Contacts of the strand formed by residues 422 - 427 (chain B) in PDB entry 1F89
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 LEU 422 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372B ASN* 4.0 33.4 - - + +
373B PRO 4.7 12.6 - - - +
380B VAL* 4.1 14.4 - - + -
414B ILE* 3.8 15.0 - - + -
415B ILE 3.0 27.6 - - - +
416B PHE* 3.8 18.4 - - + -
420B GLY 3.8 2.8 + - - -
421B LYS* 1.3 80.2 - - - +
423B ILE* 1.3 66.3 + - - +
424B ASP* 3.6 15.7 - - - +
425B LYS* 5.6 3.8 - - + -
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B ILE* 5.1 2.0 - - + -
415B ILE* 3.0 10.1 + - + +
416B PHE 4.1 5.6 - - - +
417B ASN* 3.4 45.5 - - + +
421B LYS* 2.9 18.8 + - + +
422B LEU* 1.3 74.1 - - - +
424B ASP* 1.3 65.9 + - + +
457B ILE* 3.4 35.0 - - + -
458B ASP* 4.0 15.0 - - + +
459B THR* 4.9 6.5 - - - +
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Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ILE* 3.1 27.7 + - - +
422B LEU* 3.5 8.6 - - - +
423B ILE* 1.3 83.2 - - + +
425B LYS* 1.3 88.3 + - - +
453B LYS* 3.7 25.2 + - - -
455B THR* 3.8 13.3 - - + +
456B THR 4.8 6.4 - - - +
457B ILE* 3.8 24.6 - - + +
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Residues in contact with LYS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B ASN* 4.2 30.9 + - + +
401B GLU* 2.8 33.6 + - - +
412B THR* 3.7 15.7 - - + -
413B SER 3.3 12.8 - - - +
414B ILE* 4.3 7.6 - - + -
415B ILE* 4.2 2.0 - - - -
422B LEU* 5.3 3.8 - - + -
424B ASP* 1.3 97.0 + - - +
426B HIS* 1.3 60.7 + - - +
427B ARG* 3.3 27.0 + - + +
453B LYS* 5.4 3.6 - - - +
455B THR* 3.6 8.8 + - - -
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Residues in contact with HIS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B THR* 3.1 5.9 - - - +
413B SER* 2.9 35.1 + - - +
415B ILE* 4.7 0.4 - - + +
425B LYS* 1.3 73.5 - - - +
427B ARG* 1.3 75.0 + - - +
429B VAL* 3.8 17.0 + - + -
453B LYS 3.8 9.3 + - - -
454B SER* 4.9 1.3 - - - -
455B THR* 2.6 35.8 + - + +
466B VAL* 3.5 33.9 + - + -
467B GLY* 3.8 3.9 - - - -
468B ILE* 3.5 27.2 - - + +
471B ASP* 3.1 22.1 + - - -
477B LEU* 5.0 6.5 - - + -
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B GLU* 3.1 31.5 + - - -
403B ASP* 3.5 19.8 + - - +
410B TYR* 3.0 58.7 - - + -
411B ASN 3.9 0.9 - - - -
412B THR* 3.4 19.7 - - + +
425B LYS* 3.3 21.5 + - + +
426B HIS* 1.3 81.4 + - - +
428B LYS* 1.3 68.3 + - - +
429B VAL* 3.0 7.6 + - - +
451B GLY* 3.7 22.8 - - - -
452B GLU 5.5 0.7 - - - +
453B LYS 4.9 1.4 + - - +
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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