Contacts of the strand formed by residues 477 - 484 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B GLU* 3.5 1.7 - - - -
380B MET* 3.1 36.8 + - + +
381B THR 3.4 35.4 - - - +
382B GLU* 3.5 17.0 - - - +
385B LEU* 4.4 9.6 - - + -
451B ARG* 3.7 19.7 - - + +
468B VAL* 4.9 4.5 - - + -
469B ALA 3.7 3.6 - - - -
470B ARG* 3.4 49.0 - - + +
476B MET* 1.3 84.7 - - - +
478B LYS* 1.3 59.5 + - - +
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Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP* 3.2 68.5 - - + +
378B VAL 3.6 4.0 - - - +
379B GLU* 4.5 0.4 - - - -
380B MET* 5.2 1.3 - - - -
467B TYR 3.6 1.2 - - - +
468B VAL* 3.1 28.1 - - - +
469B ALA 2.9 15.8 + - - +
471B ASP* 2.8 29.6 + - + +
476B MET* 3.7 27.5 - - + +
477B LEU* 1.3 78.3 - - - +
479B CYS* 1.3 59.1 + - - +
480B HIS* 3.5 26.1 + - + +
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Residues in contact with CYS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP* 3.3 3.5 - - - -
378B VAL* 2.8 35.7 + - - +
380B MET* 3.8 20.9 - - + -
394B VAL* 3.8 26.0 - - - -
397B CYS* 3.7 26.9 - - - -
466B ALA* 4.2 5.2 - - - -
467B TYR 3.4 4.5 - - - -
468B VAL* 3.8 8.5 - - + -
478B LYS* 1.3 72.1 - - - +
480B HIS* 1.3 64.3 + - - +
481B VAL* 3.6 15.8 + - - +
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Residues in contact with HIS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B SER* 6.2 0.2 - - - +
376B GLY 4.2 1.7 - - - -
377B TRP* 3.4 22.6 + + + +
416B TRP* 3.4 31.3 - + + -
443B HIS* 5.8 0.6 + - - -
466B ALA* 3.2 2.6 - - - -
467B TYR* 2.9 69.9 + + + -
469B ALA* 4.8 7.4 + - + +
471B ASP* 5.9 3.2 - - - -
478B LYS* 3.5 47.3 - - + +
479B CYS* 1.3 70.9 - - - +
481B VAL* 1.3 60.8 + - - +
482B PHE* 3.8 13.3 - - + -
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B SER* 3.9 1.9 + - - -
375B LEU* 2.9 44.1 + - + +
376B GLY 3.3 13.7 + - - +
397B CYS 4.5 4.9 - - - +
398B ILE* 4.1 28.3 - - + -
401B LEU* 3.9 19.5 - - + -
464B ASP* 4.5 0.9 - - + -
465B PHE 3.4 12.3 - - - +
466B ALA* 3.8 14.6 - - + -
479B CYS* 3.7 17.9 - - - +
480B HIS* 1.3 77.2 - - - +
482B PHE* 1.3 75.6 + - - +
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Residues in contact with PHE 482 (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 VAL* 3.8 29.8 - - + -
373B ARG 3.4 7.6 - - - +
374B SER* 3.8 31.2 - - - -
375B LEU* 4.3 2.9 - - - +
416B TRP* 4.8 3.4 - + - -
422B LEU* 4.2 4.3 - - + -
424B LEU* 4.3 6.7 - - + -
433B LEU* 3.8 33.7 - - + -
464B ASP* 3.4 6.1 - - - +
465B PHE* 2.9 50.1 + + + +
467B TYR* 3.2 38.6 - + - -
480B HIS* 3.8 17.5 - - + -
481B VAL* 1.3 79.9 - - - +
483B ARG* 1.3 59.9 + - - +
484B CYS* 3.8 4.6 + - - -
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Residues in contact with ARG 483 (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 VAL* 3.1 3.2 - - - -
373B ARG* 2.7 55.1 + - + +
375B LEU* 3.7 25.8 - - + +
401B LEU 4.5 0.4 + - - -
402B SER* 3.5 39.2 + - - +
463B ARG* 4.1 25.4 - - - +
464B ASP* 2.6 27.6 + - - -
482B PHE* 1.3 71.2 - - - +
484B CYS* 1.3 65.8 + - - +
485B GLU* 5.7 0.3 - - - +
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Residues in contact with CYS 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B PHE* 5.9 0.4 - - + -
371B ALA 3.9 4.7 - - - +
372B VAL* 3.5 22.4 - - + -
463B ARG* 3.0 40.7 + - - +
465B PHE* 3.7 33.2 - - - -
482B PHE* 3.8 9.0 - - - -
483B ARG* 1.3 75.9 - - - +
485B GLU* 1.3 62.2 + - - +
486B ALA* 3.2 22.4 - - + +
488B ALA* 4.3 3.6 - - - -
491B ILE* 3.8 13.0 - - + -
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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