Contacts of the strand formed by residues 419 - 424 (chain C) in PDB entry 3FZ7
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 VAL 419 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381C LYS* 3.4 22.7 - - - +
382C LEU 4.5 1.2 + - - -
391C THR* 5.9 1.8 - - - -
392C LEU* 3.7 29.6 - - + +
393C TYR* 3.7 40.4 - - + +
408C ALA* 4.3 5.2 - - + -
409C PHE 3.5 6.7 - - - +
410C THR* 3.8 18.6 - - + -
417C ASP* 3.7 7.4 + - - +
418C ILE* 1.3 73.4 - - - +
420C VAL* 1.3 65.5 + - - +
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Residues in contact with VAL 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C TYR 4.5 0.2 - - - +
366C ILE* 3.8 19.7 - - + -
379C CYS* 3.8 15.7 - - - -
380C PHE 3.3 11.0 - - - +
381C LYS* 4.3 1.8 - - + -
392C LEU* 4.1 4.3 - - - -
407C PRO 3.7 0.7 - - - +
408C ALA* 3.1 6.6 - - - +
409C PHE* 2.7 74.2 + - + +
411C LEU* 3.8 34.5 - - + -
418C ILE* 4.2 4.9 - - + -
419C VAL* 1.3 76.9 - - - +
421C MET* 1.3 59.7 + - - +
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Residues in contact with MET 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378C VAL 3.6 1.3 - - - +
379C CYS* 3.4 6.4 - - - -
380C PHE* 2.9 64.3 + - + -
392C LEU* 3.5 39.2 - - + +
395C LEU* 3.7 23.3 - - + -
396C SER* 3.7 16.8 - - - +
399C LEU* 4.4 1.6 - - + -
406C VAL* 3.4 43.5 - - + +
407C PRO 3.2 6.3 - - - +
408C ALA* 4.8 0.9 - - + -
420C VAL* 1.3 74.3 - - - +
422C ARG* 1.3 60.2 + - - +
423C ILE* 4.8 0.9 - - + -
441C TYR* 4.4 5.4 - - - -
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Residues in contact with ARG 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU 4.0 1.6 - - - +
61C ALA* 3.1 31.9 + - - +
63C PHE* 4.2 8.2 - - - -
212C THR* 2.9 32.1 + - - +
213C TYR* 3.6 15.5 - - - +
214C THR* 4.4 11.0 - - - +
215C GLY 5.2 0.2 - - - +
375C ILE* 6.6 0.2 - - - -
377C ALA* 4.9 5.4 - - + -
378C VAL 3.3 6.7 - - - +
379C CYS* 4.7 3.4 - - + -
406C VAL* 4.2 0.5 - - - +
407C PRO* 3.1 41.4 + - - +
409C PHE* 3.6 32.8 - - + -
420C VAL 4.1 0.6 - - - -
421C MET* 1.3 74.3 - - - +
423C ILE* 1.3 70.6 + - - +
424C MET* 4.4 14.7 - - + +
463C PHE 4.5 0.2 + - - -
464C LYS* 3.0 36.7 + - - +
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Residues in contact with ILE 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 3.8 29.8 - - + -
353C LEU* 4.3 18.6 - - + -
357C ILE* 3.6 31.6 - - + -
377C ALA* 3.2 7.1 - - - +
378C VAL* 2.9 49.3 + - + +
380C PHE* 4.4 12.3 - - + -
406C VAL* 3.8 19.7 - - + -
421C MET* 4.8 2.2 - - + -
422C ARG* 1.3 76.8 - - - +
424C MET* 1.3 67.8 + - - +
425C CYS* 4.1 3.6 + - - -
429C PHE* 4.9 0.2 - - + -
437C LEU* 4.5 11.4 - - + -
441C TYR* 5.4 3.1 - - + -
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Residues in contact with MET 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 2.9 40.7 + - - +
61C ALA 4.6 3.8 - - - +
62C THR 3.7 15.0 - - - +
63C PHE* 3.7 37.7 - - + -
277C PHE* 3.3 33.7 - - + -
375C ILE* 3.8 26.5 - - - -
376C PRO 3.9 10.1 - - - +
377C ALA* 4.2 6.3 - - + -
422C ARG* 4.2 17.0 - - - +
423C ILE* 1.3 75.1 - - - +
425C CYS* 1.3 70.4 + - - +
426C ARG* 3.8 8.2 + - + -
429C PHE* 4.4 1.0 - - - +
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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