Contacts of the helix formed by residues 364 - 376 (chain X) in PDB entry 2W6C
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 364 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362X HIS 4.0 1.0 + - - -
363X ALA* 1.3 75.2 - - - +
365X ASP* 1.3 64.9 + - - +
366X LEU* 3.8 8.2 - - - +
367X GLY 2.7 38.9 + - - -
368X LEU* 3.0 12.1 + - - +
531X LEU* 4.6 0.3 - - - +
532X LEU* 3.4 16.3 - - + +
535X THR* 2.6 44.3 + - - -
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Residues in contact with ASP 365 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364X ASN* 1.3 72.9 - - - +
366X LEU* 1.3 63.6 + - - +
368X LEU* 3.2 17.3 + - - +
369X ASP* 2.9 30.1 + - - +
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Residues in contact with LEU 366 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364X ASN* 3.1 13.4 + - - +
365X ASP* 1.3 78.1 - - - +
367X GLY* 1.3 61.1 + - - +
369X ASP* 3.3 18.1 + - + +
370X ALA* 3.1 19.8 + - - +
531X LEU* 3.3 34.8 - - + -
535X THR* 3.6 20.2 - - + -
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Residues in contact with GLY 367 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363X ALA* 4.4 5.6 - - - -
364X ASN* 2.7 23.4 + - - -
366X LEU* 1.3 69.9 - - - +
368X LEU* 1.3 58.1 + - - -
370X ALA* 2.9 5.5 + - - +
371X VAL* 2.8 32.7 + - - +
528X LEU* 4.1 21.5 - - - +
531X LEU* 4.4 4.2 - - - +
532X LEU* 4.4 7.2 - - - -
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Residues in contact with LEU 368 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356X VAL* 3.7 29.2 - - + +
357X LYS* 3.8 43.5 - - + +
360X VAL* 4.0 9.9 - - + +
363X ALA* 3.8 24.0 - - + +
364X ASN 3.0 13.6 + - - +
365X ASP* 3.6 18.8 - - - +
367X GLY* 1.3 73.9 - - - +
369X ASP* 1.3 62.9 + - - +
371X VAL* 3.4 2.7 + - - +
372X THR* 2.7 30.5 + - - +
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Residues in contact with ASP 369 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365X ASP* 2.9 22.1 + - - +
366X LEU* 3.4 21.8 - - + +
367X GLY 3.2 0.4 - - - -
368X LEU* 1.3 73.2 - - - +
370X ALA* 1.3 57.1 + - - +
372X THR* 3.3 5.8 + - - -
373X LEU* 2.8 30.9 + - - +
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Residues in contact with ALA 370 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366X LEU* 3.1 11.6 + - + +
367X GLY* 2.9 8.9 + - - +
369X ASP* 1.3 75.2 - - - +
371X VAL* 1.3 66.7 + - - +
373X LEU* 3.3 10.3 + - + +
374X GLN* 3.0 25.3 + - - +
523X PHE* 3.9 20.5 - - + -
527X PHE* 4.3 17.0 - - + -
528X LEU* 4.9 2.0 - - + -
531X LEU* 4.3 8.3 - - + -
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Residues in contact with VAL 371 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356X VAL* 4.3 15.3 - - + -
360X VAL* 4.0 13.5 - - + -
367X GLY 2.8 20.1 + - - +
368X LEU* 3.9 4.9 - - - +
370X ALA* 1.3 73.5 - - - +
372X THR* 1.3 63.5 + - - +
374X GLN* 3.0 13.7 + - - +
375X TYR* 3.2 15.1 + - + +
394X ILE* 3.4 35.7 - - + -
523X PHE* 3.8 16.8 - - + -
524X TRP* 3.5 32.5 - - + -
528X LEU* 4.2 6.5 - - + -
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Residues in contact with THR 372 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349X ARG* 3.8 13.9 - - - +
352X PHE* 4.1 14.8 - - + -
353X MET* 5.6 8.0 - - + +
356X VAL* 4.1 17.3 - - - +
368X LEU* 2.7 23.4 + - - +
369X ASP* 3.5 6.7 - - - -
371X VAL* 1.3 74.9 - - - +
373X LEU* 1.3 68.3 + - - +
375X TYR* 3.2 1.8 + - - -
376X THR* 2.7 40.9 + - - +
378X TRP* 4.6 9.2 - - + -
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Residues in contact with LEU 373 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369X ASP 2.8 20.3 + - - +
370X ALA* 3.8 8.5 - - + +
372X THR* 1.3 75.6 - - - +
374X GLN* 1.3 71.8 + - - +
375X TYR 3.3 0.7 + - - -
376X THR 3.8 12.0 + - - +
378X TRP* 4.1 27.2 + - + +
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Residues in contact with GLN 374 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370X ALA 3.0 12.7 + - - +
371X VAL* 3.0 13.3 + - - +
373X LEU* 1.3 89.7 - - - +
375X TYR* 1.3 67.5 + - + +
376X THR 5.4 0.2 - - - -
519X GLN* 4.8 7.3 + - - +
520X MET* 3.2 43.7 - - + +
523X PHE* 4.2 31.3 - - + +
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Residues in contact with TYR 375 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352X PHE* 4.7 9.6 - - + -
371X VAL* 3.2 24.6 + - + +
372X THR 3.2 1.5 + - - +
374X GLN* 1.3 89.5 - - + +
376X THR* 1.3 61.4 + - - +
377X ASP 3.9 1.9 + - - -
386X LYS 5.3 1.7 - - - +
390X GLY* 3.8 22.3 - - - +
393X ASP* 3.8 17.0 - - + -
394X ILE* 3.4 37.9 - - + -
397X ASP* 2.3 34.1 + - - -
517X ARG* 4.5 1.6 - - - -
520X MET* 3.3 30.2 - - + +
523X PHE* 4.6 2.7 - + - -
524X TRP* 2.9 33.1 + + - -
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Residues in contact with THR 376 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349X ARG* 2.9 35.7 + - - +
352X PHE* 4.1 5.1 - - - -
372X THR* 2.7 23.2 + - - +
373X LEU 3.8 5.3 + - - +
374X GLN 3.6 1.0 - - - -
375X TYR* 1.3 78.4 - - - +
377X ASP* 1.3 69.6 + - - +
378X TRP* 3.0 52.4 + - + -
381X ASP* 4.4 3.8 - - + -
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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