Contacts of the strand formed by residues 460 - 470 (chain C) in PDB entry 5EG6
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 VAL 460 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367C TYR 3.3 17.5 - - - +
368C GLU* 5.0 5.8 - - + -
369C GLY 4.4 0.7 - - - +
373C VAL* 4.1 18.8 - - + -
377C VAL* 4.3 17.0 - - + -
455C VAL* 3.4 2.8 - - - -
456C ARG* 2.9 50.7 + - + +
458C ASP* 3.4 20.9 + - - +
459C GLY* 1.3 75.9 - - - +
461C ILE* 1.3 64.3 + - - +
462C TYR* 3.6 33.1 + - + +
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Residues in contact with ILE 461 (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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57C LEU* 3.8 31.2 - - + -
61C ALA 5.1 0.2 - - - +
62C MET* 4.3 3.1 - - - -
65C TYR* 3.6 53.8 - - + +
71C ASP* 5.2 0.2 - - - +
366C PHE* 3.5 4.7 - - - -
367C TYR* 2.7 48.6 + - + +
369C GLY* 4.0 9.0 - - - -
453C THR* 3.4 24.9 - - + -
454C LEU 3.7 2.9 - - - -
455C VAL* 4.4 3.8 - - + +
459C GLY 3.8 10.3 - - - +
460C VAL* 1.3 73.9 - - - +
462C TYR* 1.3 64.6 + - - +
463C SER 3.9 0.9 + - - -
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Residues in contact with TYR 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C THR 3.7 15.5 - - - -
366C PHE* 3.9 11.7 - - + -
377C VAL 2.5 29.9 + - - -
379C PRO 4.6 1.2 + - - -
380C VAL* 3.7 14.4 - - + -
381C PRO* 3.4 38.0 - - + +
408C LEU* 4.2 14.1 - - + -
453C THR* 3.6 2.8 - - - +
454C LEU* 2.7 49.0 + - + +
456C ARG* 3.4 26.4 + - + -
460C VAL* 3.6 29.5 - - + +
461C ILE* 1.3 71.6 - - - +
463C SER* 1.3 66.4 + - - +
464C THR* 3.5 4.2 + - + +
522C BU1 3.6 10.1 - - - +
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Residues in contact with SER 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TYR* 3.3 23.4 + - - -
69C ARG* 3.2 19.3 + - - +
71C ASP* 3.7 11.4 + - - -
365C THR* 3.8 17.9 + - - +
453C THR* 4.5 4.9 - - - -
461C ILE* 3.9 4.0 + - - +
462C TYR* 1.3 71.5 - - - +
464C THR* 1.3 67.8 + - - +
522C BU1 2.8 34.4 + - - -
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Residues in contact with THR 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ARG* 4.4 2.2 + - - +
383C VAL* 4.1 25.4 - - + +
452C VAL* 2.6 31.2 + - + +
453C THR* 4.3 0.9 - - - +
454C LEU* 4.3 11.9 - - + +
462C TYR 3.5 9.4 + - - +
463C SER* 1.3 87.6 + - - +
465C SER* 1.3 55.4 + - - +
466C LEU* 3.0 29.7 + - + +
504C EDO 2.7 24.6 + - - -
522C BU1 5.4 2.9 - - - -
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Residues in contact with SER 465 (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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464C THR* 1.3 72.9 - - - +
466C LEU* 1.3 71.0 + - - +
467C THR* 4.0 2.6 + - - +
504C EDO 3.5 11.7 - - - -
522C BU1 5.7 1.0 + - - -
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Residues in contact with LEU 466 (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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383C VAL* 3.5 41.5 - - + +
384C GLU 5.3 5.4 - - - +
385C SER* 5.2 1.3 - - - -
386C LEU* 3.8 34.1 - - + +
452C VAL* 3.0 19.4 + - + +
464C THR* 3.0 17.6 + - + +
465C SER* 1.3 89.7 - - - +
467C THR* 1.3 61.5 + - - +
504C EDO 2.8 23.4 + - - -
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Residues in contact with THR 467 (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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386C LEU* 4.0 15.4 - - - +
449C GLN* 2.9 35.4 + - + +
450C VAL 3.2 14.4 - - - +
451C PRO* 4.3 1.8 - - + -
452C VAL* 3.8 5.6 - - - -
465C SER 4.0 2.9 + - - +
466C LEU* 1.3 77.6 - - - +
468C PHE* 1.3 61.4 + - - +
469C THR* 4.7 2.4 + - - -
504C EDO 3.4 27.8 - - - +
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Residues in contact with PHE 468 (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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386C LEU* 6.1 0.4 - - + -
388C LEU* 3.9 20.2 - - + -
395C ALA* 5.7 0.2 - - + -
397C LEU* 3.8 37.0 - - + -
412C PHE* 3.9 24.7 - + + -
431C VAL* 3.7 27.8 - - + -
448C VAL 3.9 0.3 - - - +
449C GLN* 3.3 1.4 - - - +
450C VAL* 2.8 35.2 + - + +
452C VAL* 3.9 5.8 - - + +
467C THR* 1.3 74.4 - - - +
469C THR* 1.3 80.1 + - - +
470C TYR* 3.8 32.8 - + - -
501C EDO 4.2 15.3 - - - -
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Residues in contact with THR 469 (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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447C PRO* 4.5 9.0 - - + -
448C VAL 3.3 13.5 - - - +
449C GLN* 3.6 25.1 + - + +
467C THR* 4.7 1.9 + - - -
468C PHE* 1.3 89.1 - - - +
470C TYR* 1.3 74.7 + - - +
471C THR* 3.6 14.6 + - - +
501C EDO 3.4 11.3 + - - -
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Residues in contact with TYR 470 (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 PHE* 4.6 0.9 - - - -
431C VAL* 3.6 11.3 - - + +
432C PRO* 2.7 35.2 + - - +
434C ILE* 3.6 41.3 - - + -
437C PHE* 3.2 37.7 - + - -
444C VAL* 3.9 11.0 - - + -
447C PRO* 3.1 7.6 - - - +
448C VAL* 2.7 47.3 + - + +
450C VAL* 4.3 9.4 - - + -
468C PHE* 3.8 25.0 - + - -
469C THR* 1.3 74.0 - - - +
471C THR* 1.3 61.0 + - - +
501C EDO 3.7 21.1 - - - -
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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