Contacts of the helix formed by residues 458 - 469 (chain X) in PDB entry 3F6B
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 TYR 458 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403X LEU* 5.8 4.3 - - + -
429X GLY* 3.6 35.2 + - - -
430X SER 5.3 0.2 - - - -
432X ASN* 5.8 0.9 + - - -
433X TYR* 3.8 24.6 + + - -
457X THR* 1.3 69.0 + - - +
459X GLY* 1.3 63.4 + - - +
460X ALA 3.3 3.1 - - - -
461X LEU* 3.1 40.1 + - + +
462X ARG* 3.1 14.0 + - - +
475X GLY 3.5 26.0 - - - -
476X LEU* 2.8 21.6 + - - +
478X VAL* 3.6 22.4 - - + +
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Residues in contact with GLY 459 (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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377X THR* 5.7 0.4 + - - -
378X SER* 4.1 14.1 - - - -
455X ASN* 4.8 3.7 + - - +
457X THR* 3.1 22.5 + - - -
458X TYR* 1.3 73.6 - - - +
460X ALA* 1.3 62.5 + - - +
462X ARG* 3.1 7.4 + - - +
463X TRP* 3.0 20.1 + - - +
526X PRO* 4.2 15.4 - - - +
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Residues in contact with ALA 460 (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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377X THR* 3.6 43.9 + - - +
378X SER* 3.8 10.8 - - - +
458X TYR 3.3 0.8 - - - -
459X GLY* 1.3 75.5 - - - +
461X LEU* 1.3 61.7 + - + +
463X TRP* 3.2 8.1 + - - +
464X PHE* 2.9 50.1 + - + -
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Residues in contact with LEU 461 (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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458X TYR* 3.1 35.2 + - + +
460X ALA* 1.3 78.7 - - + +
462X ARG* 1.3 58.5 + - - +
464X PHE* 3.8 18.5 - - + +
465X ALA* 2.8 31.8 + - - +
476X LEU* 4.0 25.7 - - + +
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Residues in contact with ARG 462 (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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457X THR* 2.9 30.3 + - - +
458X TYR 3.1 10.4 + - - +
459X GLY 3.1 7.6 + - - +
461X LEU* 1.3 77.4 - - - +
463X TRP* 1.3 56.6 + - - +
465X ALA* 3.4 7.5 + - - +
466X GLY* 3.0 24.9 + - - -
476X LEU* 4.1 22.9 - - + +
477X ASP* 2.7 32.9 + - - -
526X PRO* 4.7 16.2 - - + -
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Residues in contact with TRP 463 (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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282X GLN* 5.9 9.0 - - + -
378X SER* 5.9 2.5 - - - -
459X GLY 3.0 12.8 + - - +
460X ALA* 3.4 12.1 - - - +
462X ARG* 1.3 73.9 - - - +
464X PHE* 1.3 104.8 + + - +
466X GLY* 3.1 4.1 + - - -
467X VAL* 3.0 51.7 + - + +
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Residues in contact with PHE 464 (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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281X HIS* 3.6 37.0 - + - -
282X GLN* 5.6 4.7 - - + -
460X ALA* 2.9 43.5 + - + +
461X LEU* 4.0 17.7 - - + +
463X TRP* 1.3 103.2 - + - +
465X ALA* 1.3 60.5 + - - +
467X VAL* 2.9 30.6 - - + +
468X LEU* 3.0 17.7 + - + +
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Residues in contact with ALA 465 (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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461X LEU 2.8 19.4 + - - +
462X ARG* 3.6 7.4 - - - +
464X PHE* 1.3 75.1 - - - +
466X GLY* 1.3 58.2 + - - +
468X LEU* 3.3 4.6 + - - -
469X GLU 2.9 8.0 + - - -
470X ALA* 2.8 54.5 + - + +
473X VAL* 4.8 10.8 - - + -
476X LEU* 4.8 7.9 - - + -
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Residues in contact with GLY 466 (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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462X ARG 3.0 15.5 + - - -
463X TRP* 3.1 4.7 + - - -
465X ALA* 1.3 77.4 - - - +
467X VAL* 1.3 61.7 + - - +
469X GLU* 3.0 15.0 + - - +
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Residues in contact with VAL 467 (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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463X TRP* 3.0 50.4 + - + +
464X PHE* 2.9 33.4 + - + +
466X GLY* 1.3 75.5 - - - +
468X LEU* 1.3 67.2 + - + +
469X GLU* 3.4 2.1 + - - +
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Residues in contact with LEU 468 (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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464X PHE* 3.0 25.9 + - + +
465X ALA* 3.7 8.1 - - - +
467X VAL* 1.3 80.7 - - + +
469X GLU* 1.3 69.5 + - - +
470X ALA* 4.1 14.4 - - + +
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Residues in contact with GLU 469 (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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465X ALA 2.9 5.6 + - - -
466X GLY* 3.0 14.2 + - - +
467X VAL 3.1 2.0 - - - +
468X LEU* 1.3 80.7 - - - +
470X ALA* 1.3 60.4 + - - +
471X GLU* 3.6 17.3 + - + +
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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