Contacts of the helix formed by residues 393 - 411 (chain A) in PDB entry 2JDQ
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 393 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A GLU* 3.6 37.6 + - - +
392A ALA* 1.3 75.1 - - - +
394A PHE* 1.3 67.7 + - - +
395A ARG* 4.4 14.0 - - - +
396A THR* 3.0 12.2 + - - +
397A ARG 3.0 17.7 + - - -
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Residues in contact with PHE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ALA 3.7 1.2 + - - -
393A GLU* 1.3 71.1 - - - +
395A ARG* 1.3 84.2 + - + +
397A ARG* 3.0 16.6 + - + +
398A LYS* 2.9 43.6 + - + +
431A LEU* 6.1 0.2 - - + -
434A VAL* 4.0 19.3 - - + -
436A ASP* 3.1 45.3 - - + -
439A ILE* 4.1 15.3 - - + -
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Residues in contact with ARG 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.6 34.8 + - + +
393A GLU* 3.1 14.0 + - - +
394A PHE* 1.3 98.5 - - + +
396A THR* 1.3 61.8 + - - +
398A LYS* 3.8 7.7 + - + +
399A GLU* 3.7 21.7 + - - +
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Residues in contact with THR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU* 2.7 36.8 + - - +
355A LYS* 4.4 9.9 - - + -
356A LYS* 3.8 35.4 - - - +
359A CYS* 4.4 2.9 - - - -
388A ILE* 3.7 22.4 - - + -
392A ALA* 4.0 4.7 - - + -
393A GLU* 3.0 10.3 + - - +
395A ARG* 1.3 76.0 - - - +
397A ARG* 1.3 65.4 + - - +
399A GLU* 2.9 15.4 + - - +
400A ALA* 3.1 11.1 + - - +
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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
----------------------------------------------------------
388A ILE 3.5 22.4 - - - +
389A LEU* 3.1 31.5 + - + +
390A GLN* 5.0 7.9 + - - +
391A THR 5.0 1.6 - - - +
392A ALA* 3.1 28.8 + - - +
393A GLU 3.0 6.1 + - - +
394A PHE* 3.3 19.0 - - - +
396A THR* 1.3 76.5 - - - +
398A LYS* 1.3 57.0 - - - +
400A ALA* 3.4 4.9 + - - +
401A ALA* 3.0 28.2 + - - +
427A PRO* 4.9 0.4 + - - +
430A ASP* 4.5 17.8 + - - +
431A LEU* 3.8 27.4 - - - +
434A VAL* 4.4 15.6 - - - +
439A ILE* 4.2 6.5 - - + -
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Residues in contact with LYS 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A PHE* 2.9 27.0 + - + +
395A ARG* 3.8 9.6 - - + +
397A ARG* 1.3 77.2 - - - +
399A GLU* 1.3 71.0 + - - +
401A ALA* 3.4 3.5 + - - +
402A TRP* 3.2 50.1 + - + +
436A ASP* 4.0 11.0 - - - +
438A LYS* 4.0 40.2 + - - +
439A ILE* 3.4 26.9 - - + +
442A VAL* 4.9 1.0 - - + +
739E ARG* 4.9 3.6 - - - +
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Residues in contact with GLU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LYS* 3.7 33.1 + - + +
359A CYS* 3.6 23.6 - - + +
360A TRP* 3.5 16.3 - - + +
363A SER* 4.0 0.5 - - - -
395A ARG 3.7 14.9 + - - +
396A THR 2.9 8.0 + - - +
398A LYS* 1.3 86.3 - - - +
400A ALA* 1.3 65.7 + - - +
402A TRP* 3.3 7.0 + - - +
403A ALA* 3.0 20.6 + - - +
739E ARG* 2.7 45.3 + - - -
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Residues in contact with ALA 400 (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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359A CYS* 3.8 14.7 - - - +
385A LEU* 3.8 19.9 - - + +
388A ILE* 3.8 28.7 - - + -
389A LEU* 4.4 6.5 - - + +
396A THR 3.1 5.0 + - - +
397A ARG 3.7 7.6 - - - +
399A GLU* 1.3 77.5 - - - +
401A ALA* 1.3 56.7 + - - +
403A ALA* 3.2 7.9 + - - +
404A ILE* 3.0 33.5 + - - +
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 4.0 8.9 - - + +
397A ARG 3.0 15.1 + - - +
398A LYS* 3.4 13.9 - - - +
399A GLU 3.2 0.2 - - - -
400A ALA* 1.3 73.9 - - - +
402A TRP* 1.3 59.6 + - - +
404A ILE* 3.3 4.1 + - - +
405A THR* 2.9 32.9 + - - -
428A LEU* 4.8 4.3 - - + +
431A LEU* 3.9 25.1 - - + -
439A ILE* 4.4 6.1 - - + +
442A VAL* 3.7 12.8 - - + -
443A ALA 5.6 0.4 - - - +
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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
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363A SER* 3.7 4.7 - - - -
398A LYS* 3.2 45.7 + - + +
399A GLU 3.4 9.4 - - - +
401A ALA* 1.3 75.5 - - - +
403A ALA* 1.3 64.9 + - - +
405A THR* 5.4 0.7 - - + -
406A ASN* 2.9 59.9 + - - -
442A VAL* 3.4 29.6 - - + +
695E LEU* 3.7 29.4 - - + -
735E MET* 4.3 22.0 - - + -
737E ARG* 4.0 24.2 - - + -
739E ARG* 3.5 54.8 - - - +
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Residues in contact with ALA 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A CYS 4.1 4.7 - - - +
362A ILE* 4.4 2.9 - - + -
363A SER* 3.4 31.4 - - - +
366A THR* 2.9 21.2 + - + +
385A LEU* 3.6 24.9 - - + -
399A GLU 3.0 12.3 + - - +
400A ALA* 3.4 11.0 - - - +
401A ALA 3.2 0.2 - - - -
402A TRP* 1.3 77.0 - - - +
404A ILE* 1.3 62.6 + - - +
407A ALA* 3.2 10.2 + - - +
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 3.6 28.3 - - + -
385A LEU* 4.0 19.3 - - + +
386A ILE* 4.1 17.7 - - + -
389A LEU* 4.3 16.2 - - + -
400A ALA 3.0 22.7 + - - +
401A ALA 3.8 3.8 - - - +
403A ALA* 1.3 74.9 - - - +
405A THR* 1.3 58.0 + - - +
407A ALA* 3.3 8.5 - - - +
408A THR* 3.1 30.7 + - + +
419A LEU* 4.9 5.6 - - + -
424A CYS* 4.2 20.9 - - + -
428A LEU* 4.3 23.3 - - + -
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Residues in contact with THR 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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401A ALA 2.9 18.7 + - - -
402A TRP* 4.0 2.7 - - + -
404A ILE* 1.3 74.5 - - - +
406A ASN* 1.3 67.0 + - - +
408A THR* 2.8 22.6 + - - -
409A SER* 3.0 7.4 + - - -
428A LEU* 4.3 9.5 - - - +
442A VAL* 2.8 38.8 + - + +
445A ASN* 3.3 25.6 - - + +
446A GLY* 3.5 15.4 - - - +
449A ASN* 3.7 1.4 + - - -
695E LEU* 5.7 0.4 - - + -
737E ARG* 3.8 8.5 - - - +
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Residues in contact with ASN 406 (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 SER* 2.8 25.3 + - - -
366A THR* 3.3 25.4 - - - +
367A ALA* 3.7 9.1 - - - +
402A TRP* 2.9 36.6 + - - +
405A THR* 1.3 75.4 - - - +
407A ALA* 1.3 64.3 + - - +
409A SER* 2.6 24.5 + - - +
410A GLY* 3.1 5.7 + - - -
737E ARG* 3.1 48.6 + - - +
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Residues in contact with ALA 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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366A THR* 3.6 14.2 + - - -
373A ILE* 3.6 14.0 - - + +
382A PHE* 3.7 29.2 - - + -
403A ALA 3.2 12.3 + - - +
404A ILE 3.3 10.5 - - - +
406A ASN* 1.3 78.7 - - - +
408A THR* 1.3 57.7 + - - +
411A GLY* 2.9 31.0 + - - -
416A ILE* 4.2 2.9 - - - +
419A LEU* 3.9 10.1 - - + -
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Residues in contact with THR 408 (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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404A ILE* 3.1 22.8 + - + +
405A THR* 2.8 14.9 + - - -
407A ALA* 1.3 75.7 - - - +
409A SER* 1.3 60.9 + - - +
411A GLY 4.1 3.5 + - - -
416A ILE* 3.9 19.3 - - + +
419A LEU* 4.4 13.9 - - + -
424A CYS* 5.5 0.9 - - - -
428A LEU* 5.2 0.4 - - + -
446A GLY* 3.4 13.6 - - - +
449A ASN* 3.0 32.6 + - - +
450A ILE* 3.9 28.5 - - + -
452A ARG* 4.1 6.8 + - - -
453A LEU* 4.3 2.6 - - - +
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Residues in contact with SER 409 (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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367A ALA* 5.5 1.0 - - - -
405A THR 3.0 7.7 + - - -
406A ASN* 2.6 21.9 + - - -
408A THR* 1.3 77.6 + - - +
410A GLY* 1.3 59.8 + - - +
411A GLY 5.0 0.3 - - - +
449A ASN* 3.3 15.5 - - - +
452A ARG* 4.1 13.8 + - - +
692E ARG* 4.4 13.0 + - - +
737E ARG* 3.2 47.0 + - - -
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Residues in contact with GLY 410 (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 THR 5.4 0.2 - - - -
368A GLY 4.8 1.1 - - - -
370A ARG* 3.3 15.0 + - - +
373A ILE* 3.5 10.3 - - - -
406A ASN 3.1 5.0 + - - -
409A SER* 1.3 83.3 + - - +
411A GLY* 1.3 59.8 + - - +
692E ARG* 2.7 49.5 + - - -
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Residues in contact with GLY 411 (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 ARG* 3.8 9.9 + - - -
373A ILE* 3.6 5.4 - - - +
407A ALA 2.9 17.0 + - - -
408A THR 4.1 2.3 + - - +
409A SER 3.6 1.2 - - - +
410A GLY* 1.3 81.2 - - - +
412A SER* 1.3 65.3 - - - +
415A GLN* 3.1 15.3 - - - -
416A ILE* 3.9 8.3 - - - -
452A ARG* 4.9 3.1 + - - -
453A LEU* 4.0 15.9 - - - +
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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