Contacts of the strand formed by residues 378 - 383 (chain B) in PDB entry 1JV5
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 378 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B SER* 4.0 6.1 - - - -
322B CYS 3.3 17.7 - - - +
323B LYS* 3.0 26.8 + - + +
329B PHE* 3.7 3.9 - - - -
372B VAL* 3.4 3.8 - - - +
373B ASP 2.8 31.8 + - - -
376B SER* 3.2 20.0 + - - -
377B SER* 1.3 78.1 - - - +
379B ALA* 1.3 71.9 + - - +
380B TYR* 3.5 34.2 + - + +
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B SER* 3.6 1.6 - - - -
322B CYS* 2.7 44.9 + - + +
329B PHE* 3.9 6.6 - - + -
334B ILE* 3.8 37.9 - - + -
336B TRP* 3.8 6.6 - - - +
351B ILE* 5.3 0.7 - - + -
371B THR 3.8 4.5 - - - +
372B VAL* 4.1 9.0 - - + -
378B THR* 1.3 76.8 - - - +
380B TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LYS* 3.4 39.0 - - + -
320B LEU 3.3 11.7 - - - +
321B SER* 3.9 11.4 - - - -
336B TRP* 4.0 8.2 + - - -
370B LEU* 3.4 4.5 - - - +
371B THR* 2.7 55.2 + - - +
372B VAL* 4.3 4.5 - - - -
373B ASP* 3.8 25.9 + - + +
376B SER* 4.3 5.7 + - - -
378B THR* 3.5 33.1 + - + +
379B ALA* 1.3 77.1 - - - +
381B MET* 1.3 61.8 + - - +
382B GLN 4.3 0.7 - - - +
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Residues in contact with MET 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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318B VAL 3.7 0.9 - - - +
319B LYS* 3.4 2.8 - - - -
320B LEU* 2.7 58.0 + - + +
336B TRP* 3.8 41.1 - - + -
348B ILE* 4.1 10.3 - - + -
368B ALA* 4.0 21.3 - - + -
369B THR 3.5 3.4 - - - -
370B LEU* 3.7 22.9 - - + -
380B TYR* 1.3 75.1 - - - +
382B GLN* 1.3 63.2 + - - +
383B LEU* 3.9 10.0 + - + -
394B TYR* 3.5 35.9 - - + -
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Residues in contact with GLN 382 (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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317B SER* 3.2 24.3 + - - +
318B VAL 3.1 16.2 - - - +
319B LYS* 4.1 20.7 - - + +
367B LYS 3.3 2.6 - - - +
368B ALA* 3.3 6.4 - - - -
369B THR* 3.0 48.0 + - + +
371B THR* 6.4 0.7 - - + -
380B TYR* 5.4 0.2 - - - +
381B MET* 1.3 73.8 - - - +
383B LEU* 1.3 59.6 + - - +
384B SER* 4.0 15.2 + - - -
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Residues in contact with LEU 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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317B SER* 3.3 7.2 + - - -
318B VAL* 2.7 45.0 + - + -
320B LEU* 4.2 14.8 - - + -
348B ILE* 5.9 0.7 - - + -
364B PHE* 5.8 4.5 - - + -
367B LYS* 3.6 22.9 - - + -
368B ALA* 4.3 12.8 - - + -
381B MET* 4.2 18.4 - - + +
382B GLN* 1.3 72.7 - - - +
384B SER* 1.3 60.7 + - - +
386B LEU* 3.6 24.0 - - + +
390B ASP* 5.1 2.5 - - + +
394B TYR* 3.6 42.0 - - + +
414B VAL* 4.9 4.3 - - + -
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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