Contacts of the strand formed by residues 477 - 484 (chain C) in PDB entry 3D8F
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 477 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C GLU* 3.3 6.2 - - - -
380C MET* 2.8 41.6 + - + +
382C GLU* 3.5 36.8 - - + +
385C LEU* 3.3 31.9 - - + -
451C ARG* 3.3 28.5 - - + +
468C VAL* 4.6 2.9 - - + -
469C ALA 3.6 4.5 - - - +
470C ARG* 3.9 38.3 - - + +
475C GLN 4.1 0.8 + - - -
476C MET* 1.3 76.2 - - - +
478C LYS* 1.3 60.2 + - - +
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Residues in contact with LYS 478 (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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377C TRP* 3.4 54.1 - - + +
378C VAL 3.9 3.6 - - - -
380C MET* 5.1 0.9 - - - -
467C TYR 3.7 2.1 - - - +
468C VAL* 3.2 6.4 - - - +
469C ALA 3.0 32.0 + - - +
471C ASP* 2.5 39.7 + - + +
474C THR* 4.4 1.8 + - - +
476C MET* 3.5 24.9 + - + +
477C LEU* 1.3 79.5 - - - +
479C CYS* 1.3 60.0 + - - +
480C HIS* 3.8 29.4 + - + +
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Residues in contact with CYS 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C TRP* 3.4 4.1 - - - -
378C VAL* 3.0 28.2 + - - +
380C MET* 3.7 17.0 - - - +
394C VAL* 4.5 5.8 - - - -
397C CYS* 3.4 41.7 - - - -
466C ALA* 3.9 26.2 - - - -
467C TYR 3.5 4.7 - - - -
468C VAL* 3.8 13.7 - - + -
478C LYS* 1.3 71.6 - - - +
480C HIS* 1.3 60.0 + - - +
481C VAL* 3.7 6.3 + - - +
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Residues in contact with HIS 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C GLY 3.4 8.7 + - - +
377C TRP* 3.4 27.6 - + + +
443C HIS* 5.1 9.9 + + - -
466C ALA* 3.2 4.7 - - - -
467C TYR* 2.9 67.4 + + + +
469C ALA* 5.2 4.1 + - + +
478C LYS* 3.8 32.6 + - + +
479C CYS* 1.3 70.1 - - - +
481C VAL* 1.3 59.7 + - - +
482C PHE* 3.6 25.6 - + + -
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Residues in contact with VAL 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C LEU* 3.2 43.0 + - + -
376C GLY 3.1 10.2 + - - +
397C CYS* 3.8 17.3 - - + +
398C ILE* 3.9 38.8 - - + +
401C LEU* 3.7 28.7 - - + -
464C ASP* 4.7 0.4 - - - +
465C PHE 3.3 6.1 - - - +
466C ALA* 4.4 0.4 - - + -
479C CYS* 4.1 12.6 - - - +
480C HIS* 1.3 73.2 - - - +
482C PHE* 1.3 77.5 + - - +
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Residues in contact with PHE 482 (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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372C VAL* 4.3 26.7 - - + -
373C ARG 3.4 7.2 - - - +
374C SER* 3.9 28.3 - - - -
375C LEU* 4.1 5.8 - - - -
376C GLY 5.8 0.2 - - - -
422C LEU* 5.5 0.2 - - + -
424C LEU* 4.5 7.6 - - + -
433C LEU* 3.8 35.2 - - + -
464C ASP* 3.3 9.4 - - - +
465C PHE* 2.6 56.4 + + + +
467C TYR* 3.5 34.8 - + - -
480C HIS* 3.6 23.1 - + + -
481C VAL* 1.3 80.7 - - - +
483C ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 483 (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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372C VAL* 3.2 3.5 - - - -
373C ARG* 2.8 49.1 + - + +
375C LEU* 3.9 18.6 - - + +
402C SER* 3.1 25.7 + - - +
403C TYR 2.8 33.5 + - - +
404C HIS* 4.7 10.5 - - - +
463C ARG* 3.4 18.0 - - + +
464C ASP* 2.9 31.1 + - - +
482C PHE* 1.3 72.6 - - - +
484C CYS* 1.3 64.5 + - - +
485D GLU* 3.8 14.6 + - - -
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Residues in contact with CYS 484 (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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370C PHE* 5.5 1.6 - - + -
371C ALA 3.5 6.1 - - - +
372C VAL* 3.8 14.8 - - + -
463C ARG* 2.7 39.2 + - - +
465C PHE* 3.6 29.6 - - - -
482C PHE 4.5 1.1 - - - -
483C ARG* 1.3 78.6 - - - +
485C GLU* 1.3 64.9 + - - +
486C ALA* 3.3 20.2 - - + +
487C PRO 4.9 0.2 - - - -
488C ALA* 4.0 8.1 - - - -
491C ILE* 3.7 22.2 - - + -
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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