Contacts of the helix formed by residues 370 - 389 (chain J) in PDB entry 5IJO
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 370 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365J LEU* 3.8 4.6 + - - +
367J SER* 5.4 0.3 - - - -
368J GLY 3.2 8.7 - - - +
369J GLY* 1.3 82.2 - - - +
371J ASP* 1.3 69.2 + - - +
372J CYS 4.6 0.9 - - - +
373J THR* 3.9 24.2 - - - +
374J THR* 3.2 20.7 + - - -
803J GLY* 4.6 3.1 - - - +
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Residues in contact with ASP 371 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367J SER* 5.5 8.5 - - - +
368J GLY 5.3 1.0 - - - +
370J ASN* 1.3 76.0 - - - +
372J CYS* 1.3 63.5 + - + +
374J THR* 3.4 6.8 + - - -
375J SER* 3.6 12.6 + - - -
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Residues in contact with CYS 372 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145J THR* 5.6 10.5 - - - -
370J ASN* 4.6 0.6 - - - +
371J ASP* 1.3 77.1 - - + +
373J THR* 1.3 68.7 + - - +
374J THR 3.4 0.2 + - - -
376J THR* 4.0 16.1 + - - -
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Residues in contact with THR 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216J GLU* 5.5 12.1 - - - -
370J ASN* 3.8 21.3 + - - +
371J ASP 3.4 0.8 - - - -
372J CYS* 1.3 80.2 - - - +
374J THR* 1.4 64.5 + - - +
376J THR* 3.6 3.1 + - - -
377J ALA* 3.1 21.7 + - - +
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Residues in contact with THR 374 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J LEU* 2.7 51.4 - - - +
366J ALA* 4.9 1.1 - - - -
367J SER 5.5 0.2 - - - -
370J ASN 3.2 13.5 + - - -
371J ASP 3.9 1.8 - - - -
372J CYS 3.3 0.2 - - - -
373J THR* 1.4 75.8 - - - +
375J SER* 1.3 63.3 + - - +
377J ALA* 2.8 5.8 + - - +
378J CYS* 2.6 30.1 + - - +
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Residues in contact with SER 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371J ASP 3.6 10.9 + - - -
372J CYS 4.1 0.4 + - - -
374J THR* 1.3 81.3 - - - +
376J THR* 1.3 64.1 + - - +
378J CYS* 4.1 9.1 - - - +
379J MET* 3.5 15.4 + - - +
421J TRP* 4.9 18.8 - - - -
422J GLY 5.1 7.9 - - - +
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Residues in contact with THR 376 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223J ALA* 5.5 11.4 - - - -
372J CYS 4.0 11.4 + - - -
373J THR 3.6 7.5 + - - -
374J THR 3.1 0.8 - - - -
375J SER* 1.3 76.7 - - - +
377J ALA* 1.4 57.4 + - - +
379J MET* 2.9 27.1 - - - +
380J CYS* 4.0 1.7 + - - +
421J TRP* 5.8 2.6 - - - +
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Residues in contact with ALA 377 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219J PHE* 6.4 1.6 - - + -
271J LEU* 4.7 18.8 - - + +
365J LEU* 5.1 6.5 - - + -
373J THR* 3.1 15.2 + - - +
374J THR* 2.8 12.7 + - - +
376J THR* 1.4 73.9 - - - +
378J CYS* 1.3 65.4 + - - +
379J MET 3.0 2.5 - - - -
380J CYS* 2.9 25.9 + - - +
381J VAL* 3.8 0.9 + - - +
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Residues in contact with CYS 378 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362J LEU* 5.9 7.2 - - + +
365J LEU* 5.6 5.8 - - + -
374J THR* 2.6 18.1 + - - +
375J SER* 4.1 10.3 - - - +
376J THR 3.4 0.2 - - - -
377J ALA* 1.3 72.5 - - - +
379J MET* 1.3 61.5 + - - +
381J VAL* 2.9 22.4 + - - +
382J TYR* 3.1 11.5 + - - +
410J VAL* 4.7 22.3 - - + +
413J ASP* 5.7 4.5 - - + -
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Residues in contact with MET 379 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375J SER 3.5 8.9 + - - +
376J THR* 2.9 20.2 + - - +
378J CYS* 1.3 78.3 - - - +
380J CYS* 1.3 60.2 + - - +
382J TYR* 3.1 11.8 + - - +
383J GLY* 3.0 19.4 + - - -
423J THR* 6.2 5.8 - - - +
424J GLU 6.4 0.2 - - - +
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Residues in contact with CYS 380 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271J LEU* 4.2 26.2 - - + +
274J VAL* 4.8 15.0 - - + +
275J GLU* 4.8 9.9 - - + +
376J THR 4.0 1.5 + - - +
377J ALA* 2.9 18.0 + - - +
379J MET* 1.3 79.8 - - - +
381J VAL* 1.3 59.8 + - - +
383J GLY* 3.2 10.7 + - - -
384J LEU* 3.4 9.9 + - - +
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Residues in contact with VAL 381 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J VAL* 6.3 0.4 - - - -
358J LEU* 5.4 12.6 - - + +
362J LEU* 6.3 1.8 - - + -
377J ALA 3.8 0.6 + - - -
378J CYS* 2.9 15.5 + - - +
380J CYS* 1.3 78.0 - - - +
382J TYR* 1.3 62.6 + - - +
384J LEU* 3.1 18.4 + - - +
385J LEU* 3.3 11.4 + - - +
410J VAL* 5.0 12.3 - - + -
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Residues in contact with TYR 382 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378J CYS 3.1 8.8 + - - +
379J MET* 3.2 17.0 - - - +
381J VAL* 1.3 76.8 - - - +
383J GLY* 1.3 62.6 + - - +
385J LEU* 3.1 9.4 + - - +
386J SER* 3.0 20.7 + - - -
410J VAL* 5.6 6.7 - - + +
423J THR* 5.9 7.2 - - - -
424J GLU* 5.8 9.2 - - + +
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Residues in contact with GLY 383 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279J ILE* 5.6 2.5 - - - +
280J GLU* 5.1 18.8 + - - +
379J MET 3.0 12.8 + - - -
380J CYS 3.2 4.6 + - - -
381J VAL 3.2 0.4 - - - -
382J TYR* 1.3 75.6 - - - +
384J LEU* 1.3 62.6 + - - +
386J SER* 3.1 16.8 + - - -
387J PHE* 3.4 12.0 + - - +
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Residues in contact with LEU 384 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J VAL* 6.3 2.9 - - + -
279J ILE* 5.5 8.5 - - - +
321J PRO* 5.6 6.5 - - + +
324J LEU* 6.3 2.0 - - + -
325J ALA* 5.2 15.5 - - + +
380J CYS 3.4 7.9 + - - +
381J VAL* 3.1 14.6 + - - +
383J GLY* 1.3 77.4 - - - +
385J LEU* 1.3 62.6 + - - +
387J PHE* 3.3 5.0 + - - +
388J VAL* 3.0 22.4 + - - +
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Residues in contact with LEU 385 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381J VAL 3.3 7.1 + - - +
382J TYR* 3.1 11.5 + - - +
384J LEU* 1.3 76.0 - - - +
386J SER* 1.3 69.1 + - - +
388J VAL* 3.1 16.6 + - - +
389J LEU* 3.2 13.0 + - - +
403J ILE* 5.6 5.8 - - + +
407J ALA* 4.9 18.8 - - + +
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Residues in contact with SER 386 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280J GLU* 6.3 1.8 - - - -
382J TYR 3.0 12.4 + - - -
383J GLY* 3.1 13.2 + - - -
385J LEU* 1.3 78.9 - - - +
387J PHE* 1.3 61.2 + - - +
389J LEU* 3.5 14.4 + - - +
390J THR 4.6 1.0 + - - -
427J SER* 4.8 19.9 - - - +
428J GLY* 5.2 10.8 - - - -
431J ILE* 6.0 0.7 - - - +
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Residues in contact with PHE 387 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279J ILE* 5.5 10.1 - - + +
280J GLU* 5.8 6.5 - - - -
283J HIS* 5.9 7.9 - - + -
328J LEU* 5.3 13.7 - - + -
383J GLY 3.4 5.5 + - - +
384J LEU* 3.3 8.3 + - - +
385J LEU 3.3 0.4 - - - -
386J SER* 1.3 76.8 - - - +
388J VAL* 1.3 64.9 + - - +
389J LEU 3.1 1.2 + - - -
390J THR* 3.3 16.3 + - - -
396J THR 3.4 7.8 + - - -
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Residues in contact with VAL 388 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328J LEU* 6.4 1.3 - - - -
384J LEU 3.0 17.4 + - - +
385J LEU* 3.1 11.2 + - - +
387J PHE* 1.3 75.9 - - - +
389J LEU* 1.3 51.3 + - - +
396J THR 2.7 13.2 + - - +
397J LEU* 2.6 50.9 + - + +
403J ILE* 6.3 2.5 - - + -
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Residues in contact with LEU 389 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385J LEU 3.2 9.2 + - - +
386J SER* 3.8 11.9 - - - +
387J PHE 3.1 1.8 + - - -
388J VAL* 1.3 71.9 - - - +
390J THR* 1.3 63.8 + - - +
391J SER 3.4 1.7 - - - +
397J LEU* 2.5 23.1 - - - +
398J GLY* 3.7 11.3 - - - +
399J ASN* 4.7 2.1 + - - +
403J ILE* 6.4 2.5 - - + -
431J ILE* 4.6 20.6 - - + -
432J ILE* 6.5 0.7 - - + -
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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