Contacts of the helix formed by residues 367 - 377 (chain K) in PDB entry 6X5A
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 PHE 367 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318K TRP* 4.5 25.4 - + - -
319K PRO* 6.4 1.1 - - + -
322K THR* 5.1 6.7 - - + -
345K PHE* 4.0 25.1 - + + -
365K LEU* 3.5 47.1 - - + -
366K SER* 1.3 78.5 - - - +
368K SER* 1.3 62.2 + - - +
369K HIS* 3.2 11.7 - + - -
370K THR* 3.0 28.7 - - + +
371K GLU* 2.7 26.2 + - - +
467K HIS* 4.5 13.2 - + - -
469K PHE* 4.0 40.2 - + + -
470K ILE* 4.6 4.5 - - + -
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Residues in contact with SER 368 (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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195K LEU* 6.3 1.1 - - - -
197K THR* 3.1 30.7 - - - +
215K MET* 3.6 28.6 - - - +
346K TYR* 4.8 4.3 - - - -
366K SER* 3.7 6.4 - - - +
367K PHE* 1.3 76.8 - - - +
369K HIS* 1.3 58.9 + - - +
371K GLU* 3.3 12.0 + - - +
372K LYS* 2.9 28.2 + - - +
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Residues in contact with HIS 369 (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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195K LEU* 5.9 1.8 - - + -
196K ASN 5.8 5.6 - - - +
197K THR* 6.0 0.9 - - - -
318K TRP* 4.8 2.3 - + - -
343K GLU* 3.1 40.7 + - + +
344K PRO* 2.7 32.9 + - + -
345K PHE* 4.5 1.3 - - - -
346K TYR* 3.2 38.7 - + + +
367K PHE* 3.7 16.9 - + + -
368K SER* 1.3 71.4 + - - +
370K THR* 1.3 71.8 + - + -
372K LYS* 3.3 7.0 + - - +
373K TYR* 2.9 29.2 + - - +
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Residues in contact with THR 370 (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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318K TRP* 4.9 5.2 - - + -
326K LEU* 4.1 0.5 - - - +
340K LEU* 3.1 46.6 - - - +
367K PHE* 3.0 39.9 - - + +
369K HIS* 1.3 90.0 - - + +
371K GLU* 1.3 57.5 + - - +
373K TYR* 3.2 3.8 + - - +
374K ILE* 2.9 30.7 + - - +
469K PHE* 3.4 24.7 - - + -
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Residues in contact with GLU 371 (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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367K PHE* 2.7 35.0 + - - +
368K SER* 3.3 10.1 + - - +
370K THR* 1.3 76.8 - - - +
372K LYS* 1.3 61.7 + - - +
374K ILE* 3.0 10.2 - - - +
375K LEU* 2.9 26.2 + - - +
421K TYR* 4.9 16.7 - - - -
424K LYS* 5.2 8.3 - - + +
428K PHE* 3.4 31.0 - - + -
467K HIS* 5.5 4.3 + - - -
469K PHE* 3.7 19.7 - - + -
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Residues in contact with LYS 372 (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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196K ASN* 4.4 15.9 - - - +
197K THR* 3.1 37.6 - - - +
198K GLY* 3.2 24.3 - - - +
203K HIS* 3.9 21.3 - - + +
368K SER 2.9 17.9 + - - +
369K HIS* 3.7 6.7 - - - +
370K THR 3.3 0.2 - - - -
371K GLU* 1.3 76.2 - - - +
373K TYR* 1.3 54.0 + - - +
375K LEU* 3.8 9.6 - - + +
376K ASN* 2.4 53.1 + - + +
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Residues in contact with TYR 373 (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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332K LEU* 5.7 1.6 - - + -
336K VAL* 3.7 22.9 - - + +
340K LEU* 4.6 21.5 - - + -
343K GLU* 5.7 4.9 - - - +
369K HIS 2.9 17.2 + - - +
370K THR* 3.2 9.4 + - - +
372K LYS* 1.3 77.6 - - - +
374K ILE* 1.3 64.4 + - + +
376K ASN* 3.0 12.4 - - - +
377K ASN* 2.8 54.4 + - + +
382K LYS* 2.6 34.1 + - - -
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Residues in contact with ILE 374 (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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326K LEU* 5.3 6.5 - - + -
328K ILE* 4.9 12.8 - - + -
331K TRP* 4.0 29.8 - - + -
332K LEU* 6.2 2.9 - - + -
340K LEU* 5.7 3.4 - - + -
370K THR* 2.9 18.1 + - - +
371K GLU* 3.0 25.6 - - - +
373K TYR* 1.3 83.5 - - + +
375K LEU* 1.3 58.9 + - - +
377K ASN* 2.8 36.5 - - - +
378K HIS* 2.8 7.2 + - - -
428K PHE* 3.5 34.5 - - + +
431K TRP* 5.1 4.9 - - + -
468K TYR* 5.2 7.6 - - + -
469K PHE* 5.6 2.5 - - + -
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Residues in contact with LEU 375 (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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202K GLU* 3.3 46.7 - - + +
203K HIS* 4.6 9.0 - - + +
371K GLU 2.9 19.0 + - - +
372K LYS* 3.8 8.5 - - + +
374K ILE* 1.3 78.0 - - + +
376K ASN* 1.3 54.3 + - + +
378K HIS* 2.7 36.7 + - + +
385K CYS* 5.6 0.2 - - - -
395K LYS* 5.3 4.7 - - + -
398K LEU* 3.6 23.1 - - + -
424K LYS* 6.5 0.4 - - - -
428K PHE* 5.1 4.5 - - + -
431K TRP* 3.6 35.0 - - + -
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Residues in contact with ASN 376 (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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203K HIS* 5.4 10.3 - - + +
372K LYS* 2.4 56.1 + - + +
373K TYR* 3.0 9.3 - - - +
375K LEU* 1.3 77.9 - - + +
377K ASN* 1.3 87.1 + - - +
378K HIS* 3.6 5.6 + - - -
382K LYS 4.9 0.5 - - - +
384K CYS* 4.1 13.2 - - - +
385K CYS* 4.9 6.1 - - + +
386K GLU* 4.5 5.7 - - - +
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Residues in contact with ASN 377 (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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331K TRP* 5.0 2.1 - - - -
332K LEU* 5.4 2.5 - - + +
373K TYR* 2.8 34.8 + - + +
374K ILE* 2.8 11.1 - - - +
376K ASN* 1.3 100.6 + - - +
378K HIS* 1.3 57.7 + - - +
379K GLY 2.8 21.0 + - - +
381K GLU 5.0 0.2 - - - -
382K LYS* 3.3 56.6 + - + +
384K CYS* 3.3 8.3 - - - -
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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