Contacts of the strand formed by residues 379 - 383 (chain B) in PDB entry 3LPJ
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 ASP 379 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B PHE* 6.0 1.7 - - - +
221B PRO* 5.6 7.3 - - - +
330B CYS* 3.4 0.5 - - - -
331B TRP* 2.9 31.9 + - - +
332B GLN 5.0 0.4 - - - +
333B ALA* 4.2 2.8 - - - +
334B GLY* 2.9 32.7 + - - +
336B THR* 3.8 9.4 + - - +
377B GLN 4.2 3.8 - - - +
378B ASP* 1.3 75.2 - - - +
380B CYS* 1.3 62.1 + - - +
381B TYR* 3.6 28.8 + - + +
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Residues in contact with CYS 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PRO* 5.1 2.8 - - - +
328B LEU* 4.1 11.9 - - + -
329B VAL 3.2 5.2 - - - +
330B CYS* 2.0 46.9 - - - -
369B PRO* 3.5 2.3 - - - +
370B VAL* 3.1 35.1 + - - +
372B ASP* 3.4 25.6 - - - -
378B ASP* 3.8 9.3 + - - -
379B ASP* 1.3 75.2 - - - +
381B TYR* 1.3 73.0 + - - +
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Residues in contact with TYR 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY 4.7 6.4 + - - -
322B PHE* 4.3 5.6 - - + -
327B GLN 4.3 0.2 - - - +
328B LEU* 3.1 5.0 - - - -
329B VAL* 3.0 30.2 + - + +
331B TRP* 3.7 19.5 - + + -
336B THR* 2.9 35.5 + - + -
338B TRP* 3.3 30.3 - + - -
367B LEU* 3.9 31.4 - - + -
368B ARG 3.1 8.7 - - - +
369B PRO* 3.7 31.2 - - + -
370B VAL* 4.0 4.9 - - - -
379B ASP* 3.6 26.9 + - + +
380B CYS* 1.3 85.8 - - - +
382B LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PHE* 4.3 2.9 - - - -
325B GLY 4.0 18.7 + - - +
326B GLU* 3.6 21.8 + - - +
327B GLN 4.3 6.5 - - - +
328B LEU* 4.2 20.2 - - + +
367B LEU* 3.5 3.9 - - - -
368B ARG* 2.9 60.2 + - + +
370B VAL* 4.1 16.8 - - + -
381B TYR* 1.3 79.9 - - - +
383B PHE* 1.3 64.5 + - - +
384B ALA* 3.2 1.1 + - - -
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Residues in contact with PHE 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B ASN* 4.1 3.8 + - - -
306B VAL* 4.1 16.2 - - + -
309B ILE* 4.1 11.9 - - + -
322B PHE* 3.2 36.7 + + + +
323B TRP* 3.5 60.8 - + - -
325B GLY* 3.5 20.2 - - - +
327B GLN 5.0 0.2 + - - -
341B PHE* 6.0 0.2 - + - -
366B TYR* 4.0 15.9 - + - -
367B LEU* 4.1 16.2 - - + -
382B LYS* 1.3 71.8 - - - +
384B ALA* 1.3 59.9 + - - +
385B ILE* 3.3 58.5 + - + +
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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
------------------------------------------------------------
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