Contacts of the helix formed by residues 356 - 376 (chain J) in PDB entry 4E2I
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 THR 356 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354J GLN 3.5 4.7 + - - +
355J LEU* 1.3 77.5 - - - +
357J ARG* 1.3 64.6 + - - +
358J GLU* 3.0 11.4 + - - +
359J GLN* 3.0 45.8 + - - +
360J MET* 3.1 9.8 + - - +
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Residues in contact with ARG 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355J LEU 3.8 0.2 + - - -
356J THR* 1.3 72.6 - - - +
358J GLU* 1.3 59.6 + - - +
360J MET* 3.5 24.8 + - + +
361J LEU* 3.6 14.4 + - - +
412J MET 2.8 22.6 + - - -
413J VAL* 3.7 20.1 - - + +
415J ASN* 3.7 32.4 + - - +
467J GLN 4.8 4.2 + - - -
468J PHE* 3.0 75.5 + - + +
522J PRO* 5.5 2.4 - - - +
523J PRO* 3.5 19.0 - - - +
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Residues in contact with GLU 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356J THR* 3.0 9.0 + - - +
357J ARG* 1.3 78.4 - - - +
359J GLN* 1.3 56.2 + - + +
360J MET 3.3 0.2 - - - -
361J LEU* 3.3 7.2 + - + +
362J THR* 2.7 34.8 + - - +
410J LYS* 3.3 26.1 + - - +
413J VAL* 3.5 28.2 - - + +
587J GLU 5.1 1.2 - - - +
588J PHE 5.4 0.3 - - - -
589J ALA* 4.9 15.8 + - + -
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Residues in contact with GLN 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354J GLN 4.7 0.9 - - - +
355J LEU* 3.4 28.6 - - + +
356J THR* 3.0 41.1 + - - +
358J GLU* 1.3 78.0 - - + +
360J MET* 1.3 64.0 + - - +
362J THR* 3.0 21.4 + - - +
363J ASN* 2.8 22.5 + - - +
309K GLU* 5.5 5.9 + - - +
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Residues in contact with MET 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351J ASP* 4.0 18.6 - - + +
352J SER* 4.2 19.1 - - - +
355J LEU* 3.8 26.2 - - + +
356J THR 3.1 11.3 + - - +
357J ARG* 3.5 52.3 - - + +
358J GLU 3.3 0.2 - - - -
359J GLN* 1.3 78.5 - - - +
361J LEU* 1.3 61.4 + - - +
363J ASN* 3.5 12.6 + - - +
364J ARG* 3.3 17.8 + - - +
443J CYS 5.9 0.2 - - - -
466J ASP 5.9 1.6 - - - +
467J GLN 5.6 5.2 - - - +
468J PHE* 4.5 14.6 - - + -
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Residues in contact with LEU 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357J ARG 3.6 3.5 + - - +
358J GLU* 3.3 9.1 + - + +
359J GLN 3.1 0.6 - - - -
360J MET* 1.3 76.4 - - - +
362J THR* 1.3 58.5 + - - +
364J ARG* 2.9 4.8 + - - +
365J PHE* 2.8 55.3 + - + -
409J LEU* 4.2 18.8 - - + +
413J VAL* 3.5 31.9 - - + -
443J CYS* 3.7 32.8 - - + +
468J PHE* 3.5 38.6 - - + -
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Residues in contact with THR 362 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358J GLU* 2.7 23.0 + - - +
359J GLN* 3.1 15.5 - - - +
361J LEU* 1.3 77.2 - - - +
363J ASN* 1.3 59.9 + - - +
365J PHE* 3.5 7.4 + - - +
366J ASN* 2.7 42.9 + - - +
589J ALA* 3.5 25.8 - - + +
591J SER* 3.6 24.0 - - - +
592J ILE* 4.1 8.9 - - + +
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Residues in contact with ASN 363 (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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281J LYS* 5.7 3.1 - - - +
355J LEU* 3.6 28.1 - - - +
359J GLN* 2.8 23.3 + - - +
360J MET* 3.8 8.0 - - - +
361J LEU 3.2 0.2 - - - -
362J THR* 1.3 75.8 - - - +
364J ARG* 1.3 62.8 + - - +
366J ASN* 3.3 10.8 + - - +
367J ASP* 2.7 37.3 + - - +
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Residues in contact with ARG 364 (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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360J MET 3.3 10.6 + - - +
361J LEU* 2.9 10.5 + - - +
363J ASN* 1.3 79.1 - - - +
365J PHE* 1.3 64.4 + - + +
367J ASP* 3.0 15.5 + - - +
368J LEU* 2.9 39.5 + - + +
371J ARG* 4.0 18.5 - - - +
441J GLU* 2.8 50.3 + - - +
442J LEU 3.5 15.7 - - - +
443J CYS 3.2 26.7 + - - +
444J GLY* 4.2 9.6 - - - -
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Residues in contact with PHE 365 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361J LEU* 2.8 55.3 + - + +
362J THR* 3.8 2.7 - - - +
364J ARG* 1.3 73.0 - - + +
366J ASN* 1.3 61.3 + - - +
368J LEU* 3.5 10.8 + - + +
369J LEU* 3.3 28.5 + - + +
409J LEU* 3.9 27.4 - - + -
442J LEU* 4.0 21.5 - - + -
576J LEU* 3.5 21.2 - - + +
579J LEU* 3.5 27.6 - - + -
588J PHE* 4.2 25.1 - + - -
592J ILE* 3.7 19.3 - - + -
596J ILE* 5.6 0.7 - - + -
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Residues in contact with ASN 366 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362J THR* 2.7 32.3 + - - +
363J ASN* 3.3 11.3 + - - +
364J ARG 3.1 0.8 - - - -
365J PHE* 1.3 76.4 - - - +
367J ASP* 1.3 56.7 + - - +
368J LEU 3.2 0.2 - - - -
369J LEU* 3.1 2.1 + - - -
370J ASP* 2.7 37.8 + - - +
591J SER 5.3 2.9 + - - +
592J ILE* 3.4 28.0 - - - +
595J ARG* 3.2 33.0 + - - +
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Residues in contact with ASP 367 (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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281J LYS* 3.5 27.1 + - - -
363J ASN* 2.7 28.7 + - - +
364J ARG* 3.0 19.8 + - - +
366J ASN* 1.3 77.8 - - - +
368J LEU* 1.3 62.2 + - + +
370J ASP* 3.1 26.2 + - - +
371J ARG* 3.5 20.3 + - - +
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Residues in contact with LEU 368 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364J ARG* 2.9 37.0 + - + +
365J PHE* 3.7 11.7 - - + +
367J ASP* 1.3 76.9 - - + +
369J LEU* 1.3 59.1 + - - +
371J ARG* 3.7 13.7 + - - +
372J MET* 3.1 24.3 + - - +
441J GLU* 3.7 21.3 - - + +
442J LEU* 3.5 41.5 - - + +
572J GLY 4.6 3.4 - - - +
573J ILE* 3.3 28.5 - - + +
576J LEU* 3.5 20.4 - - + -
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Residues in contact with LEU 369 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365J PHE 3.3 18.3 + - - +
366J ASN* 3.1 3.0 + - - +
368J LEU* 1.3 76.9 - - - +
370J ASP* 1.3 54.0 + - - +
371J ARG 3.2 0.4 - - - -
372J MET* 3.1 27.2 + - - +
373J ASP* 2.8 36.9 + - - +
576J LEU* 3.5 12.3 - - + -
580J ILE* 3.9 17.0 - - + -
592J ILE* 4.5 9.2 - - + -
595J ARG* 3.2 50.3 - - + +
596J ILE* 4.7 10.5 - - + -
599J TRP* 3.8 20.8 - - + +
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Residues in contact with ASP 370 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366J ASN* 2.7 24.6 + - - +
367J ASP* 3.1 25.1 + - - +
368J LEU 3.3 0.2 - - - -
369J LEU* 1.3 77.7 - - - +
371J ARG* 1.3 62.6 + - + +
373J ASP* 3.3 11.2 + - - +
374J ILE* 3.2 25.6 + - + +
595J ARG* 3.2 18.9 + - - +
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Residues in contact with ARG 371 (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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506I LYS* 6.0 2.0 - - - +
364J ARG* 4.0 24.7 - - - +
367J ASP* 3.5 18.6 + - - +
368J LEU* 3.8 15.4 - - - +
369J LEU 3.2 0.2 - - - -
370J ASP* 1.3 77.1 - - + +
372J MET* 1.3 58.6 + - - +
374J ILE* 3.1 12.0 + - - +
375J MET* 2.9 41.5 + - - +
441J GLU* 3.4 30.3 + - - +
573J ILE* 4.1 17.1 - - + +
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Residues in contact with MET 372 (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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368J LEU 3.1 11.7 - - - +
369J LEU* 3.1 20.8 + - + +
371J ARG* 1.3 71.8 - - - +
373J ASP* 1.3 56.0 + - - +
374J ILE 3.0 4.9 - - - -
375J MET* 3.4 9.2 - - - -
376J PHE* 2.8 60.6 + - + +
573J ILE* 3.5 20.9 - - + -
576J LEU* 3.5 31.4 - - + -
577J LEU* 3.4 39.0 - - + -
580J ILE* 5.5 0.7 - - + -
599J TRP* 3.6 19.1 - - + -
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Residues in contact with ASP 373 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369J LEU* 2.8 21.7 + - - +
370J ASP* 3.3 9.3 + - - +
372J MET* 1.3 74.8 - - - +
374J ILE* 1.3 60.3 + - + +
376J PHE 5.3 0.4 - - - -
377J GLY* 4.0 15.0 - - - -
595J ARG* 2.8 24.3 + - - -
599J TRP* 3.2 25.3 + - - -
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Residues in contact with ILE 374 (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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308J LYS 6.1 0.2 - - - +
311J PRO* 3.7 31.6 - - + -
314J TYR* 4.3 11.7 - - - +
315J LYS* 5.4 8.5 - - + +
370J ASP* 3.2 21.1 - - + +
371J ARG* 3.1 8.7 + - - +
372J MET 3.0 0.4 - - - -
373J ASP* 1.3 81.9 - - + +
375J MET* 1.3 62.6 + - - +
376J PHE 3.3 1.1 - - - -
377J GLY* 3.2 7.7 + - - -
379J THR* 3.5 27.3 + - - +
380J GLY* 3.1 23.1 + - - -
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Residues in contact with MET 375 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371J ARG* 2.9 30.5 + - - +
372J MET* 3.4 18.4 - - - -
374J ILE* 1.3 77.1 - - - +
376J PHE* 1.3 86.8 + - + +
377J GLY 3.2 2.0 + - - +
380J GLY* 3.3 18.2 - - - +
381J SER 4.5 0.7 - - - +
382J ALA* 3.3 43.1 + - + +
387J TRP* 3.5 39.5 - - + -
573J ILE* 4.4 8.1 - - + -
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Residues in contact with PHE 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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372J MET* 2.8 65.1 + - + +
373J ASP* 4.6 1.1 - - - -
375J MET* 1.3 97.1 - - + +
377J GLY* 1.3 58.4 + - - +
382J ALA* 3.8 14.1 - - + -
383J ASP 4.0 1.1 - - - -
384J ILE* 3.4 52.5 - - + -
387J TRP* 3.8 25.8 - + + -
573J ILE* 4.7 0.7 - - + -
577J LEU* 4.5 0.9 - - + -
599J TRP* 3.9 17.4 - + + -
602J ARG* 3.5 30.9 + - - +
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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