Contacts of the strand formed by residues 419 - 426 (chain L) in PDB entry 2B4X
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 419 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52L SER* 3.4 19.1 - - - +
55L ASN* 5.7 4.7 - - + +
56L SER* 4.4 2.2 - - - -
81L LEU* 4.6 9.3 - - + +
126L LEU* 4.0 24.5 - - + -
130L LEU* 3.9 21.8 - - - +
413L ARG* 3.4 4.6 - - - +
414L GLU* 3.1 32.0 + - - +
417L LEU* 3.2 19.0 - - + +
418L ASN* 1.3 78.7 - - - +
420L ILE* 1.3 66.3 + - - +
421L ILE* 3.4 8.5 + - - +
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Residues in contact with ILE 420 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L SER* 4.1 24.9 + - - +
59L ALA* 4.2 18.4 - - + -
60L THR* 4.7 7.6 - - + -
80L PRO* 3.8 14.1 - - + +
81L LEU* 3.7 15.6 + - - +
301L PRO* 6.3 1.3 - - + -
304L LEU* 5.3 10.5 - - + -
411L PHE* 4.2 24.7 - - + -
412L ILE 4.2 3.1 - - - -
413L ARG* 4.4 9.2 - - + -
418L ASN 5.9 0.2 - - - -
419L THR* 1.3 73.3 - - - +
421L ILE* 1.3 60.6 + - - +
422L PHE 3.3 22.4 - - - +
423L MET* 3.7 24.9 - - + -
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Residues in contact with ILE 421 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L SER* 2.5 34.4 + - - +
80L PRO* 3.8 1.4 - - - +
81L LEU* 4.0 18.3 - - + +
130L LEU* 5.5 0.9 - - + -
140L LEU* 3.5 33.9 - - + -
219L ILE* 4.1 19.1 - - + -
221L PHE* 5.4 0.9 - - + -
279L ILE* 5.0 6.5 - - + -
412L ILE* 3.1 20.4 + - + +
413L ARG 4.4 1.8 - - - -
414L GLU* 4.2 18.4 - - + +
419L THR* 3.8 18.4 - - - +
420L ILE* 1.3 75.0 - - - +
422L PHE* 1.3 83.3 + - + +
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Residues in contact with PHE 422 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L PHE* 3.7 26.7 - + + -
78L LEU 3.4 10.1 - - - +
79L SER* 3.7 11.9 - - - -
80L PRO* 4.1 1.1 - - - -
219L ILE* 4.3 12.8 - - + -
221L PHE* 3.7 15.9 - - + -
382L ALA* 3.3 40.8 - - + -
383L ALA* 3.6 24.7 - - - -
384L ALA* 3.9 9.4 - - + -
411L PHE* 3.4 0.5 - - - -
412L ILE* 3.0 41.1 + - + -
420L ILE* 3.3 11.6 - - - +
421L ILE* 1.3 102.1 - - + +
423L MET* 1.3 65.9 + - - +
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Residues in contact with MET 423 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L ALA* 3.2 44.4 - - + +
60L THR* 4.2 2.7 - - + +
63L TYR* 3.7 32.3 - - + -
77L PHE* 3.3 9.3 - - - -
78L LEU* 3.1 46.3 + - + +
80L PRO* 3.6 13.2 - - + -
299L LEU* 5.5 2.0 - - - -
410L VAL 2.9 13.9 - - - +
411L PHE* 3.9 20.2 - - + -
420L ILE* 3.7 12.8 - - + -
422L PHE* 1.3 79.4 - - - +
424L GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 424 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L TYR* 4.4 16.9 - - - -
76L ILE 3.2 14.6 - - - -
77L PHE* 4.2 4.2 - - - -
78L LEU* 4.6 0.4 - - - -
409L LEU* 3.3 6.8 - - - +
410L VAL* 2.8 34.5 + - - +
423L MET* 1.3 79.2 - - - +
425L ARG* 1.3 60.8 + - - +
426L VAL* 4.0 2.0 - - - -
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Residues in contact with ARG 425 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L TYR* 3.5 11.9 - - - +
67L ALA* 3.7 21.6 + - - +
70L LYS* 4.8 2.8 + - - +
71L ASN 3.2 22.2 + - - -
72L ASP* 4.0 16.2 + - - +
74L ASP* 3.0 30.6 + - - +
75L ASN* 3.5 3.3 - - - +
76L ILE* 2.8 51.6 + - + +
292L LEU* 5.0 2.9 - - + +
296L GLU* 2.8 41.6 + - - +
325L ILE* 4.7 0.2 - - - +
407L PRO* 3.7 29.7 - - + +
408L PHE 3.5 7.2 - - - +
409L LEU* 4.1 5.4 - - + -
424L GLY* 1.3 75.7 - - - +
426L VAL* 1.3 60.6 + - - +
427L ALA* 3.3 3.0 + - - -
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Residues in contact with VAL 426 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ASN* 4.0 3.4 - - - +
76L ILE 5.7 0.2 - - - +
77L PHE* 6.2 1.1 - - + -
323L PHE* 3.6 43.5 - - + -
325L ILE* 4.6 12.1 - - + -
373L LEU* 4.8 5.4 - - + -
406L ARG 4.6 0.2 - - - +
407L PRO* 3.1 2.7 - - - +
408L PHE* 2.8 62.5 + - + -
410L VAL* 3.7 21.3 - - + -
424L GLY 4.0 0.6 - - - -
425L ARG* 1.3 72.8 - - - +
427L ALA* 1.3 65.6 + - - +
428L ASN 4.7 2.2 - - - +
429L PRO* 4.9 10.3 - - + -
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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