Contacts of the helix formed by residues 380 - 405 (chain A) in PDB entry 4C2M
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 380 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 4.2 2.8 + - - +
367A PHE 4.2 4.2 + - - -
368A ARG* 3.1 40.7 - - - +
369A LEU 3.0 25.8 + - - +
370A PRO* 4.2 4.0 - - - +
371A SER* 5.6 1.8 - - - -
378A HIS 3.7 0.8 + - - -
379A GLU* 1.3 73.2 - - - +
381A SER* 1.3 64.3 + - - +
382A GLN* 2.9 33.8 + - - +
383A ASN* 3.0 30.3 + - - +
384A GLN* 3.2 12.0 + - - +
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU 3.6 3.6 + - - -
380A ASN* 1.3 74.3 + - - +
382A GLN* 1.3 66.0 + - - +
384A GLN* 3.1 26.5 + - - +
385A LEU* 3.1 17.5 + - - +
453A ILE* 3.4 25.3 - - - +
454A PRO* 4.7 11.4 + - - +
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Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.6 19.7 - - - +
367A PHE* 4.6 4.2 - - - +
368A ARG* 3.5 23.0 - - + +
380A ASN* 2.9 12.7 + - - +
381A SER* 1.3 82.8 + - - +
383A ASN* 1.3 57.1 + - - +
385A LEU* 3.5 9.3 + - + +
386A LEU* 3.1 31.6 + - + +
437A PHE* 3.7 23.1 - - + -
454A PRO 5.6 1.3 - - - +
455A GLY 5.7 0.8 - - - -
456A VAL* 3.8 29.1 - - - +
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 5.0 8.3 - - + +
49A LEU* 3.5 26.6 - - + +
50A TYR* 3.3 42.0 + - - -
368A ARG* 2.8 39.8 + - - +
379A GLU* 5.8 3.8 - - + +
380A ASN* 3.0 21.2 + - + +
382A GLN* 1.3 74.7 - - - +
384A GLN* 1.3 65.9 + - + +
386A LEU* 3.2 0.9 + - - +
387A SER* 2.9 24.7 + - - -
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Residues in contact with GLN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU* 3.4 45.0 + - - +
380A ASN 3.2 8.2 + - - +
381A SER* 3.1 23.6 + - - +
383A ASN* 1.3 78.5 - - - +
385A LEU* 1.3 62.8 + - - +
387A SER* 3.2 18.5 + - - -
388A LYS* 3.5 21.0 + - - +
453A ILE* 3.9 23.0 - - + +
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A SER 3.1 8.8 + - - +
382A GLN* 3.8 10.5 - - - +
383A ASN 3.2 0.2 - - - -
384A GLN* 1.3 78.8 - - - +
386A LEU* 1.3 64.1 + - - +
388A LYS* 3.2 25.5 + - + +
389A VAL* 3.4 14.5 + - - +
433A ASP 4.8 2.7 - - - +
436A ALA* 3.4 42.8 - - + +
437A PHE* 4.0 20.4 - - + +
453A ILE* 3.9 31.2 - - + +
454A PRO 3.5 23.8 - - - +
455A GLY* 4.5 0.4 - - - -
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LEU* 3.8 33.2 - - + -
79A ILE* 4.1 12.8 - - + +
360A LEU* 4.1 14.1 - - + -
361A VAL 5.6 1.1 - - - +
362A VAL* 4.2 16.8 - - + -
363A PRO* 4.3 6.5 - - + -
368A ARG* 4.3 15.7 - - - -
382A GLN* 3.1 21.4 + - + +
383A ASN* 3.2 1.1 + - - +
385A LEU* 1.3 73.4 - - - +
387A SER* 1.3 61.9 + - - +
389A VAL* 3.2 9.5 + - + +
390A LEU* 3.0 29.8 + - - +
437A PHE* 3.5 41.7 - - + -
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.5 29.8 - - - +
37A VAL* 5.5 1.8 - - - -
49A LEU* 4.0 5.3 - - - +
383A ASN 2.9 15.0 + - - -
384A GLN* 3.2 14.0 + - - -
385A LEU 3.3 0.2 - - - -
386A LEU* 1.3 77.2 - - - +
388A LYS* 1.3 61.2 + - - +
390A LEU* 3.1 12.1 + - - +
391A THR* 3.0 33.3 + - - +
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Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A GLN* 3.5 17.3 + - - +
385A LEU* 3.2 22.4 + - + +
386A LEU 3.2 0.6 - - - -
387A SER* 1.3 78.8 + - - +
389A VAL* 1.3 62.2 + - - +
391A THR* 2.9 22.0 + - - +
392A THR* 3.1 15.9 + - - -
433A ASP* 3.3 20.3 - - + +
446A ARG* 4.5 22.2 - - - +
453A ILE* 6.1 4.3 - - + -
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 4.1 22.2 - - + -
81A LEU* 3.8 27.8 - - + -
360A LEU* 4.3 19.3 - - + -
385A LEU 3.4 9.4 + - - +
386A LEU* 3.2 14.7 + - + +
388A LYS* 1.3 79.2 - - - +
390A LEU* 1.3 57.2 + - - +
392A THR* 3.6 3.1 + - - -
393A SER* 3.0 26.9 + - - -
430A ILE* 4.2 4.3 - - + +
433A ASP* 3.6 36.3 - - + +
434A VAL* 4.3 2.7 - - + +
437A PHE* 4.9 2.2 - - + -
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.5 39.5 - - + +
33A THR* 3.8 12.1 - - - +
34A ASN 3.4 25.1 - - - +
35A PRO* 4.0 13.2 - - + -
49A LEU* 4.2 11.2 - - + -
79A ILE* 3.6 25.8 - - + -
386A LEU 3.0 19.7 + - - +
387A SER* 3.1 16.5 + - - +
389A VAL* 1.3 75.2 - - - +
391A THR* 1.3 65.1 + - - +
393A SER* 3.2 7.5 + - - -
394A LEU* 3.0 26.6 + - - +
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Residues in contact with THR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 3.7 25.8 - - + -
387A SER 3.0 16.8 + - - +
388A LYS* 2.9 17.3 + - - +
390A LEU* 1.3 70.4 - - - +
392A THR* 1.3 76.7 + - - +
393A SER 3.0 1.1 - - - -
394A LEU* 3.2 6.7 + - - +
395A LEU* 2.9 34.8 + - - +
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Residues in contact with THR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LYS 3.1 8.2 + - - -
389A VAL 3.9 3.4 - - - -
391A THR* 1.3 82.9 + - - +
393A SER* 1.3 58.3 + - - +
395A LEU* 3.3 10.4 + - + +
396A ILE* 2.9 36.2 + - + +
429A THR* 3.9 12.4 + - - +
430A ILE* 3.7 41.7 - - + +
433A ASP* 2.4 25.9 + - - +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ILE* 4.6 7.1 - - - +
80A GLU 3.2 14.0 + - - -
81A LEU* 4.4 2.1 - - - +
82A PRO* 3.1 33.5 - - - +
389A VAL 3.0 20.7 + - - -
390A LEU* 3.2 11.7 - - - -
391A THR 3.0 0.2 - - - -
392A THR* 1.3 75.0 - - - +
394A LEU* 1.3 68.7 + - - +
396A ILE* 3.3 3.5 + - - +
397A ARG* 3.0 30.5 + - - +
430A ILE* 4.9 1.3 - - - -
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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
----------------------------------------------------------
33A THR* 3.7 31.6 - - + +
34A ASN* 5.3 0.4 - - - -
35A PRO* 4.1 19.5 - - + -
390A LEU 3.0 16.4 + - - +
391A THR* 3.7 7.0 - - - +
393A SER* 1.3 76.0 - - - +
395A LEU* 1.3 65.8 + - + +
397A ARG* 3.2 25.9 + - + +
398A ASP* 3.2 21.1 + - - +
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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
----------------------------------------------------------
391A THR* 2.9 26.5 + - - +
392A THR* 3.6 9.4 - - + +
393A SER 3.2 0.2 - - - -
394A LEU* 1.3 81.3 - - + +
396A ILE* 1.3 61.1 + - + +
398A ASP* 3.3 15.9 + - + +
399A LEU* 3.2 19.1 + - - +
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Residues in contact with ILE 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 3.6 32.1 - - + +
83A VAL* 4.9 15.5 - - + -
392A THR* 2.9 24.7 + - + +
393A SER 3.8 0.2 - - - +
394A LEU 3.3 0.2 - - - -
395A LEU* 1.3 72.3 - - + +
397A ARG* 1.3 58.1 + - - +
398A ASP 3.0 5.4 - - - -
399A LEU* 3.2 9.1 + - + +
400A ASN* 2.9 32.0 + - + +
426A ALA* 3.6 45.3 - - + +
430A ILE* 3.7 23.1 - - + -
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Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 5.2 6.9 - - - +
33A THR* 6.1 1.6 - - - +
80A GLU* 3.1 41.3 + - - +
82A PRO* 4.1 22.0 - - + +
393A SER* 3.0 25.2 + - - +
394A LEU* 3.2 21.8 + - + +
396A ILE* 1.3 77.5 - - - +
398A ASP* 1.3 59.1 + - - +
400A ASN* 3.9 11.8 + - + +
401A ASP* 3.5 18.2 + - - +
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 3.2 17.6 + - - +
395A LEU* 3.4 18.6 - - + +
396A ILE 3.0 0.6 - - - -
397A ARG* 1.3 76.9 - - - +
399A LEU* 1.3 64.6 + - - +
400A ASN 3.1 1.1 - - - -
401A ASP* 3.0 17.6 + - - +
402A ASP* 3.1 24.5 + - - +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A LEU 3.2 10.1 + - - +
396A ILE* 3.5 12.6 - - + +
398A ASP* 1.3 78.3 - - - +
400A ASN* 1.3 58.8 + - - +
402A ASP* 3.4 6.4 + - + +
403A LEU* 3.0 47.8 + - + +
422A ARG* 3.8 36.1 - - + +
423A LEU* 4.5 12.6 - - + -
426A ALA* 3.8 29.2 - - + -
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Residues in contact with ASN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PRO* 6.0 0.8 + - + -
396A ILE* 2.9 20.5 + - + +
397A ARG* 4.0 13.6 - - - +
398A ASP 3.1 0.2 - - - -
399A LEU* 1.3 78.8 - - - +
401A ASP* 1.3 59.0 + - - +
403A LEU* 3.8 16.4 - - - +
404A SER* 3.6 19.9 + - - -
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Residues in contact with ASP 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ARG 3.5 13.7 + - - +
398A ASP* 3.0 18.4 + - - +
400A ASN* 1.3 78.4 - - - +
402A ASP* 1.3 66.7 + - - +
403A LEU 3.2 0.4 - - - -
404A SER* 2.9 21.4 + - - -
405A LYS* 2.9 44.4 + - - +
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Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASP* 3.1 18.3 + - - +
399A LEU* 4.0 7.4 - - + +
401A ASP* 1.3 84.1 - - - +
403A LEU* 1.3 66.0 + - + +
404A SER 3.3 0.2 - - - -
405A LYS* 3.3 23.5 + - - +
406A LEU* 3.7 15.5 + - - +
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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
----------------------------------------------------------
399A LEU* 3.0 36.2 + - + +
400A ASN* 3.9 17.0 - - - +
401A ASP 3.2 0.2 - - - -
402A ASP* 1.3 79.7 - - + +
404A SER* 1.3 60.9 + - - +
406A LEU* 3.5 34.8 + - + +
419A ILE* 4.0 22.4 - - + -
422A ARG* 6.1 2.2 - - + -
423A LEU* 3.9 35.7 - - + -
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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
----------------------------------------------------------
400A ASN 3.6 10.2 + - - -
401A ASP* 2.9 22.5 + - - -
403A LEU* 1.3 75.0 - - - +
405A LYS* 1.3 60.4 + - - +
406A LEU 3.1 17.0 + - - +
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Residues in contact with LYS 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ASP* 2.9 42.0 + - - +
402A ASP* 3.3 20.0 + - - +
403A LEU 3.3 1.2 - - - -
404A SER* 1.3 77.3 + - - +
406A LEU* 1.3 63.0 + - - +
407A GLN* 3.8 8.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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