Contacts of the strand formed by residues 409 - 414 (chain B) in PDB entry 1FA0
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 PHE 409 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B PHE* 3.6 31.0 - + - -
405B PHE* 3.7 30.3 - + - -
407B LYS* 4.0 4.5 - - + -
408B PRO* 1.3 75.7 - - - +
410B GLU* 1.3 60.8 + - - +
411B SER* 5.1 0.5 + - - -
428B TYR* 4.5 1.7 + - - -
461B LEU 3.6 1.7 - - - +
462B SER* 3.6 1.6 - - - -
463B THR* 2.7 40.3 + - - +
465B TYR* 3.7 21.8 - + + -
520B GLU* 3.4 57.9 - - + +
521B VAL* 3.6 9.9 - - + -
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Residues in contact with GLU 410 (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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375B HIS* 4.2 10.4 - - + -
376B LEU* 5.3 6.4 - - - +
379B SER* 4.5 3.8 + - - -
383B GLU* 4.6 6.8 - - - +
408B PRO* 3.8 22.6 + - + +
409B PHE* 1.3 77.6 - - - +
411B SER* 1.3 65.6 + - - +
461B LEU 3.1 5.4 - - - +
462B SER* 3.0 29.1 + - - +
520B GLU* 4.8 2.2 - - - +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE 5.1 0.3 + - - -
410B GLU* 1.3 77.7 - - - +
412B SER* 1.3 61.7 + - - +
413B TYR* 4.9 8.7 + - - -
428B TYR* 4.7 4.7 + - - -
442B LEU* 4.8 13.7 - - - -
460B TYR* 3.6 1.1 - - - +
461B LEU* 2.8 52.9 + - - +
520B GLU* 4.2 13.3 + - - -
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Residues in contact with SER 412 (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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411B SER* 1.3 76.6 - - - +
413B TYR* 1.3 71.5 + - - +
442B LEU* 3.5 7.0 - - - +
443B VAL* 3.0 49.7 + - - +
458B LYS* 5.1 1.3 - - - -
459B ALA 3.2 15.0 - - - -
460B TYR* 3.7 26.3 - - - -
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Residues in contact with TYR 413 (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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411B SER* 4.9 9.1 + - - -
412B SER* 1.3 76.7 - - - +
414B CYS* 1.3 63.0 + - - +
415B CYS* 3.4 0.4 + - - -
424B ILE* 4.1 28.9 - - + -
428B TYR* 5.7 1.0 - + - -
437B LEU* 3.6 45.8 - - + +
438B ASN* 5.8 1.7 - - - -
440B LEU* 4.0 22.7 - - + -
441B LYS 3.5 5.8 - - - +
442B LEU* 3.3 51.8 - - + +
443B VAL* 3.4 6.5 - - - -
458B LYS* 3.0 6.9 - - - +
459B ALA* 3.0 30.8 + - + +
461B LEU* 4.3 15.5 - - + -
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Residues in contact with CYS 414 (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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413B TYR* 1.3 71.6 - - - +
415B CYS* 1.3 60.2 + - - +
416B PRO* 2.9 17.0 - - + +
440B LEU* 4.0 15.8 - - - +
441B LYS* 3.2 32.8 + - + +
443B VAL* 3.8 19.3 - - - -
457B PRO* 3.2 12.6 - - + +
458B LYS* 4.3 1.1 - - - +
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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