Contacts of the helix formed by residues 482 - 490 (chain X) in PDB entry 3F6E
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 ASP 482 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480X GLY 4.2 1.6 + - - -
481X ILE* 1.3 74.3 - - - +
483X PHE* 1.3 56.5 + - - +
484X ARG* 3.1 18.2 + - - +
485X ALA* 3.0 32.8 + - + +
486X LEU* 3.1 26.5 + - - +
520X GLU* 4.2 4.5 - - - +
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Residues in contact with PHE 483 (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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428X ASP* 3.4 43.7 - - + -
431X ALA* 3.7 23.8 - - + -
432X ASN* 4.0 8.1 - - - -
435X ILE* 4.8 5.4 - - + -
452X ILE* 4.0 19.1 - - + -
454X ASN* 4.0 7.4 - - - -
481X ILE* 3.4 38.4 - - + -
482X ASP* 1.3 69.4 - - - +
484X ARG* 1.3 59.8 + - - +
486X LEU* 3.4 16.1 + - + +
487X ALA* 2.9 28.8 + - - +
518X LEU* 3.8 23.3 - - + +
520X GLU* 3.0 30.8 + - + +
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Residues in contact with ARG 484 (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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482X ASP* 3.1 9.0 + - - +
483X PHE* 1.3 77.3 - - - +
485X ALA* 1.3 59.4 + - - +
487X ALA* 3.5 2.1 + - - +
488X LYS* 3.0 27.4 + - - +
494X ALA* 3.8 24.3 + - + +
495X LEU* 4.0 17.9 - - - +
496X LYS* 3.5 54.2 - - - +
518X LEU* 4.8 1.1 - - + -
520X GLU* 4.0 11.0 - - + +
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Residues in contact with ALA 485 (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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482X ASP* 3.0 33.3 + - + +
484X ARG* 1.3 75.1 - - - +
486X LEU* 1.3 61.3 + - + +
488X LYS* 3.3 11.1 + - + +
489X GLY* 2.8 26.2 + - - -
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Residues in contact with LEU 486 (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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432X ASN* 4.4 5.2 - - - +
435X ILE* 4.0 34.5 - - + -
438X LEU* 4.5 2.0 - - + -
481X ILE* 3.7 29.2 - - + -
482X ASP 3.1 11.5 + - - +
483X PHE* 3.4 21.3 + - + +
485X ALA* 1.3 75.8 - - + +
487X ALA* 1.3 63.0 + - - +
489X GLY* 3.1 11.4 + - - +
490X TYR* 3.2 23.3 + - + -
518X LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 487 (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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438X LEU* 4.1 12.4 - - + +
483X PHE 2.9 17.7 + - - +
484X ARG 3.8 0.2 - - - +
485X ALA 3.3 0.2 - - - -
486X LEU* 1.3 75.7 - - - +
488X LYS* 1.3 62.5 + - - +
490X TYR* 3.0 4.7 + - - +
491X GLY 3.0 5.2 + - - -
492X VAL* 2.9 42.6 + - + +
494X ALA* 3.8 16.4 - - + -
518X LEU* 4.1 22.0 - - + -
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Residues in contact with LYS 488 (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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484X ARG 3.0 15.9 + - - +
485X ALA* 3.5 12.1 - - + +
487X ALA* 1.3 74.3 - - - +
489X GLY* 1.3 65.6 + - - +
491X GLY* 3.1 13.8 + - - +
492X VAL 3.8 6.6 + - - +
494X ALA* 5.9 0.4 - - + -
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Residues in contact with GLY 489 (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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439X TRP* 5.5 0.3 - - - -
485X ALA 2.8 18.4 + - - -
486X LEU* 3.1 7.3 + - - -
488X LYS* 1.3 74.3 - - - +
490X TYR* 1.3 67.4 + - - +
491X GLY 3.8 0.2 + - - -
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Residues in contact with TYR 490 (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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45X LEU* 3.7 18.9 - - + +
435X ILE* 3.9 27.6 - - + +
436X SER* 3.6 30.6 - - - -
438X LEU* 3.9 11.9 - - + -
439X TRP* 3.6 49.1 - + + +
442X ALA* 3.2 20.1 - - - +
443X GLN* 5.6 0.3 + - - -
486X LEU* 3.2 17.0 + - + +
487X ALA 3.0 4.7 + - - +
489X GLY* 1.3 81.8 - - - +
491X GLY* 1.3 58.2 + - - +
492X VAL* 3.5 2.7 - - - -
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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