Contacts of the helix formed by residues 366 - 378 (chain C) in PDB entry 2W93
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 LYS 366 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363C THR* 5.8 2.8 - - + +
364C PRO* 3.4 31.3 + - - +
365C LEU* 1.3 81.4 - - - +
367C GLN* 1.3 65.8 + - - +
368C GLU* 3.3 5.6 - - + +
369C TRP* 3.2 15.0 + - + +
370C MET* 2.9 21.3 + - - +
540C LEU* 4.0 4.3 - - - -
541C PRO* 3.8 26.0 - - + -
544C ASP* 3.3 15.9 - - + +
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Residues in contact with GLN 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366C LYS* 1.3 71.7 - - - +
368C GLU* 1.3 64.4 + - - +
370C MET* 3.1 6.6 + - + -
371C TRP* 2.8 57.6 + - - +
390C THR* 3.0 35.0 + - - +
469C LEU* 4.1 5.9 - - - +
471C ASN* 4.2 7.3 - - - +
540C LEU* 3.9 28.2 - - + +
541C PRO 5.9 0.2 + - - -
544C ASP* 2.5 34.2 + - + +
545C ALA* 3.8 16.6 - - - -
546C PRO* 3.4 14.2 - - - +
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Residues in contact with GLU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C ASN* 4.8 0.4 - - - +
366C LYS* 3.3 4.7 - - + +
367C GLN* 1.3 78.9 - - - +
369C TRP* 1.3 65.2 + - - +
371C TRP* 4.4 1.2 - - - +
372C ASN* 3.4 19.6 + - - +
397C GLN* 2.9 29.3 + - - +
544C ASP* 5.0 1.0 + - - +
545C ALA 4.5 5.9 + - - +
546C PRO* 3.6 0.6 - - - +
547C GLN* 2.7 57.0 + - + +
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Residues in contact with TRP 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ASN* 3.0 48.9 + - + +
357C ALA 4.6 2.9 + - - -
359C VAL* 4.2 19.1 - - + +
363C THR* 6.1 1.8 - - + -
365C LEU* 3.4 29.6 - - + -
366C LYS* 3.2 17.7 + - + +
367C GLN 3.2 0.2 - - - -
368C GLU* 1.3 79.7 - - - +
370C MET* 1.3 87.3 + - - +
372C ASN 3.1 2.6 + - - -
373C GLN* 2.9 55.0 + - + +
515C THR* 3.4 34.9 + - - -
518C TRP* 3.7 22.7 - + - -
519C ASP* 3.8 8.3 - - - -
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Residues in contact with MET 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LEU* 5.0 4.5 - - + -
366C LYS 2.9 16.9 + - - +
367C GLN* 3.1 5.4 + - - +
369C TRP* 1.3 90.5 - - + +
371C TRP* 1.3 103.5 + - + +
373C GLN* 3.0 3.1 + - - +
374C LEU* 2.8 28.3 + - + +
441C PHE* 4.2 3.4 - - + -
469C LEU* 4.0 18.4 - - + -
518C TRP* 3.6 44.3 - - + -
538C VAL* 3.9 19.3 - - - -
540C LEU* 4.6 10.5 - - + -
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Residues in contact with TRP 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C GLN* 2.8 51.6 + - + +
368C GLU* 4.5 2.0 - - - +
370C MET* 1.3 94.6 - - + +
372C ASN* 1.3 59.5 + - - +
374C LEU* 3.6 19.8 + - + +
375C GLY 4.3 0.5 + - - -
391C SER* 3.6 36.1 - - - -
394C GLY* 3.3 40.9 - - - +
395C ILE* 3.9 12.1 - - + -
397C GLN* 4.3 12.3 - - + +
398C THR* 2.7 41.5 + - - +
399C THR 4.9 0.2 + - - -
441C PHE* 3.6 38.1 - + + -
469C LEU* 3.9 8.7 - - + -
546C PRO* 4.3 7.6 - - + -
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Residues in contact with ASN 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C THR* 4.2 22.3 - - - +
354C PRO 3.0 27.7 + - - +
355C ALA* 3.9 2.8 - - - -
356C ASN* 3.0 34.0 + - - +
368C GLU 3.4 11.6 + - - +
369C TRP 3.1 9.7 + - - +
371C TRP* 1.3 77.6 - - - +
373C GLN* 1.3 61.7 + - - +
375C GLY* 4.4 4.1 + - - -
376C ASN* 5.0 3.6 - - - +
397C GLN* 4.4 12.2 + - + +
398C THR* 5.4 0.2 - - - +
399C THR 6.2 0.2 - - - +
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Residues in contact with GLN 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C ASN* 2.9 27.7 + - - +
369C TRP* 2.9 48.2 + - + +
370C MET 3.0 4.5 + - - +
372C ASN* 1.3 75.0 - - - +
374C LEU* 1.3 66.4 + - - +
375C GLY 3.1 2.5 - - - -
376C ASN* 3.0 47.1 + - + +
377C PHE* 4.2 0.9 + - - +
518C TRP* 3.8 11.7 + - - +
519C ASP* 2.8 35.4 + - - +
523C GLN* 5.0 1.4 - - - +
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Residues in contact with LEU 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C MET* 2.8 16.6 + - + +
371C TRP* 3.8 16.4 - - + +
372C ASN 3.4 1.0 - - - -
373C GLN* 1.3 77.8 - - - +
375C GLY* 1.3 62.7 - - - +
377C PHE* 2.9 38.0 + - + +
378C LEU* 3.4 20.6 + - + +
384C VAL* 5.2 0.9 - - + -
395C ILE* 3.9 27.1 - - + -
398C THR* 3.9 10.8 - - + +
441C PHE* 3.6 42.6 - - + -
518C TRP* 4.1 15.5 - - + +
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Residues in contact with GLY 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C TRP 4.3 2.0 + - - -
372C ASN 4.4 3.4 + - - -
373C GLN 3.1 2.2 + - - -
374C LEU* 1.3 77.4 - - - +
376C ASN* 1.3 62.3 + - - +
377C PHE 3.3 0.5 + - - -
378C LEU* 3.5 17.3 + - - +
398C THR* 3.9 7.7 - - - +
399C THR* 3.5 29.6 - - - +
401C PRO* 5.1 2.9 - - - +
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Residues in contact with ASN 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355C ALA* 6.1 0.7 - - - +
372C ASN 5.0 2.6 - - - +
373C GLN* 3.0 43.7 + - + +
375C GLY* 1.3 79.2 - - - +
377C PHE* 1.3 60.9 + - + +
378C LEU 4.1 3.3 - - - +
519C ASP* 5.3 0.2 + - - -
522C THR* 6.1 0.9 - - - +
523C GLN* 5.1 14.0 - - + +
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Residues in contact with PHE 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C GLN 5.2 0.7 - - - +
374C LEU* 2.9 29.6 + - + +
376C ASN* 1.3 77.9 - - + +
378C LEU* 1.3 69.8 + - + +
379C GLN* 4.6 1.2 - - - +
437C ARG* 2.8 32.6 + - - -
439C ILE* 3.6 27.1 - - + -
465C TYR* 3.8 27.6 - + - -
467C PHE* 4.1 16.8 - + - -
518C TRP* 5.6 1.3 - - - +
522C THR* 3.5 36.3 - - + +
527C PHE* 3.5 23.6 - + - -
528C ASN* 3.4 27.0 - - - +
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C LEU* 3.4 21.3 + - + +
375C GLY 3.9 9.3 - - - +
376C ASN 3.5 4.4 - - - +
377C PHE* 1.3 90.8 - - + +
379C GLN* 1.3 60.0 + - - +
382C ASP* 3.4 6.3 - - + +
384C VAL* 3.9 16.6 - - + -
398C THR* 3.9 19.7 - - + -
399C THR 4.1 5.8 - - - +
400C PHE* 3.7 32.8 - - + -
401C PRO* 3.6 24.0 - - + +
439C ILE* 3.8 28.7 - - + -
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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