Contacts of the helix formed by residues 391 - 407 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363F LYS 5.4 0.6 + - - -
364F GLY 3.3 22.6 + - - -
365F TYR* 4.0 10.5 - - - +
388F ASP* 3.0 17.8 + - + +
390F THR* 1.3 79.9 + - - +
392F PRO* 1.3 72.7 - - - +
393F ASP* 3.2 17.5 + - - +
394F ALA* 2.9 19.6 + - + +
395F CYS* 3.0 14.7 + - - -
428F PHE* 3.3 43.3 - - + +
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Residues in contact with PRO 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390F THR 3.5 10.0 - - - +
391F ASN* 1.3 86.7 - - - +
393F ASP* 1.3 70.3 + - - +
395F CYS* 3.0 20.6 + - + +
396F LYS* 3.0 13.2 + - - +
428F PHE* 3.9 15.5 - - + -
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Residues in contact with ASP 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365F TYR* 3.5 30.1 + - + +
391F ASN* 3.2 7.8 + - - +
392F PRO* 1.3 84.6 - - - +
394F ALA* 1.3 56.2 + - - +
396F LYS* 3.5 8.9 + - - +
397F TRP* 3.1 27.0 + - - +
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Residues in contact with ALA 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365F TYR* 3.7 39.9 - - + +
387F TYR* 5.4 5.3 - - + -
388F ASP 3.6 19.7 - - - +
389F PHE* 5.0 3.8 - - + -
391F ASN* 2.9 20.6 + - + +
393F ASP* 1.3 76.0 - - - +
395F CYS* 1.3 66.0 + - - +
397F TRP* 3.3 4.2 + - - +
398F TYR* 3.0 23.9 + - - +
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Residues in contact with CYS 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F PHE* 2.9 39.7 - - - -
391F ASN 3.0 13.4 + - - -
392F PRO* 3.0 11.0 + - + +
394F ALA* 1.3 77.8 - - - +
396F LYS* 1.3 52.2 + - - +
398F TYR* 3.1 3.9 + - - +
399F ALA* 2.7 37.7 + - - +
443F ILE* 5.5 2.7 - - - -
447F LEU* 3.8 25.8 - - + +
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Residues in contact with LYS 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392F PRO 3.0 12.0 + - - +
393F ASP* 3.8 11.9 - - - +
395F CYS* 1.3 77.3 - - - +
397F TRP* 1.3 55.7 + - - +
399F ALA* 3.7 6.3 - - + +
400F ASP* 2.9 63.5 + - - +
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Residues in contact with TRP 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F ASP 4.7 1.1 - - - -
318F PHE* 4.3 8.5 - + - -
356F VAL* 3.4 35.0 - - + -
359F GLU* 3.3 28.4 + - - -
360F LEU* 3.7 14.4 - - + -
363F LYS* 4.5 5.2 - - - -
365F TYR* 3.8 24.9 - + + +
387F TYR* 3.5 32.5 - + - -
393F ASP 3.1 16.0 + - - +
394F ALA 3.5 7.4 - - - +
395F CYS 3.2 0.2 - - - -
396F LYS* 1.3 76.0 - - - +
398F TYR* 1.3 69.7 + - + +
400F ASP* 3.4 8.8 + - - +
401F LYS* 3.3 63.0 + - + +
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Residues in contact with TYR 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F PHE* 3.3 28.9 - + - -
346F ILE* 3.8 14.2 - - - +
347F ASN 2.8 27.2 + - - -
387F TYR* 3.7 36.3 - + + -
389F PHE* 3.7 31.6 - + + -
394F ALA 3.0 12.8 + - - +
395F CYS 3.5 6.7 - - - +
397F TRP* 1.3 83.1 - - + +
399F ALA* 1.3 65.6 + - - +
401F LYS* 3.0 15.3 + - - +
402F LEU* 3.1 32.4 + - + +
444F TYR* 3.8 4.8 - + - -
447F LEU* 3.7 19.7 - - + -
448F VAL* 4.4 9.0 - - + -
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Residues in contact with ALA 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395F CYS 2.7 21.2 + - - +
396F LYS* 3.7 8.7 - - + +
398F TYR* 1.3 73.2 - - - +
400F ASP* 1.3 59.0 + - - +
402F LEU* 3.0 5.2 + - - +
403F LYS* 2.9 37.5 + - - +
447F LEU* 4.2 12.8 - - + +
451F VAL* 3.6 25.4 - - + +
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Residues in contact with ASP 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F LYS* 2.9 58.1 + - - +
397F TRP* 3.7 9.4 + - + +
398F TYR 3.2 0.2 - - - -
399F ALA* 1.3 77.7 - - - +
401F LYS* 1.3 62.4 + - + +
403F LYS* 3.4 20.2 + - - +
404F GLY* 3.1 18.4 + - - -
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Residues in contact with LYS 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F ASP 4.1 3.4 - - - -
318F PHE* 3.3 43.5 - - + +
319F GLU* 3.7 18.8 - - - +
356F VAL* 5.2 4.2 - - - +
359F GLU* 5.3 0.8 + - - -
397F TRP* 3.3 52.0 + - + +
398F TYR 3.0 7.7 + - - +
400F ASP* 1.3 78.8 - - - +
402F LEU* 1.3 64.2 + - - +
404F GLY* 3.2 3.3 + - - -
405F LEU* 3.2 24.5 + - - +
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Residues in contact with LEU 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318F PHE* 3.9 25.1 - - + -
346F ILE* 4.0 13.7 - - + -
398F TYR* 3.1 35.1 + - + +
399F ALA 3.0 7.2 + - - +
401F LYS* 1.3 73.3 - - - +
403F LYS* 1.3 66.3 + - - +
405F LEU* 2.9 16.7 + - + +
406F VAL* 3.0 17.4 + - - +
413F PHE* 3.8 25.7 - - + -
447F LEU* 3.9 16.4 - - + -
448F VAL* 4.0 23.3 - - + -
451F VAL* 3.8 15.5 - - + -
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Residues in contact with LYS 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399F ALA* 2.9 21.1 + - - +
400F ASP* 3.7 21.7 + - - +
402F LEU* 1.3 75.5 - - - +
404F GLY* 1.3 58.9 + - - +
406F VAL* 3.1 10.5 + - - +
407F ALA* 2.8 31.9 + - - +
451F VAL* 4.1 21.1 - - + +
454F ASP* 4.9 16.0 - - - +
455F THR* 4.1 20.0 - - + +
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Residues in contact with GLY 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400F ASP 3.1 14.3 + - - -
401F LYS* 3.2 5.1 + - - -
402F LEU 3.1 0.6 - - - -
403F LYS* 1.3 77.5 - - - +
405F LEU* 1.3 61.5 + - - +
407F ALA* 3.7 7.7 + - - +
408F MET* 3.5 24.0 + - - +
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Residues in contact with LEU 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F TRP* 3.7 33.2 - - + -
318F PHE* 4.1 23.3 - - + +
320F TRP* 3.5 35.0 - - + +
344F VAL* 4.1 5.2 - - + -
346F ILE* 4.9 0.4 - - + -
401F LYS 3.2 10.6 + - - +
402F LEU* 2.9 9.7 + - + +
404F GLY* 1.3 75.2 - - - +
406F VAL* 1.3 64.7 + - - +
408F MET* 3.0 25.1 + - + +
410F VAL* 3.2 27.5 + - + +
413F PHE* 4.0 22.0 - - + -
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Residues in contact with VAL 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402F LEU 3.0 18.6 + - - +
403F LYS* 3.4 10.8 - - - +
405F LEU* 1.3 72.2 - - - +
407F ALA* 1.3 55.5 + - - +
408F MET 2.8 5.9 + - - -
409F GLY* 2.8 25.1 + - - -
410F VAL* 3.6 20.3 + - - +
413F PHE* 3.8 23.8 - - + -
451F VAL* 4.4 3.4 - - + -
452F LEU* 4.2 7.6 - - + -
455F THR* 3.6 36.1 - - + +
456F VAL* 4.2 13.5 - - + -
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Residues in contact with ALA 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403F LYS 2.8 19.9 + - - +
404F GLY* 3.9 8.7 - - - +
405F LEU 3.3 0.2 - - - -
406F VAL* 1.3 73.4 - - - +
408F MET* 1.3 57.2 + - - +
409F GLY 3.4 0.2 - - - -
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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