Contacts of the strand formed by residues 378 - 383 (chain C) in PDB entry 4BUR
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 LYS 378 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C ARG* 4.1 3.4 - - - +
301C LYS* 6.1 2.2 - - - +
374C VAL* 3.3 7.6 - - - +
375C SER* 2.7 40.9 + - - +
376C SER 4.5 11.4 - - - +
377C GLY* 1.3 82.1 - - - +
379C LEU* 1.3 63.9 + - - +
390C GLU* 4.0 27.4 - - + +
391C THR 3.7 8.7 - - - +
392C ASP* 3.5 27.4 + - - +
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Residues in contact with LEU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL* 3.9 33.2 - - + +
280C ARG* 4.0 46.0 - - + +
281C THR* 5.3 0.2 - - - +
372C VAL* 4.8 3.8 - - + -
373C GLY 3.5 4.7 - - - +
374C VAL* 4.2 7.0 - - + -
378C LYS* 1.3 72.7 - - - +
380C LEU* 1.3 60.8 + - - +
381C ILE 4.2 0.4 - - - -
389C VAL 3.7 0.2 - - - +
390C GLU* 3.4 6.3 - - - +
391C THR* 2.8 48.5 + - + +
392C ASP 4.1 12.6 - - - +
393C HIS* 4.2 1.3 - - - -
394C ILE* 3.7 36.6 - - + +
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Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C SER* 3.9 0.5 + - - +
372C VAL* 3.4 4.6 - - - +
373C GLY* 2.8 36.9 + - - +
375C SER* 4.2 26.5 - - - +
379C LEU* 1.3 73.5 - - - +
381C ILE* 1.3 65.0 + - - +
382C LYS* 3.6 37.8 + - + +
388C LYS* 4.6 18.6 - - + +
389C VAL 3.3 10.3 - - - +
390C GLU* 4.3 19.3 - - + +
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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
----------------------------------------------------------
304C THR* 3.9 26.9 - - + -
306C ILE* 4.8 5.2 - - + -
333C LEU* 4.4 6.5 - - + -
369C VAL* 3.7 35.9 - - + -
371C SER 3.6 4.0 - - - +
372C VAL* 4.1 7.9 - - + +
379C LEU 5.1 0.2 - - - -
380C LEU* 1.3 76.9 - - - +
382C LYS* 1.3 63.4 + - - +
383C LEU* 3.9 11.1 + - + +
387C ARG 3.9 0.2 - - - +
388C LYS* 3.2 6.2 - - - +
389C VAL* 2.8 52.8 + - + +
391C THR* 4.0 13.2 - - + -
394C ILE* 3.8 30.5 - - + -
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Residues in contact with LYS 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C GLN* 2.8 39.6 + - - +
371C SER* 2.9 31.3 + - - +
380C LEU* 3.6 30.6 + - + +
381C ILE* 1.3 73.9 - - - +
383C LEU* 1.3 63.7 + - - +
387C ARG 4.0 2.9 - - - -
388C LYS* 3.8 30.7 - - + +
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Residues in contact with LEU 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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333C LEU* 4.0 29.2 - - + -
364C MET* 4.0 10.8 - - + -
367C ALA* 3.5 23.1 - - + -
368C ILE 3.3 14.8 - - - +
369C VAL* 4.4 3.4 - - + -
370C GLN* 4.2 2.3 - - - +
381C ILE* 4.3 16.6 - - + +
382C LYS* 1.3 76.7 - - - +
384C LYS* 1.3 59.4 + - - +
385C ASP* 2.9 16.6 + - - +
386C GLY* 2.9 16.8 + - - -
387C ARG* 2.9 56.5 + - + +
389C VAL* 5.1 3.1 - - + -
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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