Contacts of the helix formed by residues 391 - 408 (chain B) in PDB entry 1XSK
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 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LYS 5.3 0.6 + - - -
364B GLY 3.4 22.0 + - - +
365B TYR* 4.3 4.9 - - - -
388B ASP* 3.2 17.8 + - + +
389B PHE 3.1 0.6 - - - -
390B THR* 1.3 78.2 - - - +
392B PRO* 1.3 64.5 - - - +
393B ASP* 3.0 26.7 + - - +
394B ALA* 3.1 15.9 + - + +
395B CYS* 3.0 30.7 + - - -
428B PHE* 3.1 41.1 - - + +
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Residues in contact with PRO 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B THR 3.4 9.2 - - - +
391B ASN* 1.3 84.7 - - - +
393B ASP* 1.3 69.3 + - - +
395B CYS* 3.3 9.4 + - + +
396B LYS* 3.1 21.7 + - - +
428B PHE* 3.5 20.9 - - + -
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Residues in contact with ASP 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TYR* 3.3 29.1 + - + +
391B ASN* 3.0 10.9 + - - +
392B PRO* 1.3 77.8 - - - +
394B ALA* 1.3 67.4 + - - +
396B LYS* 3.1 9.5 + - - +
397B TRP* 2.9 23.7 + - - +
428B PHE* 5.6 3.5 - - - -
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TYR* 3.7 39.4 - - + +
387B TYR* 5.5 5.4 - - + -
388B ASP 3.4 25.8 - - - +
389B PHE* 5.1 3.2 - - + -
391B ASN* 3.1 14.9 + - + +
393B ASP* 1.3 80.1 - - - +
395B CYS* 1.3 62.2 + - - +
397B TRP* 3.3 3.3 + - - +
398B TYR* 3.1 24.3 + - - +
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Residues in contact with CYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.0 38.8 - - - -
391B ASN 3.0 14.9 + - - -
392B PRO* 3.5 10.8 - - + +
394B ALA* 1.3 77.6 - - - +
396B LYS* 1.3 57.4 + - - +
398B TYR* 3.7 1.7 - - - +
399B ALA* 2.9 32.1 + - - +
443B ILE* 5.5 2.0 - - - -
447B LEU* 3.8 28.7 - - + +
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Residues in contact with LYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392B PRO 3.1 13.1 + - - +
393B ASP* 3.6 11.4 - - - +
395B CYS* 1.3 75.1 - - - +
397B TRP* 1.3 58.6 + - - +
399B ALA* 3.2 6.1 + - - +
400B ASP* 2.8 57.2 + - - +
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Residues in contact with TRP 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ASP 4.8 1.6 - - - -
318B PHE* 4.3 8.1 - + - -
356B VAL* 3.3 35.7 - - + -
359B GLU* 3.6 24.7 + - - +
360B LEU* 3.7 14.5 - - + +
363B LYS* 4.3 9.4 - - - +
365B TYR* 3.9 25.6 - + + -
387B TYR* 3.7 31.4 - + - -
393B ASP 2.9 12.5 + - - +
394B ALA 3.4 8.7 - - - +
395B CYS 3.3 0.2 - - - -
396B LYS* 1.3 78.5 - - - +
398B TYR* 1.3 81.6 + - + +
400B ASP* 3.0 14.5 + - - +
401B LYS* 3.0 54.3 + - + +
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Residues in contact with TYR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B PHE* 3.4 26.8 - + - -
346B ILE* 4.0 6.1 - - - +
347B ASN 2.7 38.2 + - - -
387B TYR* 3.8 36.1 - + + -
389B PHE* 3.8 29.4 - + + -
394B ALA 3.1 12.7 + - - +
395B CYS 3.7 3.1 - - - +
397B TRP* 1.3 88.4 - - + +
399B ALA* 1.3 63.2 + - - +
401B LYS* 3.1 15.5 + - - +
402B LEU* 3.2 35.3 + - + +
444B TYR* 3.9 8.1 - + - -
447B LEU* 3.8 10.8 - - + -
448B VAL* 4.4 10.8 - - + -
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B CYS 2.9 19.2 + - - +
396B LYS* 3.6 7.2 - - - +
398B TYR* 1.3 76.5 - - - +
400B ASP* 1.3 63.3 + - - +
402B LEU* 3.0 7.7 + - - +
403B LYS* 3.0 32.5 + - - +
447B LEU* 4.2 13.5 - - + -
451B VAL* 3.8 24.6 - - + +
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LYS* 2.8 55.2 + - - +
397B TRP* 3.4 7.9 + - - +
399B ALA* 1.3 70.9 - - - +
401B LYS* 1.3 66.9 + - - +
403B LYS* 3.1 26.3 + - - +
404B GLY* 3.0 19.4 + - - -
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Residues in contact with LYS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ASP 4.2 3.4 - - - -
318B PHE* 3.5 41.5 - - + +
319B GLU* 4.0 18.4 - - - +
356B VAL* 5.5 3.4 - - - -
359B GLU* 5.1 1.0 + - - -
397B TRP* 3.0 57.2 + - + +
398B TYR 3.1 7.7 + - - +
400B ASP* 1.3 76.4 - - - +
402B LEU* 1.3 62.9 + - - +
404B GLY* 3.1 10.8 + - - -
405B LEU* 3.2 17.7 + - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 3.7 25.4 - - + -
346B ILE* 4.0 14.1 - - + -
398B TYR* 3.6 35.4 - - + +
399B ALA 3.0 7.5 + - - +
401B LYS* 1.3 74.9 - - - +
403B LYS* 1.3 65.0 + - - +
405B LEU* 3.1 6.5 + - - +
406B VAL* 2.9 27.1 + - - +
413B PHE* 3.7 27.6 - - + -
447B LEU* 4.2 5.6 - - + -
448B VAL* 3.9 31.6 - - + -
451B VAL* 4.1 14.6 - - + -
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Residues in contact with LYS 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399B ALA* 3.0 23.0 + - - +
400B ASP* 3.1 26.4 + - - +
402B LEU* 1.3 76.0 - - - +
404B GLY* 1.3 58.5 + - - +
406B VAL* 3.1 8.3 + - - +
407B ALA* 2.8 32.8 + - - +
451B VAL* 3.6 26.5 - - + +
454B ASP* 5.6 8.4 + - - +
455B THR* 4.1 17.1 - - + +
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Residues in contact with GLY 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B ASP 3.0 12.8 + - - -
401B LYS* 3.5 5.8 - - - -
402B LEU 3.1 0.6 - - - -
403B LYS* 1.3 78.5 - - - +
405B LEU* 1.3 60.6 + - - +
407B ALA* 3.5 7.0 + - - +
408B MET* 3.1 26.8 + - - +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B TRP* 3.7 27.8 - - + -
318B PHE* 4.0 24.9 - - + +
320B TRP* 3.7 28.7 - - + +
344B VAL* 4.1 9.2 - - + -
346B ILE* 5.0 0.9 - - + -
401B LYS 3.2 10.3 + - - +
402B LEU* 3.1 9.7 + - + +
404B GLY* 1.3 73.9 - - - +
406B VAL* 1.3 62.7 + - - +
408B MET* 3.2 21.3 + - + +
410B VAL* 2.9 41.0 + - + +
413B PHE* 4.0 21.8 - - + -
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B LEU 2.9 18.9 + - - +
403B LYS* 3.1 11.4 + - - +
405B LEU* 1.3 73.6 - - - +
407B ALA* 1.3 59.3 + - - +
408B MET 3.0 5.2 - - - -
409B GLY* 2.9 20.3 + - - -
410B VAL 3.5 16.1 - - - +
413B PHE* 3.8 24.0 - - + -
451B VAL* 4.6 3.6 - - + -
452B LEU* 4.2 9.0 - - + -
455B THR* 3.4 35.2 - - + +
456B VAL* 4.1 14.4 - - + -
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B GLU* 4.5 6.3 - - - +
403B LYS 2.8 17.5 + - - +
404B GLY* 3.8 7.2 - - - +
406B VAL* 1.3 77.9 - - - +
408B MET* 1.3 58.4 + - - +
409B GLY* 3.2 1.6 + - - -
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Residues in contact with MET 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B TRP* 3.5 35.9 - - + +
328B PRO* 3.7 19.7 - - + -
329B GLU* 3.2 37.7 - - + +
332B ILE* 2.9 35.7 - - + +
404B GLY 3.1 14.4 + - - +
405B LEU* 3.3 24.2 - - + +
406B VAL 3.0 0.4 - - - -
407B ALA* 1.3 78.6 - - - +
409B GLY* 1.3 56.2 + - - +
410B VAL* 3.6 3.4 - - + -
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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