Contacts of the helix formed by residues 388 - 407 (chain A) in PDB entry 3CKM
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 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A PRO* 2.9 26.4 + - - +
387A GLN* 1.3 76.5 + - - +
389A ASP* 1.3 67.3 + - - +
390A LEU* 3.3 11.9 + - - +
391A GLY* 2.8 32.9 + - - -
392A GLN* 3.0 21.5 + - - +
414A TYR* 5.3 1.1 - - - -
465A ARG* 5.8 3.0 - - - +
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Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASN* 1.3 76.1 - - - +
390A LEU* 1.3 63.8 + - - +
392A GLN* 3.2 8.6 + - - +
393A ARG* 3.0 46.0 + - - +
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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
----------------------------------------------------------
362A PRO* 3.9 18.8 - - + -
363A GLU* 4.2 4.7 - - - +
386A PRO* 5.7 1.8 - - + -
388A ASN* 3.2 11.0 + - - +
389A ASP* 1.3 78.2 - - - +
391A GLY* 1.3 58.2 + - - +
393A ARG* 3.1 30.4 + - - +
394A VAL* 2.9 53.1 + - + +
465A ARG* 4.3 20.0 - - - +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A MSE 3.4 25.2 - - - +
386A PRO* 3.4 28.6 - - - +
388A ASN* 2.8 12.4 + - - -
390A LEU* 1.3 76.2 - - - +
392A GLN* 1.3 57.3 + - - +
394A VAL* 4.6 1.6 - - - -
395A GLY* 2.8 25.8 + - - -
414A TYR* 4.0 3.2 - - - -
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Residues in contact with GLN 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ASN 3.0 12.9 + - - +
389A ASP* 3.5 10.9 + - - +
391A GLY* 1.3 77.0 - - - +
393A ARG* 1.3 84.5 + - - +
395A GLY* 3.9 0.5 - - - -
396A ASN* 3.0 37.8 + - - +
414A TYR* 3.9 27.2 + - + +
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A THR* 5.9 0.4 - - - -
347A PRO* 3.5 35.5 - - + +
363A GLU* 3.3 19.6 + - - +
389A ASP* 3.0 41.6 + - - +
390A LEU* 3.6 38.1 - - - +
392A GLN* 1.3 92.8 - - - +
394A VAL* 1.3 62.4 + - - +
396A ASN* 3.4 6.6 + - - +
397A ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A PRO* 3.7 39.3 - - + +
363A GLU* 4.1 10.5 - - - +
366A ALA* 3.6 21.8 - - + +
385A MSE 3.7 20.6 - - + -
390A LEU* 2.9 30.1 + - + +
391A GLY* 4.6 0.9 - - - -
393A ARG* 1.3 76.1 - - - +
395A GLY* 1.3 65.2 + - - +
397A ALA* 3.2 4.0 + - - +
398A PHE* 3.1 18.7 + - - +
436A TYR* 4.9 0.7 - - + +
438A VAL* 4.2 18.4 - - + -
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Residues in contact with GLY 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A VAL* 4.9 0.4 - - - -
385A MSE 3.6 18.9 - - - -
391A GLY 2.8 18.7 + - - -
392A GLN* 3.9 0.9 - - - -
394A VAL* 1.3 77.7 - - - +
396A ASN* 1.3 56.9 + - - +
398A PHE* 3.2 7.7 + - - +
399A ASN* 2.8 29.2 + - - +
412A ILE* 3.8 19.4 - - - +
414A TYR* 5.6 0.9 - - - -
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Residues in contact with ASN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PRO* 5.3 4.9 - - - +
348A ASN* 4.6 12.0 + - - +
392A GLN* 3.0 31.6 + - - +
393A ARG* 3.6 7.8 - - - +
395A GLY* 1.3 75.0 - - - +
397A ALA* 1.3 58.4 + - - +
399A ASN* 3.2 8.7 + - - +
400A VAL* 2.8 52.8 + - - +
414A TYR* 5.7 0.4 + - - -
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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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363A GLU* 3.7 39.5 - - + +
366A ALA* 4.3 0.4 - - + -
367A GLU* 3.8 17.2 - - + +
393A ARG 3.1 13.2 + - - +
394A VAL 3.2 8.7 + - - +
396A ASN* 1.3 77.0 - - - +
398A PHE* 1.3 67.6 + - - +
400A VAL* 3.5 5.0 + - - +
401A ARG* 3.3 20.4 + - - +
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Residues in contact with PHE 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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366A ALA* 3.4 28.4 - - + +
369A ALA 4.0 0.7 - - - -
370A ALA* 3.6 28.1 - - - +
373A MSE 3.9 24.0 - - - -
381A PRO* 4.2 5.2 - - + -
383A VAL* 3.5 33.2 - - + -
385A MSE 6.1 0.2 - - - -
394A VAL 3.1 12.4 + - - +
395A GLY* 3.5 11.0 - - - +
397A ALA* 1.3 75.7 - - - +
399A ASN* 1.3 60.4 + - - +
401A ARG* 3.2 5.0 + - - +
402A TRP* 2.8 46.0 + + + -
410A ALA* 3.8 18.8 - - + -
412A ILE* 4.4 0.4 - - + -
436A TYR* 3.6 25.1 - + + -
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Residues in contact with ASN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLY 2.8 17.1 + - - +
396A ASN* 3.6 11.2 + - - +
398A PHE* 1.3 82.5 - - - +
400A VAL* 1.3 60.0 + - + +
402A TRP* 3.2 1.7 + - - +
403A GLN* 2.8 44.7 + - - +
409A ASP* 3.3 27.3 - - - +
410A ALA* 2.8 40.0 + - - +
412A ILE* 4.3 11.0 - - + -
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASN* 2.8 41.7 + - - +
397A ALA* 4.1 4.9 - - - +
399A ASN* 1.3 77.2 - - + +
401A ARG* 1.3 62.6 + - - +
403A GLN* 3.4 19.3 + - - +
404A GLN* 3.3 38.5 + - - +
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Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLU* 3.5 36.5 + - + +
370A ALA* 3.6 18.6 - - + -
371A ASN* 3.0 45.4 - - - +
397A ALA 3.3 10.5 + - - +
398A PHE 3.2 7.9 + - - +
400A VAL* 1.3 78.0 - - - +
402A TRP* 1.3 65.9 + - - +
404A GLN* 3.1 27.7 + - - +
405A LEU* 3.0 28.0 + - + +
557A GLU* 3.3 25.3 + - - -
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Residues in contact with TRP 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 3.5 27.8 - - + +
373A MSE 4.2 6.5 - - + -
374A TRP* 3.8 29.6 - + + -
378A VAL* 3.5 26.9 - - + -
379A ARG* 4.4 4.9 - - - -
380A ASN* 4.4 1.8 - - - +
381A PRO* 3.3 34.2 - - + +
398A PHE* 2.8 39.8 + + + +
399A ASN 3.6 3.6 - - - +
401A ARG* 1.3 76.5 - - - +
403A GLN* 1.3 58.5 + - - +
405A LEU* 4.4 4.9 - - + +
406A ALA* 2.8 51.2 + - + +
408A THR* 3.4 29.3 - - - +
409A ASP 4.0 3.2 + - - -
410A ALA* 3.8 23.3 - - + +
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Residues in contact with GLN 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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399A ASN* 2.8 28.3 + - - +
400A VAL* 3.6 24.8 + - - +
401A ARG 3.2 0.2 - - - -
402A TRP* 1.3 76.5 - - - +
404A GLN* 1.3 58.8 + - + +
407A GLY* 3.0 27.3 + - - -
408A THR 3.5 17.0 + - - +
409A ASP* 2.5 32.1 - - - +
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Residues in contact with GLN 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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400A VAL* 3.3 29.7 + - + +
401A ARG* 3.1 32.9 + - - +
403A GLN* 1.3 79.6 - - + +
405A LEU* 1.3 63.4 + - + +
407A GLY* 4.6 1.2 + - - -
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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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370A ALA* 3.5 29.8 - - + +
371A ASN* 3.5 30.5 - - - +
374A TRP* 3.4 49.8 + - + +
375A ASN* 5.9 0.4 - - - +
401A ARG* 3.0 26.3 + - + +
402A TRP* 3.9 6.1 - - + +
404A GLN* 1.3 80.9 - - + +
406A ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TRP* 3.4 27.3 - - + -
379A ARG* 5.9 0.2 - - - -
402A TRP* 2.8 45.3 + - + +
405A LEU* 1.3 74.4 - - - +
407A GLY* 1.3 63.0 + - - +
408A THR* 3.4 13.5 + - + +
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Residues in contact with GLY 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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403A GLN* 3.0 21.0 + - - -
404A GLN 4.5 1.1 + - - -
405A LEU 3.6 1.6 - - - -
406A ALA* 1.3 77.7 - - - +
408A THR* 1.3 60.0 + - - +
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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