Contacts of the strand formed by residues 353 - 359 (chain A) in PDB entry 1FLL
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 VAL 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A SER* 2.6 30.8 + - - +
351A ASN* 3.6 15.4 - - - +
352A GLY* 1.3 86.8 - - - +
354A LEU* 1.3 69.3 + - - +
355A ILE* 4.8 8.7 - - + -
381A PHE* 3.0 17.8 - - - -
493A LYS* 4.8 5.6 - - + -
494A VAL 3.3 16.6 - - - +
495A ILE* 4.3 18.4 - - + -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A SER* 4.7 4.7 - - - -
353A VAL* 1.3 77.3 - - - +
355A ILE* 1.3 110.1 + - - +
356A TRP* 3.2 9.9 - - + +
378A SER* 3.4 28.7 - - - +
379A GLN* 3.6 25.4 - - - +
381A PHE* 3.7 33.7 - - + -
392A ALA* 3.9 11.7 - - + -
492A ILE 4.1 0.9 - - - +
493A LYS* 3.1 0.9 - - - +
494A VAL* 2.9 46.9 + - + +
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Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A SER* 5.7 0.6 - - - -
353A VAL* 4.8 7.6 - - + -
354A LEU* 1.3 97.4 - - - +
356A TRP* 1.3 58.3 + - - +
357A LYS* 3.8 3.3 + - - +
379A GLN* 3.8 8.7 + - - -
435A MET* 4.5 8.1 - - + -
491A PHE* 4.1 26.0 - - + -
492A ILE 3.3 4.5 - - - +
493A LYS* 3.3 37.0 - - + -
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Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 3.2 8.9 - - + +
355A ILE* 1.3 71.1 - - - +
357A LYS* 1.3 73.5 + - - +
358A ILE* 3.4 24.7 + - + +
376A LEU* 3.6 15.7 - - + -
377A TYR 2.9 32.3 + - - -
378A SER* 3.4 32.6 - - - +
379A GLN* 4.1 13.2 - - - +
392A ALA* 4.1 5.8 - - + -
393A ARG 4.4 1.1 - - - -
394A VAL* 3.2 49.6 - - + -
409A LEU* 5.6 0.7 - - + -
491A PHE* 3.5 6.0 - - - -
492A ILE* 3.1 56.0 + - + +
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ILE 3.8 3.9 + - - +
356A TRP* 1.3 81.7 + - - +
358A ILE* 1.3 63.9 + - - +
359A ARG* 3.1 39.6 + - - +
379A GLN* 5.4 0.4 + - - -
489A THR* 4.8 13.0 - - - -
491A PHE* 3.0 47.4 - - + -
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Residues in contact with ILE 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TRP* 3.4 58.6 - - + +
357A LYS* 1.3 72.5 - - - +
359A ARG* 1.3 72.0 + - - +
361A TYR* 5.1 6.1 - - + +
364A ARG* 4.9 4.9 - - + +
376A LEU* 4.8 14.1 - - + -
394A VAL* 3.9 11.0 - - + -
396A LEU* 4.7 6.3 - - + -
489A THR* 3.1 5.3 - - - -
490A ILE* 2.5 76.1 + - + +
492A ILE* 3.8 8.5 - - + -
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Residues in contact with ARG 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A GLN* 5.9 3.4 - - - +
357A LYS* 3.1 55.9 + - - +
358A ILE* 1.3 78.4 - - - +
360A ASP* 1.3 80.4 + - - +
361A TYR* 2.7 11.9 + - - +
364A ARG* 3.3 22.9 + - - +
488A ASP 3.8 1.1 - - - -
489A THR* 3.3 25.1 - - + -
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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