Contacts of the strand formed by residues 467 - 474 (chain F) in PDB entry 1D00
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 SER 467 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410F PHE* 3.6 6.1 - - - -
411F PHE* 2.9 31.7 + - - +
447F PHE* 4.2 2.6 - - - -
453F SER* 5.5 0.4 - - - -
455F SER* 3.5 11.8 - - - -
456F PHE* 3.2 33.8 - - - -
465F ILE 3.8 0.2 + - - -
466F ALA* 1.3 76.9 - - - +
468F GLY* 1.3 61.0 + - - +
250N PRO* 3.8 8.9 - - - +
251N VAL 3.2 16.2 - - - -
252N GLN* 3.6 11.2 - - - -
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Residues in contact with GLY 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F LEU 3.9 4.7 - - - -
410F PHE* 3.2 6.2 - - - -
432F LEU* 5.0 0.7 - - - -
447F PHE* 4.0 18.6 - - - -
467F SER* 1.3 76.9 - - - +
469F CYS* 1.3 65.5 + - - -
470F PRO* 3.4 8.1 - - - +
249N ACE 4.8 0.7 - - - +
250N PRO* 3.7 6.0 - - - +
251N VAL* 2.8 31.7 + - - +
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Residues in contact with CYS 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B ARG* 5.2 7.2 - - - +
409F LEU 2.8 32.7 + - - +
410F PHE* 4.2 2.2 - - - -
432F LEU* 4.1 19.7 - - - -
445F ASP* 3.4 36.3 - - - +
447F PHE* 4.5 9.6 - - - -
468F GLY* 1.3 78.2 - - - +
470F PRO* 1.3 66.9 - - - +
471F LEU 3.1 2.5 - - - +
472F PHE* 3.1 29.3 + - + +
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Residues in contact with PRO 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448B ARG* 6.3 0.2 - - - +
399F ASP* 3.8 14.1 - - - +
400F GLY* 5.4 0.7 - - - -
401F THR* 3.7 23.6 - - - +
402F GLY* 3.6 12.5 - - - -
406F HIS* 3.9 1.2 - - - +
407F LEU 3.9 1.9 - - - +
408F SER* 2.7 29.9 + - - +
410F PHE* 4.0 15.0 - - + -
468F GLY 3.4 11.4 - - - +
469F CYS* 1.3 84.3 - - - +
471F LEU* 1.3 62.1 + - + +
472F PHE 3.5 1.5 + - - -
251N VAL* 3.7 32.1 - - + -
252N GLN 5.9 0.2 - - - +
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Residues in contact with LEU 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B LYS* 5.7 1.7 + - - -
448B ARG* 4.9 17.9 + - - +
499B THR* 4.2 29.2 - - + +
401F THR* 3.7 24.5 - - - +
402F GLY* 3.5 28.9 - - - +
406F HIS* 3.6 37.0 + - + +
407F LEU 4.2 0.2 - - - -
469F CYS* 3.1 2.8 - - - +
470F PRO* 1.3 82.0 - - + +
472F PHE* 1.3 63.5 + - - +
473F CYS 3.4 2.5 + - - -
474F PRO* 5.4 0.5 - - - +
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Residues in contact with PHE 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B LYS* 5.0 8.5 + - - +
407F LEU* 3.5 18.9 + - + +
409F LEU* 4.0 29.4 - - + +
432F LEU* 3.5 37.0 - - + -
433F MET* 3.7 14.1 - - - -
434F LEU* 3.8 25.6 - - + -
443F VAL* 3.7 25.4 - - + +
444F ILE 4.2 2.0 - - - -
445F ASP* 4.0 21.5 - - + -
469F CYS* 3.1 35.4 + - + +
471F LEU* 1.3 78.1 - - - +
473F CYS* 1.3 68.3 + - + +
474F PRO* 4.6 1.4 - - - +
492F ILE* 5.2 1.1 - - + -
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Residues in contact with CYS 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406F HIS* 3.2 4.4 - - - -
407F LEU* 2.6 44.1 + - + +
434F LEU* 3.7 12.6 - - + -
443F VAL* 4.1 16.8 - - + -
471F LEU 3.4 0.8 + - - -
472F PHE* 1.3 94.4 - - + +
474F PRO* 1.3 80.5 - - - +
477F LYS* 4.4 6.1 - - - -
478F MET* 3.6 30.5 - - - -
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Residues in contact with PRO 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405F THR 3.6 8.7 - - - +
406F HIS* 3.7 23.3 - - + +
443F VAL* 6.0 0.7 - - + -
471F LEU 5.4 0.2 - - - +
472F PHE 4.6 1.8 - - - +
473F CYS* 1.3 94.6 - - - +
475F VAL* 1.3 66.6 + - - +
476F SER* 4.0 14.8 - - - +
477F LYS* 3.0 35.0 + - + +
478F MET* 4.0 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