Contacts of the strand formed by residues 343 - 349 (chain B) in PDB entry 3UO8
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340B ALA* 3.6 15.5 - - + -
342B ASP* 1.3 93.2 + - - +
344B VAL* 1.3 63.0 + - - +
376B LEU 2.6 28.9 + - - -
377B ASP* 4.1 7.2 + - - +
378B PHE* 3.3 30.9 - - + -
379B LYS 2.9 24.4 + - - -
407B TYR* 3.4 17.7 - - + -
560B LEU 2.9 18.3 + - - +
561B THR* 3.8 5.5 + - - +
562B ASP 2.9 27.2 + - - +
564B ILE* 3.6 21.4 - - + +
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Residues in contact with VAL 344 (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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342B ASP* 4.5 4.9 - - - +
343B LYS* 1.3 80.6 - - - +
345B ALA* 1.3 65.7 + - - +
378B PHE* 3.6 5.1 - - - -
379B LYS* 3.5 26.0 - - + +
398B PHE* 3.7 23.9 - - + -
401B LEU* 3.9 46.7 - - + +
402B LEU* 3.9 10.8 - - + -
406B VAL* 4.1 10.3 - - + -
407B TYR 2.8 8.5 + - - +
408B GLY* 3.3 4.3 - - - -
409B LEU 2.9 23.2 + - - -
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Residues in contact with ALA 345 (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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344B VAL* 1.3 77.1 - - - +
346B LEU* 1.3 60.0 + - - +
347B LEU* 3.8 18.6 - - + -
373B LEU* 4.0 12.8 - - + -
378B PHE* 3.9 15.0 - - + -
379B LYS 2.9 10.4 + - - +
380B VAL* 3.4 7.3 - - + +
381B VAL* 2.9 27.0 + - - +
398B PHE* 4.0 5.1 - - - -
409B LEU* 3.2 14.1 - - + +
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Residues in contact with LEU 346 (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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345B ALA* 1.3 72.7 - - - +
347B LEU* 1.3 66.7 + - - +
348B ILE* 3.8 30.5 - - + -
381B VAL* 3.5 28.5 - - + +
383B LEU* 4.3 1.6 - - + -
394B ALA* 3.9 27.1 - - + +
395B VAL* 3.8 21.3 - - + -
398B PHE* 3.6 24.7 - - + -
409B LEU 3.0 5.3 + - - -
410B LEU* 3.4 26.7 - - + +
411B TYR 3.0 24.3 + - - +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA* 3.8 13.9 - - + -
346B LEU* 1.3 81.6 - - - +
348B ILE* 1.3 64.1 + - - +
366B VAL* 3.7 17.7 - - + +
369B LEU* 3.7 18.2 - - + -
370B THR* 3.4 42.2 - - - +
373B LEU* 3.7 20.2 - - + -
380B VAL* 4.1 6.3 - - + -
381B VAL 2.8 12.5 + - - +
382B SER* 3.3 2.9 - - - -
383B LEU* 2.8 26.2 + - - +
409B LEU* 4.3 1.6 - - + -
411B TYR* 3.3 27.8 - - + +
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Residues in contact with ILE 348 (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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346B LEU* 3.8 33.4 - - + -
347B LEU* 1.3 79.7 - - - +
349B GLY* 1.3 61.2 + - - +
350B ASN* 4.0 17.5 - - - +
366B VAL* 4.0 5.7 - - - +
383B LEU* 3.3 8.3 - - + +
386B LEU* 4.0 29.6 - - + -
391B MET* 4.2 25.6 - - + +
394B ALA* 4.6 4.5 - - + -
395B VAL* 5.0 3.4 - - + -
410B LEU* 5.0 5.2 - - + -
411B TYR 3.0 8.0 + - - +
412B TYR* 3.4 25.2 - - + -
413B ALA 2.9 24.6 + - - -
425B MET* 6.1 2.0 - - + -
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Residues in contact with GLY 349 (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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348B ILE* 1.3 74.0 - - - +
350B ASN* 1.3 63.1 + - - -
351B MET* 4.0 1.9 + - - +
362B PRO* 4.0 10.3 - - - -
366B VAL* 3.7 17.8 - - - +
383B LEU 2.8 11.6 + - - -
384B LEU* 3.2 12.8 - - - +
385B ASP* 2.9 21.8 + - - +
413B ALA 3.2 8.1 - - - -
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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