Contacts of the helix formed by residues 420 - 430 (chain E) in PDB entry 6O81
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 THR 420 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336E TYR* 3.7 14.0 - - - -
403E LEU* 3.8 32.2 - - + +
404E GLY 5.6 0.4 + - - +
414E VAL* 4.9 8.1 - - + +
416E SER* 3.9 21.3 - - - +
417E ARG 2.8 22.6 + - - -
418E VAL 3.1 4.2 + - - -
419E GLY* 1.3 76.3 - - - +
421E ALA* 1.3 58.0 + - - +
422E GLN 3.2 1.5 - - - +
423E LEU* 3.1 4.6 + - - +
424E ALA* 2.6 35.7 + - + +
490E ASP* 4.5 2.7 - - - -
492E THR* 4.4 10.8 - - - +
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Residues in contact with ALA 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PHE* 3.7 21.2 - - + -
420E THR* 1.3 75.9 - - - +
422E GLN* 1.3 60.2 + - - +
424E ALA* 3.8 1.5 - - - +
425E LEU* 2.9 29.1 + - - +
490E ASP* 3.8 12.1 + - - +
491E VAL 3.3 25.4 - - - +
492E THR* 3.4 28.7 + - + +
496E LEU* 4.1 3.5 - - - +
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Residues in contact with GLN 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP 3.0 20.3 + - - +
220D ALA* 3.3 15.0 - - - +
222D ILE* 3.1 34.6 + - - +
223D PHE* 3.7 22.3 - - + +
224D ALA 5.4 0.4 - - - +
253D THR* 3.4 31.7 + - + +
388E ILE* 3.4 23.6 + - + +
418E VAL 5.0 0.9 - - - +
419E GLY* 4.9 5.6 - - - -
420E THR 4.2 0.4 - - - +
421E ALA* 1.3 78.1 - - - +
423E LEU* 1.3 60.0 + - + +
425E LEU* 3.3 5.4 + - - +
426E VAL* 3.0 33.9 + - + +
490E ASP* 4.6 1.6 + - - -
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Residues in contact with LEU 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E LEU* 3.7 31.9 - - + -
336E TYR* 3.7 27.8 - - + -
361E VAL* 4.6 5.8 - - + -
388E ILE* 5.1 4.7 - - + -
391E ALA* 3.8 28.7 - - + -
395E LEU* 4.4 9.6 - - + -
401E VAL* 4.4 6.5 - - + -
403E LEU* 3.8 17.3 - - + -
419E GLY 3.4 17.7 + - - +
420E THR 3.1 5.1 + - - +
422E GLN* 1.3 80.4 - - - +
424E ALA* 1.3 58.2 + - - +
426E VAL* 3.8 4.5 - - + +
427E ALA* 2.9 30.0 + - - +
434E VAL* 5.3 0.2 - - - -
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Residues in contact with ALA 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E LEU* 4.9 4.9 - - + +
420E THR* 2.6 20.9 + - + +
421E ALA* 3.8 9.4 - - - +
423E LEU* 1.3 72.3 - - - +
425E LEU* 1.3 57.1 + - - +
427E ALA* 3.8 1.2 - - - +
428E ARG* 2.9 29.6 + - - +
434E VAL* 3.9 33.8 - - + +
492E THR* 4.2 15.0 - - + -
496E LEU* 4.4 11.0 - - + +
497E VAL* 4.8 1.3 - - + -
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Residues in contact with LEU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D PHE* 3.6 31.2 - - + -
253D THR 5.5 0.7 - - - +
256D LEU* 4.1 9.4 - - + +
257D ALA* 3.8 24.7 - - + +
260D HIS* 3.7 33.0 - - + +
421E ALA 2.9 18.5 + - - +
422E GLN* 3.3 4.9 + - - +
424E ALA* 1.3 75.0 - - - +
426E VAL* 1.3 62.8 + - + +
428E ARG* 3.4 5.8 + - + +
429E ALA* 2.9 28.7 + - + +
496E LEU* 4.2 20.1 - - + +
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Residues in contact with VAL 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D THR* 3.4 37.5 - - + +
256D LEU* 4.2 12.1 - - + -
391E ALA* 4.8 1.3 - - + -
392E SER* 3.9 22.0 - - - +
395E LEU* 3.7 12.8 - - + -
422E GLN* 3.0 18.6 + - + +
423E LEU* 4.0 6.1 - - + +
425E LEU* 1.3 78.4 - - + +
427E ALA* 1.3 57.8 + - - +
429E ALA* 3.2 6.7 + - - +
430E HIS* 2.9 54.2 + - + +
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Residues in contact with ALA 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E LEU* 3.7 12.0 - - + +
401E VAL* 4.0 12.6 - - + -
423E LEU 2.9 19.2 + - - +
424E ALA 3.8 0.2 - - - +
426E VAL* 1.3 75.5 - - - +
428E ARG* 1.3 56.9 + - - +
430E HIS* 3.2 1.3 + - - +
431E ASN 3.1 6.9 + - - -
432E VAL* 2.6 57.2 + - + +
434E VAL* 3.7 17.9 - - + -
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Residues in contact with ARG 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E ALA 2.9 17.6 + - - +
425E LEU* 3.8 9.2 - - + +
427E ALA* 1.3 76.0 - - - +
429E ALA* 1.3 60.3 + - - +
431E ASN* 3.2 18.6 + - - +
432E VAL 4.0 5.3 + - - +
434E VAL* 5.3 0.6 - - + +
495E GLU 3.2 22.3 + - - -
496E LEU* 3.3 38.9 + - + +
498E ASP* 2.6 34.2 + - - -
279G SER* 5.7 3.4 + - - -
223H ASN* 4.4 2.8 - - - +
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Residues in contact with ALA 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D LEU* 3.7 37.7 - - + -
425E LEU* 2.9 20.1 + - + +
426E VAL 3.2 6.5 + - - +
428E ARG* 1.3 75.1 - - - +
430E HIS* 1.3 63.1 + - + +
431E ASN 3.5 0.4 - - - -
223H ASN* 2.8 28.6 + - - +
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Residues in contact with HIS 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D HIS* 3.7 25.1 + + - -
392E SER 3.3 15.5 + - - -
395E LEU* 3.8 31.8 - - + +
396E PRO* 3.6 28.4 - - + +
426E VAL* 2.9 39.6 + - + +
427E ALA 3.2 2.2 + - - +
428E ARG 3.2 0.4 - - - -
429E ALA* 1.3 81.9 + - + +
431E ASN* 1.3 69.9 + - - +
432E VAL* 3.3 10.0 - - + +
223H ASN* 4.5 6.7 + - - +
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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