Contacts of the strand formed by residues 379 - 386 (chain O) in PDB entry 5C7O
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 PHE 379 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318O THR* 3.7 25.4 - - + -
319O CYS 3.5 16.2 - - - -
320O ARG* 4.1 9.2 - - + -
375O LEU* 3.0 35.8 + - + +
376O ASN* 3.0 18.2 + - - +
377O ASP 3.7 0.2 - - - -
378O ASN* 1.3 79.3 - - - +
380O VAL* 1.3 61.1 + - - +
244P GLU* 3.6 40.6 - - + +
245P GLY* 3.7 22.0 - - - -
246P LEU* 3.7 29.1 - - + +
318P THR 4.0 11.4 - - - -
320P ARG* 5.1 2.0 - - + -
379P PHE* 4.0 24.2 - + - -
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Residues in contact with VAL 380 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317O LEU 3.5 0.9 - - - +
318O THR* 3.4 2.8 - - - -
319O CYS* 3.0 52.3 + - - +
321O LEU* 4.1 16.6 - - + -
325O ALA 4.5 5.8 - - - +
327O TYR* 5.4 0.9 - - + -
330O ILE* 4.1 17.0 - - + -
373O ILE 3.7 7.0 - - - +
374O ALA* 3.6 20.9 - - + -
376O ASN 3.7 8.1 - - - +
377O ASP 4.9 0.4 - - - +
379O PHE* 1.3 82.5 - - - +
381O LYS* 1.3 60.1 + - - +
382O LEU* 4.0 22.4 - - + -
246P LEU* 3.5 7.2 - - - +
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Residues in contact with LYS 381 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316O ASP* 2.8 35.8 + - - +
317O LEU 3.3 3.8 - - - +
318O THR* 2.9 21.7 + - - +
327O TYR* 4.7 0.3 - - - -
372O GLY* 3.2 7.0 - - - -
373O ILE* 2.8 46.4 + - + +
380O VAL* 1.3 72.9 - - - +
382O LEU* 1.3 64.7 + - - +
383O ILE* 4.1 6.1 - - + -
246P LEU* 4.1 22.3 + - + -
247P MET 3.6 16.8 - - - -
248P THR* 2.9 27.2 + - - +
303P MET* 3.7 24.2 - - + -
316P ASP* 5.3 2.0 + - - -
318P THR* 5.0 2.6 + - - -
381P LYS* 5.4 2.2 - - - +
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Residues in contact with LEU 382 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232O LEU* 4.3 12.5 - - + +
236O ILE* 3.8 35.7 - - + -
315O VAL* 3.6 3.3 - - - +
317O LEU* 2.8 51.6 + - + +
319O CYS* 4.2 17.0 - - - -
327O TYR* 3.9 23.3 - - + -
330O ILE* 4.1 15.9 - - + -
367O PHE* 4.1 16.2 - - + -
372O GLY* 4.8 1.1 - - - -
380O VAL* 4.0 20.0 - - + -
381O LYS* 1.3 80.8 - - - +
383O ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 383 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314O VAL* 3.4 24.0 - - + -
315O VAL 3.3 1.1 - - - -
316O ASP* 3.9 23.3 - - - +
367O PHE* 3.7 10.1 - - - -
368O ASP* 2.8 35.0 + - + +
371O ALA* 3.9 25.6 - - + +
372O GLY* 3.9 24.7 - - - +
381O LYS* 4.1 11.2 - - + -
382O LEU* 1.3 82.9 - - - +
384O SER* 1.3 64.4 + - - +
385O TRP* 4.7 3.4 - - + +
303P MET* 4.4 3.8 - - + -
305P PHE* 3.9 24.7 - - + -
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Residues in contact with SER 384 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228O CYS* 3.5 11.1 - - - -
232O LEU* 4.2 19.5 - - - -
314O VAL* 3.5 4.4 - - - +
315O VAL* 2.8 40.0 + - - -
346O LEU* 4.8 0.2 - - - +
365O SER* 2.6 29.2 + - - -
366O ILE 3.1 22.6 + - - -
367O PHE* 3.5 3.9 + - - +
382O LEU 4.3 0.2 - - - -
383O ILE* 1.3 76.2 - - - +
385O TRP* 1.3 59.5 + - - +
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Residues in contact with TRP 385 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228O CYS* 3.9 0.5 - - - -
312O VAL* 3.9 11.2 - - + -
313O SER 3.6 20.9 - - - -
314O VAL* 3.6 26.1 - - + +
353O VAL* 3.7 9.1 - - + +
354O VAL 4.3 0.2 - - - -
355O SER* 3.5 29.4 - - - -
358O PHE* 3.3 42.6 - + + -
365O SER* 3.4 5.2 - - - -
366O ILE* 2.8 43.4 + - + +
368O ASP* 2.9 33.3 + - + +
383O ILE* 4.7 0.6 - - + +
384O SER* 1.3 75.6 - - - +
386O TYR* 1.3 66.3 + - - +
278P ILE* 3.5 34.5 - - + -
280P PRO* 3.6 28.0 - - + -
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Residues in contact with TYR 386 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224O OCS 3.5 42.4 - - + -
225O THR* 2.7 22.9 + - - +
228O CYS* 3.4 15.9 - - + -
249O THR* 2.6 22.9 + - - -
251O HIS* 3.3 4.2 - - - -
312O VAL* 3.4 5.0 - - - -
313O SER* 2.8 68.7 + - - +
314O VAL 3.6 3.6 - - - -
315O VAL* 3.8 19.3 - - + -
358O PHE* 5.3 0.9 - - - -
363O HIS 5.0 1.3 - - - +
364O SER 3.4 20.0 - - - +
366O ILE* 4.4 6.5 - - - -
384O SER 4.1 0.7 - - - -
385O TRP* 1.3 76.5 - - - +
387O ASP* 1.3 61.5 + - - +
388O ASN* 3.1 15.9 + - + -
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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