Contacts of the strand formed by residues 343 - 349 (chain A) in PDB entry 3V4O
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 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A ALA* 3.6 11.9 - - + -
342A ASP* 1.3 92.5 + - - +
344A VAL* 1.3 57.7 + - - +
376A LEU 2.8 26.1 + - - -
377A ASP* 4.2 5.4 + - - +
378A PHE* 3.3 27.3 - - + -
379A LYS* 2.8 31.2 + - - +
407A TYR* 3.6 21.8 - - + -
560A LEU 2.7 30.0 + - - +
561A THR* 3.7 6.5 + - - +
562A ASP 2.7 27.5 + - - +
563A PRO* 5.0 0.8 - - - +
564A ILE* 4.0 19.4 - - + +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A ASP* 4.0 16.2 - - - +
343A LYS* 1.3 80.3 - - - +
345A ALA* 1.3 66.3 + - - +
378A PHE* 3.6 3.8 - - - -
379A LYS* 3.5 13.9 - - + +
398A PHE* 3.7 23.4 - - + -
401A LEU* 3.8 40.8 - - + +
402A LEU* 4.0 9.0 - - + -
406A VAL* 3.8 18.4 - - + -
407A TYR 2.9 12.5 + - - +
408A GLY* 3.5 1.2 - - - -
409A LEU 2.9 22.5 + - - -
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A VAL* 1.3 78.3 - - - +
346A LEU* 1.3 60.8 + - - +
347A LEU* 3.9 7.9 - - + -
373A LEU* 3.9 23.1 - - + -
378A PHE* 3.8 16.1 - - + -
379A LYS 2.8 12.5 + - - +
380A VAL* 4.4 5.6 - - + -
381A VAL* 3.1 26.9 + - - +
398A PHE* 4.0 5.3 - - - -
409A LEU* 3.1 13.9 - - + +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ALA* 1.3 73.7 - - - +
347A LEU* 1.3 69.9 + - - +
348A ILE* 4.1 17.0 - - + -
381A VAL* 3.6 26.5 - - + +
383A LEU* 4.3 2.0 - - + -
394A ALA* 3.8 36.1 - - + +
395A VAL* 3.9 19.5 - - + -
398A PHE* 3.7 27.9 - - + -
409A LEU 2.8 8.7 + - - -
410A LEU* 3.4 26.2 - - + +
411A TYR 2.9 25.8 + - - +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A ALA* 3.9 11.0 - - + -
346A LEU* 1.3 83.5 - - - +
348A ILE* 1.3 65.9 + - - +
366A VAL* 3.8 15.0 - - + +
369A LEU* 3.8 20.9 - - + +
370A THR* 3.2 45.5 - - - +
373A LEU* 3.9 20.9 - - + -
380A VAL* 4.0 5.4 - - + -
381A VAL 2.9 11.6 + - - +
382A SER* 3.4 6.3 - - - +
383A LEU* 3.0 24.1 + - - +
409A LEU* 4.3 1.8 - - + -
411A TYR* 3.4 20.6 - - + +
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Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A LEU* 4.1 31.4 - - + -
347A LEU* 1.3 80.5 - - - +
349A GLY* 1.3 60.3 + - - +
350A ASN* 3.7 23.8 - - - +
366A VAL* 3.8 6.0 - - - +
383A LEU* 3.4 4.0 - - + +
386A LEU* 3.9 32.5 - - + -
391A MET* 4.3 20.4 - - + -
394A ALA* 4.5 5.2 - - + -
395A VAL* 4.9 5.8 - - + -
410A LEU* 4.9 5.6 - - + -
411A TYR 2.9 9.4 + - - +
412A TYR* 3.4 21.5 - - + -
413A ALA 2.9 25.3 + - - +
425A MET* 5.8 2.5 - - + -
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Residues in contact with GLY 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A ILE* 1.3 74.3 - - - +
350A ASN* 1.3 62.5 + - - -
351A MET* 3.9 2.2 - - - +
362A PRO* 3.8 13.2 - - - -
366A VAL* 3.6 17.5 - - - +
383A LEU 3.0 10.9 + - - -
384A LEU* 3.1 12.3 - - - +
385A ASP 2.8 21.8 + - - -
413A ALA 3.3 6.7 - - - -
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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