Contacts of the helix formed by residues 410 - 416 (chain C) in PDB entry 5FLZ
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 GLY 410 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ALA* 5.7 4.0 - - - -
110C ASP* 4.9 12.6 - - - -
406C ASN 4.5 0.4 + - - -
407C TYR 3.4 9.6 + - - +
408C ASN 2.9 17.6 - - - +
409C VAL* 1.4 79.7 - - - +
411C ASP* 1.3 64.9 + - - -
412C LEU* 3.5 3.8 + - - -
413C PHE* 3.6 5.6 + - - -
414C GLN* 3.2 6.4 + - - +
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Residues in contact with ASP 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP* 3.9 7.6 - - - +
409C VAL 3.7 1.7 + - - -
410C GLY* 1.3 71.6 - - - -
412C LEU* 1.4 84.5 + - - +
414C GLN* 3.2 7.9 + - - +
415C SER* 3.0 37.8 + - - +
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Residues in contact with LEU 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C TRP* 5.9 1.6 - - + -
106C ALA* 5.6 2.2 - - + +
109C TYR* 4.1 27.6 - - + -
110C ASP* 3.4 27.4 - - - +
410C GLY* 3.5 2.6 - - - -
411C ASP* 1.4 93.9 - - - +
413C PHE* 1.3 73.0 + - + +
415C SER* 3.8 4.9 + - - -
416C MET* 3.2 22.5 + - - +
419C VAL* 5.2 3.3 - - - +
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Residues in contact with PHE 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C TRP* 3.7 38.1 - + - -
106C ALA* 4.2 11.4 - - + -
185C TYR* 3.6 35.2 - + - -
189C LEU* 4.3 13.2 - - + -
407C TYR* 3.3 38.6 - + + +
408C ASN* 3.5 25.7 + - - +
410C GLY* 3.6 3.5 + - - +
411C ASP 3.3 0.2 - - - -
412C LEU* 1.3 86.4 - - + +
414C GLN* 1.3 61.7 + - - +
416C MET 3.0 17.3 - - - +
417C GLN* 3.7 2.9 + - - +
419C VAL* 4.2 23.8 - - + -
420C GLN* 4.4 7.0 - - + -
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Residues in contact with GLN 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ASN* 3.2 32.6 + - - +
409C VAL* 3.7 16.9 - - - +
410C GLY 3.2 12.6 + - - +
411C ASP* 3.2 11.6 + - - +
413C PHE* 1.3 77.5 - - - +
415C SER* 1.4 62.4 + - - +
416C MET* 3.3 0.9 - - - -
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Residues in contact with SER 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411C ASP* 3.0 18.3 + - - +
412C LEU* 4.2 6.0 - - - -
413C PHE 3.5 0.2 - - - -
414C GLN* 1.4 75.1 - - - +
416C MET* 1.4 79.3 + - - +
418C ASN* 5.3 0.9 + - - -
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Residues in contact with MET 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412C LEU 3.2 14.4 + - - +
413C PHE* 3.0 15.4 - - - +
414C GLN 4.6 0.2 - - - -
415C SER* 1.4 106.1 - - - +
417C GLN* 1.4 57.2 - - - +
418C ASN* 3.3 33.4 - - + +
419C VAL* 3.9 24.0 - - + +
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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