Contacts of the strand formed by residues 380 - 388 (chain C) in PDB entry 5O67
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 THR 380 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ASN* 3.3 36.8 + - + +
372C THR* 4.1 10.1 - - + -
373C ILE 3.3 11.2 - - - +
374C ALA* 4.6 1.4 - - - +
378C ASN 4.2 0.4 + - - -
379C LEU* 1.3 78.0 + - - +
381C ILE* 1.3 72.8 + - - +
382C VAL* 3.7 16.8 - - + -
401C LYS 4.2 0.2 - - - -
402C PHE* 3.4 9.7 - - - -
403C PRO* 3.3 38.9 + - + +
405C TYR* 5.0 7.6 - - - -
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Residues in contact with ILE 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C THR* 3.6 3.3 - - - -
373C ILE* 2.9 46.8 + - + +
375C ALA* 4.1 23.3 - - + -
379C LEU* 4.9 6.1 - - + -
380C THR* 1.3 76.9 - - - +
382C VAL* 1.3 63.7 + - - +
383C PRO* 3.6 9.0 - - + +
400C LEU* 4.0 20.9 - - + -
401C LYS 3.5 2.7 - - - +
402C PHE* 3.9 33.7 - - + -
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Residues in contact with VAL 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU* 3.8 34.3 - - + +
371C MET 3.5 13.7 - - - +
372C THR* 4.1 9.6 - - + -
380C THR* 3.7 18.2 - - + -
381C ILE* 1.3 79.3 - - - +
383C PRO* 1.3 66.3 - - - +
384C ASN* 3.8 4.7 + - + +
399C SER 3.5 1.7 - - - +
400C LEU* 3.4 5.5 - - - -
401C LYS* 2.9 51.5 + - + +
403C PRO* 4.4 11.7 - - + -
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Residues in contact with PRO 383 (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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370C GLY* 3.4 2.1 - - - -
371C MET* 3.0 46.6 + - + +
373C ILE* 3.7 19.3 - - + -
381C ILE* 3.6 8.3 - - + +
382C VAL* 1.3 89.1 - - - +
384C ASN* 1.3 58.8 - - - +
399C SER 3.3 7.4 - - - +
400C LEU* 3.7 20.6 - - + -
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Residues in contact with ASN 384 (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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98C GLU* 5.1 11.3 - - - +
334C SER* 6.0 0.3 - - - -
368C ASN* 3.2 32.7 + - - +
369C VAL 3.3 19.2 - - - +
370C GLY* 3.8 4.6 - - - -
382C VAL* 3.8 5.1 + - + +
383C PRO* 1.3 74.6 - - - +
385C LEU* 1.3 65.9 + - - +
386C ALA* 4.0 5.1 - - - +
397C THR 3.7 1.1 + - - +
398C PHE* 3.7 3.7 - - - -
399C SER* 3.0 46.7 + - - +
401C LYS* 6.3 2.0 - - + -
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Residues in contact with LEU 385 (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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337B VAL* 3.6 29.8 - - + -
367B PHE* 3.7 30.1 - - + -
389B MET* 4.3 7.2 - - - -
367C PHE 4.0 0.3 - - - +
368C ASN* 3.4 2.3 - - - -
369C VAL* 3.0 38.2 + - + +
384C ASN* 1.3 80.3 + - - +
386C ALA* 1.3 69.9 + - - +
387C ILE* 4.0 22.9 - - + -
396C PHE* 4.5 2.5 - - + -
397C THR 3.6 4.0 - - - +
398C PHE* 3.9 32.5 - - + +
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Residues in contact with ALA 386 (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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366C TYR* 4.4 18.5 - - + -
367C PHE 3.6 1.6 - - - -
368C ASN* 3.1 22.7 - - - +
384C ASN* 4.0 5.6 - - - +
385C LEU* 1.3 73.7 - - - +
387C ILE* 1.3 62.1 + - - +
388C GLY 3.8 0.5 + - - -
394C PRO 5.2 0.3 - - - +
396C PHE* 3.4 5.4 - - - -
397C THR* 3.0 45.9 + - + +
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Residues in contact with ILE 387 (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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387A ILE* 5.9 6.3 - - + -
367B PHE* 3.8 39.9 - - + -
387B ILE* 6.0 3.8 - - + -
389B MET* 4.2 19.7 - - + -
366C TYR* 3.4 4.9 - - - -
367C PHE* 2.9 55.3 + - + +
369C VAL* 6.0 0.7 - - + -
385C LEU* 4.0 19.3 - - + -
386C ALA* 1.3 74.4 - - - +
388C GLY* 1.3 76.0 + - - +
389C MET* 3.4 6.0 + - + +
395C ASP 4.0 7.9 - - - +
396C PHE* 4.7 1.3 - - - +
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Residues in contact with GLY 388 (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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387A ILE* 6.1 0.2 - - - +
365C GLY 3.9 6.7 - - - -
366C TYR* 4.6 3.7 - - - -
386C ALA 3.8 2.2 + - - -
387C ILE* 1.3 81.7 - - - +
389C MET* 1.3 60.0 + - - -
390C THR 3.6 3.4 - - - -
393C ALA* 4.1 9.2 - - - -
394C PRO 3.2 22.3 + - - -
395C ASP* 3.0 17.0 + - - +
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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