Contacts of the helix formed by residues 356 - 378 (chain A) in PDB entry 4CQ8
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 GLU 356 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A ARG 4.6 0.2 + - - -
353A ASP 3.2 18.2 + - - +
354A ASN 3.7 0.3 - - - +
355A GLN* 1.4 75.9 - - - +
357A ALA* 1.4 61.4 + - - +
358A GLY* 3.2 15.8 + - - -
359A LYS* 3.0 39.3 + - + +
360A LEU* 2.9 30.3 + - - +
438A GLN* 6.2 3.4 - - - +
441A GLU* 5.4 3.2 - - - +
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Residues in contact with ALA 357 (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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355A GLN 3.4 5.2 + - - -
356A GLU* 1.4 76.0 - - - +
358A GLY* 1.3 56.4 + - - +
360A LEU* 3.8 3.4 - - - +
361A LYS* 3.0 31.7 + - - +
441A GLU* 3.9 39.1 + - + +
442A ILE* 5.2 2.6 - - - +
445A VAL* 3.5 24.1 - - + +
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Residues in contact with GLY 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A GLU* 3.2 15.2 + - - -
357A ALA* 1.3 78.2 - - - +
359A LYS* 1.3 61.0 + - - +
361A LYS* 3.6 6.8 + - - +
362A ASN* 3.4 20.8 + - - +
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ASP* 3.8 31.6 + - - +
354A ASN* 4.0 25.9 + - - +
356A GLU* 3.0 23.8 + - + +
358A GLY* 1.3 71.8 - - - +
360A LEU* 1.3 66.0 + - - +
362A ASN* 3.4 7.6 + - - +
363A ILE* 3.0 27.6 + - + +
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Residues in contact with LEU 360 (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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341A ILE* 5.8 0.2 - - + -
343A VAL* 4.1 16.6 - - + -
354A ASN 3.4 18.3 + - - +
355A GLN* 4.3 4.5 - - - +
356A GLU 2.9 15.0 + - - +
357A ALA 3.8 4.5 - - - +
359A LYS* 1.3 76.8 - - - +
361A LYS* 1.3 56.1 + - - +
363A ILE* 3.2 8.4 + - + +
364A ILE* 2.9 43.6 + - + +
428A VAL* 4.0 26.2 - - + -
430A LEU* 4.8 3.1 - - + -
442A ILE* 3.8 38.1 - - + -
445A VAL* 4.4 6.7 - - + -
446A LEU* 4.2 13.9 - - + -
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Residues in contact with LYS 361 (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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357A ALA 3.0 17.3 + - - +
358A GLY* 3.8 7.2 - - - +
359A LYS 3.3 0.2 - - - -
360A LEU* 1.3 75.5 - - - +
362A ASN* 1.3 55.8 + - - +
364A ILE* 3.4 1.6 + - - +
365A LEU* 3.0 53.9 + - + +
445A VAL* 3.7 22.1 - - + +
448A GLU* 3.2 41.9 + - - +
449A THR* 3.8 17.0 - - + -
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Residues in contact with ASN 362 (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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320A ASN* 5.5 1.0 + - - -
322A VAL* 3.8 21.2 - - - +
358A GLY 3.4 8.9 + - - +
359A LYS* 3.4 10.4 + - - +
360A LEU 3.4 0.4 - - - -
361A LYS* 1.3 76.5 - - - +
363A ILE* 1.4 55.3 + - - +
365A LEU* 3.8 5.9 - - - +
366A SER* 2.8 45.6 + - - -
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Residues in contact with ILE 363 (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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321A ILE* 3.8 12.8 - - + -
322A VAL* 3.9 24.5 - - + -
325A LEU* 3.7 21.3 - - + +
341A ILE* 3.7 23.3 - - + -
343A VAL* 4.2 7.4 - - + -
354A ASN* 3.6 45.1 - - + +
359A LYS* 3.0 20.2 + - + +
360A LEU* 3.5 12.3 - - + +
362A ASN* 1.4 76.0 - - - +
364A ILE* 1.4 57.4 + - - +
366A SER* 3.4 1.7 + - - -
367A VAL* 2.9 30.5 + - - +
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Residues in contact with ILE 364 (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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341A ILE* 4.3 15.0 - - + +
360A LEU* 2.9 40.4 + - + +
361A LYS 3.9 3.1 - - - +
363A ILE* 1.4 74.8 - - - +
365A LEU* 1.3 57.1 + - - +
367A VAL* 3.3 1.9 + - - +
368A LYS* 2.9 43.2 + - + +
426A VAL* 5.3 0.2 - - + -
428A VAL* 5.0 2.7 - - + -
445A VAL* 4.2 5.8 - - + -
446A LEU* 3.7 30.1 - - + -
449A THR* 3.5 31.6 - - - +
451A ILE* 3.8 28.0 - - + -
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Residues in contact with LEU 365 (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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361A LYS* 3.0 45.4 + - + +
362A ASN* 4.1 4.5 - - - +
364A ILE* 1.3 74.8 - - - +
366A SER* 1.4 52.2 + - - +
368A LYS* 3.8 9.7 - - + +
369A GLU* 2.8 36.4 + - - +
449A THR* 3.9 29.6 - - + +
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Residues in contact with SER 366 (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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322A VAL* 3.7 30.3 - - - +
326A LYS* 4.7 8.4 - - - +
362A ASN* 2.8 36.0 + - - -
363A ILE 3.7 3.8 - - - -
365A LEU* 1.4 72.5 - - - +
367A VAL* 1.3 61.6 + - - +
369A GLU* 3.8 11.1 - - - +
370A GLU* 2.9 31.8 + - - +
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Residues in contact with VAL 367 (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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312A ILE* 4.7 1.3 - - + -
325A LEU* 3.9 26.9 - - + -
326A LYS* 5.9 0.4 - - + -
329A ILE* 3.7 27.8 - - + +
339A ILE* 4.6 5.2 - - + -
341A ILE* 3.8 21.3 - - + -
363A ILE 2.9 19.0 + - - +
364A ILE 3.8 3.1 - - - +
366A SER* 1.3 72.6 - - - +
368A LYS* 1.4 61.8 + - - +
370A GLU* 3.2 2.9 + - - +
371A ILE* 3.0 40.0 + - + +
426A VAL* 3.9 24.9 - - + -
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Residues in contact with LYS 368 (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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364A ILE* 2.9 33.1 + - + +
365A LEU* 3.8 11.2 - - + +
367A VAL* 1.4 74.6 - - - +
369A GLU* 1.3 58.1 + - - +
371A ILE* 3.4 6.6 + - - +
372A ASP* 2.9 49.3 + - - +
423A LYS* 5.3 6.7 - - - +
426A VAL* 4.1 21.2 - - + +
449A THR 3.5 26.5 - - - +
450A ASN* 3.7 19.4 - - - +
451A ILE* 4.9 2.7 - - - +
452A ASP* 5.0 9.6 + - - -
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Residues in contact with GLU 369 (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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326A LYS* 6.0 0.9 - - - +
365A LEU 2.8 20.1 + - - +
366A SER* 3.8 10.1 + - - +
367A VAL 3.3 0.2 - - - -
368A LYS* 1.3 76.0 - - - +
370A GLU* 1.4 60.7 + - - +
372A ASP* 3.4 8.1 + - - +
373A ASN* 2.9 51.3 + - - +
376A LYS* 6.4 0.2 - - - -
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Residues in contact with GLU 370 (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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326A LYS* 3.3 36.2 - - + +
329A ILE* 3.8 20.9 - - + -
330A ASN* 2.7 38.9 + - - +
366A SER 2.9 18.2 + - - +
367A VAL 3.2 4.7 + - - +
369A GLU* 1.4 78.4 - - - +
371A ILE* 1.3 62.2 + - - +
373A ASN* 3.4 24.6 + - - +
374A LEU* 3.4 17.0 + - - +
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Residues in contact with ILE 371 (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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329A ILE* 3.7 21.1 - - + -
339A ILE* 4.2 20.4 - - + -
367A VAL* 3.0 27.7 + - + +
368A LYS* 3.8 4.0 - - - +
370A GLU* 1.3 72.3 - - - +
372A ASP* 1.4 67.0 + - - +
374A LEU* 3.1 24.5 + - + +
375A GLU* 4.0 2.4 + - - +
416A TRP* 4.2 6.0 - - + -
423A LYS* 4.0 20.1 - - + +
424A PRO* 3.9 35.0 - - + +
426A VAL* 3.4 33.0 - - + -
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Residues in contact with ASP 372 (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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368A LYS* 2.9 37.1 + - - +
369A GLU* 3.8 8.2 - - + +
371A ILE* 1.4 75.9 - - - +
373A ASN* 1.4 60.6 + - - +
375A GLU* 3.5 15.4 + - - +
376A LYS* 3.4 42.9 + - - +
423A LYS* 2.8 35.9 + - - +
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Residues in contact with ASN 373 (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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330A ASN* 6.1 0.4 - - - +
369A GLU* 2.9 39.2 + - - +
370A GLU* 3.7 20.6 + - - +
371A ILE 3.2 0.6 - - - -
372A ASP* 1.4 73.6 - - - +
374A LEU* 1.4 54.4 + - - +
375A GLU 3.2 0.7 - - - -
376A LYS* 3.4 26.8 - - + +
377A ASN* 2.8 48.7 + - - +
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Residues in contact with LEU 374 (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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329A ILE* 4.0 24.7 - - + +
330A ASN* 3.6 39.5 - - - +
333A GLY* 4.4 2.9 - - - -
334A ARG* 4.4 16.8 - - + +
370A GLU 3.4 9.3 + - - +
371A ILE* 3.1 19.0 + - + +
373A ASN* 1.4 74.3 - - - +
375A GLU* 1.3 56.7 + - - +
377A ASN* 5.0 1.3 - - - -
378A ASN* 3.3 40.5 + - - +
415A LEU* 3.8 8.3 - - + +
416A TRP* 4.0 26.9 - - + -
424A PRO* 5.5 0.2 - - + -
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Residues in contact with GLU 375 (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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371A ILE 4.0 1.3 + - - +
372A ASP* 3.5 13.2 + - - +
374A LEU* 1.3 75.7 - - - +
376A LYS* 1.4 66.3 + - + +
378A ASN 3.2 21.0 - - - -
415A LEU* 3.7 20.8 - - + +
416A TRP* 3.4 26.9 + - + +
423A LYS* 4.1 23.1 + - - +
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Residues in contact with LYS 376 (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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372A ASP* 3.4 34.9 + - - +
373A ASN* 3.4 32.2 + - + +
375A GLU* 1.4 81.2 + - + +
377A ASN* 1.3 59.8 + - - +
378A ASN 3.7 0.9 + - - -
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Residues in contact with ASN 377 (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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373A ASN* 2.8 36.5 + - - +
374A LEU* 4.5 1.1 - - - +
376A LYS* 1.3 73.6 - - - +
378A ASN* 1.4 74.7 + - - +
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Residues in contact with ASN 378 (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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334A ARG* 5.8 3.8 - - - +
374A LEU* 3.3 27.6 + - - +
375A GLU* 3.2 19.9 + - - -
376A LYS 4.9 1.0 - - - +
377A ASN* 1.4 91.2 - - - +
414A PHE* 6.6 0.4 - - + -
415A LEU* 3.7 27.1 - - + +
467B LYS* 5.9 3.0 - - - +
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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