Contacts of the helix formed by residues 396 - 403 (chain C) in PDB entry 5Y9F
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 ASN 396 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C ASP* 5.1 6.9 + - - -
326C HIS* 4.7 3.9 - - - -
392C ILE 2.7 21.1 + - - +
393C HIS* 4.3 0.2 - - - -
395C MET* 1.3 89.7 + - - +
397C THR* 1.3 66.6 + - - +
398C THR* 3.1 22.3 - - + +
399C ILE* 3.1 38.6 + - + +
400C LEU 4.1 1.6 + - - -
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Residues in contact with THR 397 (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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393C HIS* 3.2 56.1 + - + +
396C ASN* 1.3 73.0 + - - +
398C THR* 1.3 58.5 + - - +
399C ILE 3.2 0.5 + - - -
400C LEU* 3.4 6.0 + - - +
401C GLU* 2.9 29.1 + - - +
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Residues in contact with THR 398 (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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326C HIS* 3.0 27.0 + - + -
396C ASN* 3.2 26.5 - - - +
397C THR* 1.3 80.0 + - - +
399C ILE* 1.3 59.7 + - - +
401C GLU* 3.9 10.1 - - - -
402C ASP* 2.9 31.4 + - - +
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Residues in contact with ILE 399 (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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325C TRP* 3.6 43.7 - - + -
326C HIS* 3.6 22.0 - - + +
392C ILE* 3.6 23.8 - - + -
395C MET* 4.8 9.4 - - + -
396C ASN* 3.1 32.8 + - + +
398C THR* 1.3 78.8 - - - +
400C LEU* 1.3 63.6 + - - +
402C ASP* 3.8 3.1 - - - +
403C TRP* 3.1 49.8 + - + -
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Residues in contact with LEU 400 (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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384C LEU* 4.1 21.3 - - + -
389C MET* 3.2 50.0 - - + +
392C ILE* 3.9 16.2 - - + -
393C HIS* 4.1 19.3 - - + +
396C ASN 4.1 0.4 + - - -
397C THR* 3.4 6.3 + - - +
399C ILE* 1.3 74.0 - - - +
401C GLU* 1.3 66.4 + - - +
403C TRP* 3.0 46.0 + - + +
404C ASN* 3.5 2.1 + - - -
405C PHE* 4.0 14.4 + - - +
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Residues in contact with GLU 401 (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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397C THR* 2.9 20.5 + - - +
398C THR* 3.9 9.6 - - - +
400C LEU* 1.3 75.8 - - - +
402C ASP* 1.3 58.0 + - - +
403C TRP 3.1 13.3 - - - +
404C ASN* 4.6 1.9 + - - -
405C PHE* 5.7 5.5 - - - -
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Residues in contact with ASP 402 (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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79C ASP* 5.3 4.9 - - - +
326C HIS* 3.3 28.7 - - + +
327C ASN* 5.8 0.2 - - - +
398C THR* 2.9 25.1 + - - +
399C ILE 3.8 4.3 - - - +
400C LEU 3.2 0.2 - - - -
401C GLU* 1.3 72.6 - - - +
403C TRP* 1.3 71.3 + - + +
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Residues in contact with TRP 403 (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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79C ASP* 4.9 6.4 + - - -
81C ASN* 3.4 25.3 - - + +
97C ARG* 3.7 41.1 - - + +
98C LEU 3.6 19.2 + - - -
99C VAL* 4.5 8.1 - - + -
325C TRP* 4.2 4.5 - + - -
327C ASN* 5.5 5.2 + - - +
382C ILE* 3.8 26.5 - - + -
384C LEU* 4.2 10.8 - - + -
392C ILE* 4.6 4.3 - - + -
399C ILE* 3.1 32.7 + - + -
400C LEU* 3.0 37.0 + - + +
401C GLU 3.1 7.4 - - - +
402C ASP* 1.3 89.2 - - + +
404C ASN* 1.3 82.2 + - - +
405C PHE 4.8 1.3 - - - +
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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