* 4.2 3.5 - - - -
243A ALA* 3.8 23.9 - - - +
246A ILE* 3.8 41.3 - - + +
247A ILE* 4.1 7.1 - - + +
349A PRO* 3.8 30.6 - - + +
392A LEU* 2.9 20.5 + - - +
393A VAL 3.7 4.3 - - - -
395A LEU* 1.3 75.5 - - - +
397A ALA* 1.3 60.3 + - - +
399A GLY 4.1 0.2 - - - -
400A SER* 3.1 21.7 + - - -
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Residues in contact with ALA 397 (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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29A PHE* 3.2 24.0 - - + -
80A PHE* 3.4 30.3 - - + -
84A PHE* 3.8 24.8 - - + -
393A VAL 3.1 9.2 + - - +
394A THR 2.7 17.0 + - - +
396A THR* 1.3 70.5 - - - +
398A MET* 1.3 58.3 + - - +
400A SER* 2.9 21.7 - - - -
401A LEU 3.6 1.0 + - - -
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Residues in contact with MET 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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29A PHE* 4.2 8.5 - - + -
32A LEU* 4.4 3.1 - - + -
394A THR* 2.7 27.8 + - + +
395A LEU* 3.2 30.5 + - + +
397A ALA* 1.3 70.7 - - - +
399A GLY* 1.3 64.0 + - - +
401A LEU* 3.1 24.8 - - - +
402A TYR* 3.7 9.5 - - + -
424A VAL* 4.5 9.4 - - + -
425A VAL* 4.7 7.2 - - + -
428A TRP* 3.4 49.8 - - + -
484A PHE* 3.5 50.2 - - + -
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Residues in contact with GLY 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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344A PRO 3.9 9.2 - - - -
345A ALA* 3.4 19.4 - - - -
348A ALA* 3.7 18.0 - - - +
349A PRO* 4.8 1.3 - - - -
395A LEU 2.9 15.7 + - - -
396A THR 4.3 0.4 - - - -
398A MET* 1.3 73.5 - - - +
400A SER* 1.3 66.2 + - - +
402A TYR* 3.1 22.7 + - - +
403A TRP* 3.7 3.3 - - - -
425A VAL* 5.3 0.2 - - - -
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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
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25A LEU* 5.0 2.8 - - - +
29A PHE* 5.6 0.2 - - - -
84A PHE* 4.2 12.5 - - - -
88A ILE* 4.8 0.2 - - - +
246A ILE* 5.2 0.9 - - - -
396A THR 3.1 16.7 + - - -
397A ALA* 2.9 20.6 - - - -
399A GLY* 1.3 73.7 - - - +
401A LEU* 1.3 53.2 + - - +
402A TYR 2.5 14.9 + - - -
403A TRP* 2.7 34.5 + - - +
404A LEU* 2.9 41.1 + - - +
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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
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25A LEU* 5.7 1.6 - - + -
29A PHE* 3.2 42.4 - - + -
397A ALA 3.7 1.3 - - - +
398A MET 3.1 13.5 - - - +
400A SER* 1.3 77.0 + - - +
402A TYR* 1.3 68.7 + - + +
403A TRP 3.5 0.2 - - - -
405A LEU* 3.2 54.3 - - + +
406A PRO* 3.3 3.8 - - - +
413A ILE* 4.0 7.5 - - - +
484A PHE* 3.7 28.3 - - + -
488A LEU* 3.7 27.1 - - + -
491A VAL* 4.7 7.3 - - + +
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Residues in contact with TYR 402 (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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343A ASN* 4.7 2.0 - - - +
344A PRO* 3.7 33.0 - - + -
345A ALA* 3.8 16.6 - - + +
398A MET* 3.7 16.6 - - + -
399A GLY* 3.4 19.1 - - - +
400A SER 2.5 7.5 + - - -
401A LEU* 1.3 83.1 - - + +
403A TRP* 1.3 56.9 + - - +
406A PRO* 2.9 19.8 - - - +
413A ILE* 3.9 35.4 - - + +
417A GLN 3.7 17.5 + - - -
418A ARG* 4.9 0.2 - - - -
421A GLY* 2.9 30.2 + - - -
425A VAL* 5.7 3.1 - - + -
484A PHE* 6.1 1.7 - + - -
487A GLY* 6.1 1.4 - - - -
491A VAL* 5.2 9.9 - - + +
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Residues in contact with TRP 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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88A ILE* 5.5 1.1 - - + -
92A LEU* 4.6 7.2 - - + -
246A ILE* 4.2 22.9 - - + +
250A ILE* 3.5 34.6 - - + +
254A GLN* 3.0 39.3 + - - +
345A ALA* 3.9 8.7 + - + -
399A GLY 3.7 9.6 - - - -
400A SER* 2.7 30.4 + - - +
402A TYR* 1.3 74.2 - - - +
404A LEU* 1.3 94.7 + - + +
406A PRO* 3.6 6.2 - - - +
407A ASN* 3.4 20.4 + - + +
506A LEU* 3.8 16.8 - - + -
507A PRO* 3.4 31.0 - - + +
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Residues in contact with LEU 404 (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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21A THR* 5.2 2.2 - - + -
25A LEU* 3.7 16.8 - - + -
88A ILE* 3.4 29.8 - - + -
91A TYR* 4.0 24.7 - - + -
92A LEU* 5.8 1.1 - - + -
400A SER* 2.9 33.1 + - - +
401A LEU* 4.8 0.4 - - - +
403A TRP* 1.3 103.0 - - + +
405A LEU* 1.3 59.3 + - - +
407A ASN* 2.9 11.5 + - + +
408A LEU* 2.8 52.0 + - + +
506A LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 405 (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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22A LEU* 3.6 28.5 - - + -
25A LEU* 3.9 23.3 - - + -
26A VAL* 6.2 1.3 - - + -
401A LEU* 3.2 47.2 + - + +
404A LEU* 1.3 73.9 - - + +
406A PRO* 1.4 64.0 - - + +
408A LEU* 4.2 2.2 - - + +
409A THR* 2.4 40.5 + - + +
411A LYS 4.9 0.7 - - - -
488A LEU* 4.6 6.3 - - + -
491A VAL* 4.3 21.3 - - + -
492A LEU* 4.4 22.2 - - + -
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Residues in contact with PRO 406 (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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401A LEU 3.3 9.6 - - - +
402A TYR 2.9 31.4 - - - +
403A TRP* 3.6 7.2 - - - +
405A LEU* 1.4 88.2 - - + +
407A ASN* 1.3 59.0 + - - +
409A THR* 4.0 0.2 - - - +
410A GLY* 2.8 25.7 + - - +
411A LYS 3.7 17.5 - - - +
412A PRO* 4.9 0.7 - - + -
413A ILE* 3.9 19.5 - - + +
501A LEU* 3.8 27.5 - - + +
502A ALA* 3.4 7.5 - - - +
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Residues in contact with ASN 407 (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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18A LYS* 2.8 22.2 - - - -
91A TYR* 2.8 27.7 + - - -
403A TRP* 3.4 14.4 + - + +
404A LEU* 2.9 18.5 + - + +
406A PRO* 1.3 79.3 - - - +
408A LEU* 1.3 57.7 + - - +
501A LEU* 4.5 2.9 - - - -
502A ALA* 2.9 18.3 - - - +
504A ALA* 2.7 39.8 + - - +
506A LEU* 3.1 28.9 - - - +
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Residues in contact with LEU 408 (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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11A VAL* 4.3 3.5 - - - +
12A TYR* 3.5 14.9 + - - -
18A LYS* 3.7 49.0 - - + +
21A THR* 3.9 15.5 - - + -
22A LEU* 3.7 25.1 - - + +
25A LEU* 3.6 21.1 - - + -
91A TYR* 3.9 23.6 - - + -
404A LEU* 2.8 41.6 + - + +
405A LEU* 4.0 2.0 - - + +
407A ASN* 1.3 78.5 - - - +
409A THR* 1.3 60.1 + - - +
502A ALA* 4.7 1.6 - - - +
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Residues in contact with THR 409 (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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11A VAL* 5.1 5.7 - - - +
12A TYR* 4.4 1.6 - - - -
22A LEU* 3.4 39.5 - - + -
405A LEU* 2.4 35.4 + - + +
406A PRO* 3.7 0.6 - - - +
408A LEU* 1.3 79.7 - - - +
410A GLY* 1.3 60.9 + - - +
411A LYS* 3.8 39.6 + - - +
492A LEU* 5.2 2.7 - - + -
497A ARG* 3.6 28.9 + - - +
498A LYS 4.4 3.8 - - - +
502A ALA* 3.9 6.6 - - - +
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Residues in contact with GLY 410 (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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406A PRO 2.8 17.0 + - - +
409A THR* 1.3 74.8 + - - +
411A LYS* 1.3 69.8 + - - +
412A PRO* 2.9 6.0 - - - +
496A GLU 4.4 0.2 - - - -
498A LYS* 3.7 20.7 - - - +
501A LEU* 3.4 19.2 - - - +
502A ALA* 3.5 14.4 - - - -
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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