Contacts of the strand formed by residues 377 - 382 (chain C) in PDB entry 1OAT
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 377 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C SER* 5.0 1.6 - - - +
232C ILE* 4.2 16.8 - - + -
234C GLY* 5.3 2.9 - - - -
238C VAL* 3.9 23.5 - - + +
266C GLN* 3.9 26.0 - - + +
267C THR* 4.0 30.3 - - + -
271C ARG* 4.0 17.5 - - + +
272C THR* 4.3 10.8 - - + -
373C GLY* 3.2 3.8 - - - -
374C LYS 3.0 32.3 + - - +
375C GLY 3.4 0.2 - - - -
376C LEU* 1.3 75.9 - - - +
378C ASN* 1.3 60.0 + - - +
413C ARG* 4.2 12.3 - - + -
414C PHE 4.2 0.4 - - - -
415C ALA* 4.6 9.0 - - + -
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Residues in contact with ASN 378 (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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238C VAL* 4.0 4.3 - - - -
353C GLY* 4.6 1.6 - - - -
356C LEU* 3.5 29.4 - - + +
357C ARG* 2.9 37.8 + - + +
360C LEU* 5.3 5.6 - - + -
371C VAL* 6.1 0.4 - - + -
372C ARG 3.3 6.3 - - - +
373C GLY* 3.3 12.8 - - - -
374C LYS 3.7 0.2 + - - -
375C GLY 3.0 22.4 + - - -
376C LEU* 3.8 4.2 + - - +
377C LEU* 1.3 77.3 - - - +
379C ALA* 1.3 60.1 + - - +
413C ARG* 3.4 9.0 - - - +
414C PHE* 2.7 41.1 + - + +
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Residues in contact with ALA 379 (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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237C GLY 4.0 9.4 - - - +
238C VAL* 3.8 24.0 - - + -
360C LEU* 5.2 0.4 - - - +
371C VAL* 3.5 5.0 - - - +
372C ARG* 2.9 36.7 + - + +
378C ASN* 1.3 77.3 - - - +
380C ILE* 1.3 66.2 + - - +
381C VAL* 5.7 0.2 - - - -
411C ILE* 4.1 12.8 - - + -
412C ILE 3.2 13.2 - - - +
413C ARG* 4.2 2.7 - - + -
414C PHE* 4.5 2.0 - - - +
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Residues in contact with ILE 380 (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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360C LEU* 3.7 31.4 - - + -
363C LEU* 5.2 2.9 - - + -
368C VAL* 4.0 19.3 - - + -
370C ALA 3.1 8.3 - - - +
371C VAL* 4.0 15.3 - - + -
379C ALA* 1.3 79.1 - - - +
381C VAL* 1.3 62.5 + - - +
382C ILE* 3.9 24.6 + - + -
410C ASP 3.9 0.2 - - - +
411C ILE* 3.5 4.3 - - - +
412C ILE* 2.9 45.1 + - + +
414C PHE* 3.8 25.8 - - + -
432C ILE* 5.4 0.4 - - + -
436C ILE* 4.4 13.2 - - + -
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Residues in contact with VAL 381 (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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368C VAL* 3.5 5.2 - - - -
369C THR* 2.9 46.2 + - - +
370C ALA* 2.9 22.1 + - + +
372C ARG* 3.9 35.7 - - + +
379C ALA 5.7 0.9 - - - -
380C ILE* 1.3 75.9 - - - +
382C ILE* 1.3 64.7 + - - +
410C ASP* 3.2 28.7 - - - +
411C ILE* 4.2 9.6 - - + -
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Residues in contact with ILE 382 (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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367C VAL* 4.0 0.7 - - + -
368C VAL* 4.3 11.4 - - + -
369C THR* 4.8 0.9 - - - -
380C ILE* 3.9 24.5 - - + +
381C VAL* 1.3 80.9 - - - +
383C LYS* 1.3 68.4 + - - +
384C GLU* 3.2 2.6 + - - +
388C TRP* 3.6 38.8 - - + -
389C ASP* 4.2 4.3 - - - -
390C ALA* 4.1 19.7 - - + +
393C VAL* 4.7 1.8 - - + -
410C ASP* 2.6 43.2 + - - +
412C ILE* 3.8 26.0 - - + -
436C ILE* 4.3 8.1 - - + -
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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