Contacts of the strand formed by residues 377 - 382 (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 ALA 377 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C THR 4.1 6.1 - - - +
215C GLY* 4.1 15.5 - - - -
350C ALA* 3.8 1.0 - - - +
367C CYS* 3.5 6.7 - - - -
369C GLY* 3.0 24.3 + - - -
375C ILE* 2.7 25.9 + - + +
376C PRO* 1.3 75.6 - - - +
378C VAL* 1.3 64.7 + - - +
379C CYS 4.2 0.7 - - - -
422C ARG* 4.9 5.2 - - + -
423C ILE 3.2 12.1 - - - +
424C MET* 4.2 10.3 - - + -
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Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ALA* 3.2 34.3 - - + +
353C LEU* 4.2 9.9 - - + -
354C ALA* 4.0 15.9 - - + +
357C ILE* 4.9 2.0 - - + -
365C PHE* 3.8 28.3 - - + -
367C CYS 3.3 5.6 - - - +
368C THR 5.0 0.2 - - - -
377C ALA* 1.3 79.5 - - - +
379C CYS* 1.3 63.1 + - - +
380C PHE* 4.1 12.7 - - + -
421C MET 3.6 1.2 - - - +
422C ARG* 3.3 5.5 - - - +
423C ILE* 2.9 48.3 + - + +
425C CYS* 5.1 1.6 - - - -
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Residues in contact with CYS 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C TYR 4.0 6.5 - - - -
214C THR* 3.3 41.5 - - - +
365C PHE* 3.5 2.1 - - - -
366C ILE* 2.7 39.6 + - + -
367C CYS* 2.8 23.4 + - + +
378C VAL* 1.3 74.0 - - - +
380C PHE* 1.3 61.3 + - - +
420C VAL* 3.8 26.2 - - - -
421C MET 3.4 11.2 - - - +
422C ARG* 4.7 3.4 - - + -
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Residues in contact with PHE 380 (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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357C ILE* 3.9 12.1 - - + -
363C TYR* 3.6 36.1 - + + -
364C GLU 3.2 15.0 - - - +
365C PHE* 3.7 19.5 - + + +
366C ILE* 4.3 2.2 - - - +
378C VAL* 4.1 13.0 - - + -
379C CYS* 1.3 78.2 - - - +
381C LYS* 1.3 61.6 + - - +
392C LEU* 3.8 12.6 - - + +
420C VAL* 3.3 7.3 - - - -
421C MET* 2.9 66.0 + - + -
423C ILE* 4.4 16.4 - - + -
441C TYR* 3.3 28.7 - + - -
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Residues in contact with LYS 381 (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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363C TYR* 3.5 8.7 - - - +
364C GLU* 2.9 62.9 + - + +
366C ILE* 4.8 11.9 - - + -
380C PHE* 1.3 77.5 - - - +
382C LEU* 1.3 82.6 + - - +
384C ASP* 3.1 33.9 + - - +
392C LEU* 4.0 5.4 - - - -
418C ILE* 3.6 40.8 - - + +
419C VAL 3.4 20.6 - - - +
420C VAL* 4.3 3.1 - - + -
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Residues in contact with LEU 382 (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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362C PRO* 3.7 7.9 - - + +
363C TYR* 4.1 23.1 - - + +
381C LYS* 1.3 99.3 + - - +
383C LYS* 1.3 67.3 + - - +
384C ASP* 4.4 0.3 - - - -
386C GLU* 4.5 11.4 - - + +
388C PRO* 3.8 30.3 - - + -
390C TYR* 4.1 25.8 - - + +
391C THR* 4.4 12.3 - - + -
392C LEU* 4.2 16.9 - - + +
419C VAL 4.5 1.6 + - - -
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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