Contacts of the strand formed by residues 414 - 421 (chain C) in PDB entry 5FBN
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 GLY 414 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410C THR* 4.2 6.3 - - - +
411C GLY* 2.9 28.4 + - - +
412C GLN 3.2 5.2 + - - +
413C PHE* 1.3 78.6 - - - +
415C VAL* 1.3 66.9 + - - -
416C VAL* 3.9 4.0 - - - +
430C LYS* 4.3 2.5 - - - +
431C MET 3.2 11.0 - - - -
433C LYS* 4.2 9.9 - - - -
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Residues in contact with VAL 415 (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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409C GLY 3.6 4.7 - - - -
410C THR* 3.6 22.0 - - + +
414C GLY* 1.3 74.9 - - - -
416C VAL* 1.3 58.0 + - - +
417C LYS* 3.7 23.1 - - - +
429C ILE 3.8 0.3 - - - +
430C LYS* 3.5 1.7 - - - -
431C MET* 2.8 50.4 + - + +
703C CL 3.8 15.5 - - + -
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Residues in contact with VAL 416 (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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408C LEU* 2.9 34.5 + - + +
409C GLY 3.0 7.2 + - - +
411C GLY 4.4 0.9 - - - +
414C GLY 3.9 4.3 - - - +
415C VAL* 1.3 79.4 - - - +
417C LYS* 1.3 73.4 + - - +
428C ALA* 4.2 2.7 - - + -
429C ILE 3.3 10.8 - - - +
430C LYS* 3.6 31.4 - - + -
701C 5WF 3.7 58.8 - - + +
703C CL 3.6 5.7 - - - +
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Residues in contact with LYS 417 (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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404C PHE* 3.8 33.2 - - + -
406C LYS 3.3 8.5 - - - +
407C GLU* 2.6 43.4 + - + -
408C LEU* 3.9 5.2 - - - +
415C VAL* 3.7 23.7 - - - +
416C VAL* 1.3 79.3 - - - +
418C TYR* 1.3 62.6 + - - +
428C ALA* 3.3 5.4 - - - -
429C ILE* 2.8 36.8 + - - +
431C MET* 4.4 15.9 - - + -
703C CL 2.9 21.7 - - - +
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Residues in contact with TYR 418 (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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404C PHE* 3.8 2.4 - - - -
405C LEU* 2.8 50.0 + - + +
406C LYS* 2.8 33.9 + - + +
408C LEU* 3.8 24.9 - - + +
417C LYS* 1.3 74.4 - - - +
419C GLY* 1.3 72.7 + - - +
420C LYS* 3.8 12.1 + - - -
426C ASP* 2.6 38.7 + - + -
427C VAL 3.7 5.6 - - - -
428C ALA* 4.8 0.2 - - - +
429C ILE* 4.4 1.6 - - - -
476C TYR* 3.7 35.4 - + + -
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Residues in contact with GLY 419 (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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403C THR 3.0 15.0 - - - -
404C PHE* 4.3 0.2 - - - -
405C LEU* 4.0 7.2 - - - -
418C TYR* 1.3 83.6 - - - +
420C LYS* 1.3 65.2 + - - +
426C ASP* 3.6 5.5 - - - -
427C VAL* 3.0 33.3 + - - -
429C ILE* 3.9 10.3 - - - +
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Residues in contact with LYS 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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401C ASP 3.4 3.8 - - - +
402C LEU* 3.5 2.8 - - - +
403C THR* 2.8 40.3 + - - +
405C LEU* 3.6 21.3 - - + -
418C TYR* 3.8 8.1 + - - +
419C GLY* 1.3 73.5 - - - +
421C TRP* 1.3 60.3 + - - +
423C GLY* 4.1 12.9 + - - +
424C GLN* 3.1 45.0 + - - +
425C TYR 3.3 3.1 - - - -
426C ASP* 2.6 31.4 + - - +
427C VAL* 4.3 3.8 - - - +
429C ILE* 5.2 0.2 - - - +
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Residues in contact with TRP 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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397C ILE* 4.0 20.7 - - + +
401C ASP* 3.3 27.1 + - + +
402C LEU* 4.1 14.1 - - + -
420C LYS* 1.3 70.5 - - - +
422C ARG* 1.3 119.7 + - + +
423C GLY 3.2 0.7 - - - -
425C TYR* 2.8 47.2 + + - +
427C VAL* 3.9 18.1 - - + +
473C ILE* 5.3 2.0 - - + -
702C 5WE 3.6 63.0 - + + -
703D 5WE 3.9 13.7 - - + -
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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