Contacts of the helix formed by residues 484 - 494 (chain X) in PDB entry 3FEW
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 484 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349X ARG* 3.9 17.2 - - - +
356X ALA 5.1 0.2 - - - -
357X SER* 2.5 40.1 + - - +
360X LYS* 2.7 33.7 + - - +
483X ASP* 1.3 75.8 + - - +
485X LYS* 1.3 60.0 + - - +
486X PHE 3.1 2.6 + - - -
487X ALA* 3.3 10.8 + - - +
488X ASP* 3.5 13.6 + - - +
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Residues in contact with LYS 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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335X GLU* 3.8 22.8 + - - +
339X ASP* 3.7 23.4 + - - -
483X ASP* 2.9 32.4 + - + +
484X ASP* 1.3 77.8 - - - +
486X PHE* 1.3 73.6 + - + +
488X ASP* 3.5 13.6 - - + +
489X ALA* 2.9 26.5 + - - +
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Residues in contact with PHE 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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332X LEU* 3.6 20.0 - - + +
335X GLU* 3.7 23.1 - - + -
336X ILE* 3.5 34.1 - - + -
339X ASP* 3.9 17.5 - - - -
475X ALA 4.7 5.8 - - - +
479X GLY* 3.7 27.8 - - - -
482X LEU* 4.0 20.4 - - + -
483X ASP* 3.4 35.0 - - + +
484X ASP 3.1 1.2 - - - -
485X LYS* 1.3 93.5 - - + +
487X ALA* 1.3 60.8 + - - +
489X ALA* 3.2 4.3 + - + +
490X LEU* 2.9 35.9 + - + +
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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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357X SER* 3.3 33.7 - - - +
360X LYS* 4.1 15.9 - - + -
361X VAL* 3.8 15.1 - - + +
476X ALA* 6.2 0.6 - - - +
479X GLY 5.8 0.8 - - - -
483X ASP 4.5 0.8 + - - -
484X ASP* 3.3 13.1 + - - +
486X PHE* 1.3 78.3 - - - +
488X ASP* 1.3 61.8 + - - +
490X LEU* 3.2 4.9 + - - +
491X ASN* 3.0 29.1 + - - -
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Residues in contact with ASP 488 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360X LYS* 3.1 28.7 + - - -
484X ASP* 3.5 12.9 + - - +
485X LYS* 3.5 14.2 - - - +
486X PHE 3.3 0.2 - - - -
487X ALA* 1.3 76.5 - - - +
489X ALA* 1.3 56.4 + - - +
491X ASN* 3.2 7.0 + - - +
492X LYS* 2.8 43.0 + - + +
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Residues in contact with ALA 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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332X LEU* 3.5 28.5 - - + -
485X LYS 2.9 18.4 + - - +
486X PHE* 3.2 7.6 + - + +
488X ASP* 1.3 76.6 - - - +
490X LEU* 1.3 62.7 + - - +
492X LYS* 3.9 5.1 - - - +
493X GLU* 3.1 35.5 + - - +
494X ILE* 3.9 4.0 + - - +
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Residues in contact with LEU 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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329X TYR* 5.0 1.3 - - + -
332X LEU* 3.4 26.0 - - + -
361X VAL* 3.7 26.2 - - + -
472X ILE* 3.9 12.1 - - + +
475X ALA* 3.9 14.8 - - + +
476X ALA* 3.6 37.0 - - + +
486X PHE* 2.9 17.5 + - + +
487X ALA* 3.5 8.1 - - - +
489X ALA* 1.3 77.6 - - - +
491X ASN* 1.3 59.9 + - - +
494X ILE* 3.3 27.3 + - + +
495X ILE* 3.1 32.7 + - + +
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Residues in contact with ASN 491 (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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360X LYS* 3.0 41.3 + - - +
361X VAL* 3.8 8.8 - - - +
364X ASN* 3.0 31.0 + - - +
487X ALA 3.0 20.3 + - - +
488X ASP* 3.8 6.5 + - - +
490X LEU* 1.3 77.8 - - - +
492X LYS* 1.3 62.5 + - - +
495X ILE* 3.8 18.6 + - - +
496X LYS 4.9 0.9 + - - -
497X PRO* 5.2 4.7 - - - +
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Residues in contact with LYS 492 (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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488X ASP* 2.8 29.8 + - + +
489X ALA* 3.9 3.8 - - - +
491X ASN* 1.3 76.2 - - - +
493X GLU* 1.3 78.7 + - + +
494X ILE 3.9 0.2 - - - -
496X LYS 5.8 1.1 + - - -
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Residues in contact with GLU 493 (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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328X ALA* 3.8 16.7 - - + +
489X ALA* 3.1 18.4 + - - +
492X LYS* 1.3 102.2 - - + +
494X ILE* 1.3 69.9 + - + +
495X ILE 3.9 0.2 - - - -
496X LYS* 4.4 16.9 - - - -
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Residues in contact with ILE 494 (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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325X LEU* 5.0 12.5 - - + +
328X ALA* 3.9 33.2 - - + +
329X TYR* 3.9 14.6 - - + +
332X LEU* 4.7 8.5 - - + -
472X ILE* 3.0 37.7 - - + -
489X ALA 4.7 1.8 - - - +
490X LEU* 3.3 37.6 + - + +
493X GLU* 1.3 87.4 - - + +
495X ILE* 1.3 78.4 + - + +
496X LYS* 3.5 11.9 + - - +
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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