Contacts of the strand formed by residues 407 - 411 (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 LEU 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A VAL* 5.0 0.9 - - + -
396A LEU* 2.9 61.9 - - + +
406A HIS* 1.3 73.4 - - - +
408A SER* 1.3 60.4 + - - +
409A LEU* 4.6 5.6 - - + -
434A LEU* 5.7 9.0 - - + -
471A PRO 3.9 1.3 - - - -
473A PHE* 2.8 60.8 + - + +
474A VAL* 3.3 20.6 + - + +
476A GLN* 4.2 4.9 - - + -
479A LEU* 3.3 28.3 - - + -
490A ILE* 5.6 0.2 - - + -
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Residues in contact with SER 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 4.1 1.7 - - - +
395A TYR* 2.6 56.4 + - - +
398A GLY* 3.4 5.3 - - - -
399A ASP 3.5 3.7 + - - -
402A GLY 3.2 14.6 + - - -
406A HIS 4.0 0.2 - - - -
407A LEU* 1.3 73.0 - - - +
409A LEU* 1.3 56.4 + - - +
410A PHE* 3.5 14.6 - - - -
470A CYS 3.4 2.2 - - - -
471A PRO* 2.3 45.0 + - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A TRP* 5.6 0.2 - - + -
392A ALA* 5.5 4.5 - - + -
393A ARG 3.5 16.4 - - - +
394A VAL* 4.6 6.1 - - + -
395A TYR 4.7 0.2 - - - +
407A LEU* 3.9 9.7 + - + -
408A SER* 1.3 74.6 - - - +
410A PHE* 1.3 83.1 + - - +
432A LEU* 3.4 39.7 - - + +
470A CYS* 3.2 24.6 + - - +
473A PHE* 4.5 24.3 - - + +
492A ILE* 4.2 37.0 - - + -
494A VAL* 6.0 5.4 - - + -
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Residues in contact with PHE 410 (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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392A ALA* 4.3 4.0 - - - +
393A ARG* 3.4 30.9 + - + +
395A TYR* 3.0 35.9 - + + -
399A ASP* 3.1 20.9 - - - -
408A SER* 3.5 21.8 - - - -
409A LEU* 1.3 91.7 - - - +
411A PHE* 1.3 61.3 + - - +
412A VAL* 4.0 2.2 + - + -
432A LEU* 4.2 3.5 - - - +
467A ALA* 4.1 16.4 - - + -
468A SER 4.1 7.9 - - - +
469A GLY* 3.1 36.6 - - - +
470A CYS 3.3 2.7 - - - -
471A PRO* 3.3 31.2 - - + -
251X VAL* 5.5 0.7 - - + -
253X GLU* 4.7 10.3 - - - -
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Residues in contact with PHE 411 (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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381A PHE* 4.3 11.4 - + - -
390A MET* 3.8 21.3 - - + -
391A CYS 4.3 4.7 - - - -
392A ALA* 5.3 2.0 - - + +
410A PHE* 1.3 74.5 - - - +
412A VAL* 1.3 84.9 + - - +
413A ILE* 3.9 11.3 - - + +
426A PHE* 3.7 28.0 - + - -
430A VAL* 3.2 43.1 - - + -
432A LEU* 3.7 23.3 - - + +
448A PHE* 4.5 11.9 - + + -
456A SER* 5.8 0.3 - - - -
457A PHE* 4.1 18.6 - + - -
466A ILE 4.9 0.7 - - - +
467A ALA 4.4 0.7 - - - -
468A SER* 3.7 22.7 + - - -
469A GLY* 3.9 4.6 - - - +
494A VAL* 4.7 4.9 - - + -
496A VAL* 4.8 0.4 - - + -
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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