Contacts of the helix formed by residues 389 - 405 (chain K) in PDB entry 3HX0
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 ARG 389 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K PRO* 1.3 67.9 - - - +
390K GLU* 1.3 77.7 + - - +
392K ALA* 2.8 21.8 + - - +
393K THR* 2.8 17.8 + - - -
418K TYR* 3.2 64.7 + - + -
421K GLY* 3.6 15.4 - - - -
422K LYS 2.8 28.4 + - - +
423K ALA* 2.9 21.8 + - - +
424K THR* 4.5 0.2 - - - +
425K CYS* 4.6 4.0 - - - -
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Residues in contact with GLU 390 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K PRO* 3.3 22.3 - - + +
389K ARG* 1.3 84.0 + - - +
391K GLU* 1.3 63.4 - - - +
393K THR* 3.1 21.4 + - - -
394K GLU* 3.3 12.9 + - - +
423K ALA 4.8 0.9 - - - +
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Residues in contact with GLU 391 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387K MET* 3.8 8.5 - - + -
388K PRO* 2.9 28.7 + - + +
390K GLU* 1.3 73.4 - - - +
392K ALA* 1.3 67.6 + - - +
394K GLU* 3.1 23.1 + - - +
395K ILE* 3.2 13.4 + - + +
479K LEU* 3.6 23.3 - - + +
484K ARG* 4.5 11.5 + - - +
485K ARG 4.3 7.1 + - - +
487K ARG* 2.8 53.8 + - - +
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Residues in contact with ALA 392 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387K MET* 3.8 15.8 - - - -
388K PRO 3.0 9.3 + - - +
389K ARG 2.8 16.6 + - - +
391K GLU* 1.3 72.1 - - - +
393K THR* 1.3 60.3 + - - +
395K ILE* 3.2 4.2 + - - +
396K GLU* 2.9 23.4 + - - +
418K TYR* 3.7 22.4 - - + -
425K CYS* 4.1 11.7 - - - -
428K VAL* 4.0 21.8 - - + +
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Residues in contact with THR 393 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389K ARG* 2.8 18.5 + - - -
390K GLU* 3.1 12.3 + - - -
392K ALA* 1.3 77.1 - - - +
394K GLU* 1.3 51.2 + - + +
396K GLU* 3.1 9.1 + - - +
397K GLN* 2.7 55.6 + - + +
418K TYR* 2.7 29.3 + - - +
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Residues in contact with GLU 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390K GLU* 3.6 12.0 - - - +
391K GLU* 3.3 14.3 + - - +
393K THR* 1.3 77.0 - - + +
395K ILE* 1.3 51.1 + - - +
397K GLN* 2.7 29.3 + - - +
398K THR* 2.7 21.9 + - - +
479K LEU* 3.8 18.8 - - + +
484K ARG* 3.4 37.1 + - - -
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Residues in contact with ILE 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387K MET* 3.7 34.5 - - + -
391K GLU* 3.2 12.7 + - + +
392K ALA 3.6 5.6 - - - +
394K GLU* 1.3 74.0 - - - +
396K GLU* 1.3 62.1 + - - +
398K THR* 3.3 10.5 + - - -
399K VAL* 3.2 22.7 + - - +
428K VAL* 3.9 11.7 - - + -
456K PHE* 3.6 16.4 - - + -
477K CYS* 3.8 15.0 - - - -
479K LEU* 3.6 21.7 - - + +
487K ARG* 4.0 18.4 - - + -
488K ARG 5.7 0.2 - - - +
489K LEU* 4.0 21.5 - - + -
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Residues in contact with GLU 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392K ALA 2.9 14.1 + - - +
393K THR* 3.3 14.1 - - - +
395K ILE* 1.3 73.4 - - - +
397K GLN* 1.3 91.6 + - - +
399K VAL* 3.4 2.8 + - - +
400K GLN* 3.0 41.0 + - - +
412K CYS* 3.6 20.8 - - - +
413K VAL* 5.5 0.2 - - - -
414K ALA* 3.5 34.3 - - + +
418K TYR* 5.5 2.9 + - + +
428K VAL* 4.6 2.5 - - + -
430K VAL* 4.5 17.9 - - + +
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Residues in contact with GLN 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393K THR* 2.7 31.0 + - + +
394K GLU* 2.7 18.5 + - - +
396K GLU* 1.3 94.7 + - - +
398K THR* 1.3 58.4 + - - -
400K GLN* 3.5 17.3 + - - +
401K LYS* 3.2 53.9 + - - +
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Residues in contact with THR 398 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394K GLU* 2.7 19.7 + - - +
395K ILE* 3.4 10.2 - - - -
396K GLU 3.1 0.4 - - - -
397K GLN* 1.3 76.4 - - - +
399K VAL* 1.3 66.5 + - - +
401K LYS* 3.7 5.2 - - - +
402K ALA* 3.1 22.2 + - - +
451K LEU* 4.3 7.0 - - + -
454K GLU* 4.8 7.9 - - - +
456K PHE* 3.8 38.1 - - + -
479K LEU* 4.0 10.2 - - - +
480K PRO* 5.5 4.0 - - + +
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Residues in contact with VAL 399 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K ILE 3.2 15.5 + - - +
396K GLU 3.9 3.1 - - - +
398K THR* 1.3 75.3 - - - +
400K GLN* 1.3 57.9 + - - +
402K ALA* 3.4 2.6 + - - +
403K ALA* 2.9 27.7 + - - +
430K VAL* 3.8 31.9 - - + -
432K ILE* 4.1 15.5 - - + -
447K LEU* 3.9 6.5 - - + +
451K LEU* 4.0 23.1 - - + -
456K PHE* 4.3 4.5 - - + -
489K LEU* 4.1 22.0 - - + -
491K ILE* 4.1 16.4 - - + -
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Residues in contact with GLN 400 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396K GLU* 3.0 44.8 + - - +
397K GLN* 3.5 20.4 - - - +
399K VAL* 1.3 77.3 - - - +
401K LYS* 1.3 53.7 + - + +
403K ALA* 3.1 2.1 + - - +
404K GLN* 2.7 71.6 + - + +
412K CYS* 3.9 32.9 + - + +
430K VAL* 5.4 0.2 - - - +
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Residues in contact with LYS 401 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397K GLN* 3.2 46.7 + - - +
398K THR* 3.7 5.6 - - - +
400K GLN* 1.3 78.3 - - + +
402K ALA* 1.3 65.7 + - - +
404K GLN* 3.0 11.9 + - - +
405K ALA* 3.0 24.4 + - - +
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Residues in contact with ALA 402 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398K THR 3.1 8.4 + - - +
399K VAL 3.7 2.7 - - - +
401K LYS* 1.3 78.1 - - - +
403K ALA* 1.3 58.8 + - - +
405K ALA* 3.5 10.2 - - - +
406K PHE* 3.1 26.7 - - - -
447K LEU* 3.7 9.4 - - + -
450K SER* 4.3 12.1 + - - +
451K LEU* 3.5 33.0 - - + -
454K GLU* 4.3 5.4 - - - +
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Residues in contact with ALA 403 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399K VAL 2.9 19.1 + - - +
400K GLN 3.4 4.7 - - - +
402K ALA* 1.3 74.3 - - - +
404K GLN* 1.3 56.6 + - - +
405K ALA 3.0 4.9 - - - -
406K PHE* 3.0 24.2 + - - +
407K ASN 3.4 0.2 + - - -
410K LEU* 3.3 30.2 - - + +
412K CYS* 4.3 7.0 - - - -
432K ILE* 4.2 11.2 - - + -
443K ILE* 5.1 1.3 - - + -
447K LEU* 3.6 24.5 - - + -
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Residues in contact with GLN 404 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400K GLN* 2.7 56.6 + - + +
401K LYS* 3.0 9.3 + - - +
403K ALA* 1.3 68.8 - - + +
405K ALA* 1.3 58.8 + - - +
406K PHE 3.1 5.8 - - - -
407K ASN 3.3 13.9 + - - +
408K SER* 3.3 37.4 + - - -
410K LEU* 3.6 27.8 + - + +
412K CYS* 5.2 0.9 - - - -
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Residues in contact with ALA 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401K LYS 3.0 10.8 + - - +
402K ALA* 3.5 16.6 - - - +
403K ALA 3.0 1.0 - - - -
404K GLN* 1.3 78.1 - - - +
406K PHE* 1.3 64.1 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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