Contacts of the strand formed by residues 407 - 413 (chain B) in PDB entry 3UOA
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 TYR 407 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B MET* 3.9 0.2 - - - +
339B LEU 3.5 5.0 + - - -
340B ALA* 3.6 29.6 - - + -
342B ASP 2.9 11.6 + - - +
343B LYS* 3.4 16.1 - - + -
344B VAL 2.9 27.9 + - - +
378B PHE* 4.5 10.5 - + + -
405B GLY 3.8 8.5 - - - -
406B VAL* 1.3 75.6 - - - +
408B GLY* 1.3 59.3 + - - +
455B GLY* 4.2 3.1 - - - -
456B LEU* 3.6 41.7 - - + -
558B ARG* 2.9 38.8 + - + -
559B ALA 3.5 15.7 - - - -
560B LEU* 5.2 0.4 - - - -
562B ASP* 2.5 36.9 + - + +
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Residues in contact with GLY 408 (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 3.3 4.9 - - - -
398B PHE* 4.1 1.3 - - - -
402B LEU* 3.9 19.0 - - - +
406B VAL 3.7 1.8 + - - -
407B TYR* 1.3 74.3 - - - +
409B LEU* 1.3 61.2 + - - +
449B MET* 3.6 15.2 - - - +
454B THR* 4.8 1.0 - - - +
456B LEU* 2.9 14.3 + - - +
457B ASN* 3.5 2.3 - - - -
458B VAL* 2.9 24.5 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B VAL 3.0 7.5 + - - +
345B ALA* 3.2 21.4 - - + -
346B LEU 3.0 25.3 + - - -
347B LEU* 4.2 4.0 - - + -
369B LEU* 5.0 0.2 - - + -
373B LEU* 4.1 27.1 - - + -
378B PHE* 4.2 8.1 - - + -
398B PHE* 3.6 6.2 - - - -
408B GLY* 1.3 75.3 - - - +
410B LEU* 1.3 74.8 + - - +
411B TYR* 3.9 9.0 - - + +
449B MET* 5.4 0.4 - - - -
458B VAL* 3.2 32.5 - - + +
460B LEU* 4.0 15.7 - - + -
519B LEU* 6.0 0.2 - - + -
560B LEU* 4.2 22.7 - - + -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU* 3.4 38.8 - - + +
348B ILE* 4.8 8.1 - - + -
395B VAL* 5.5 3.1 - - + -
398B PHE* 4.8 10.3 - - + -
409B LEU* 1.3 77.0 - - - +
411B TYR* 1.3 69.1 + - - +
412B TYR* 4.8 1.1 - - + +
425B MET* 4.3 25.6 - - + -
442B VAL* 4.7 2.7 - - + -
445B ILE* 4.3 20.4 - - + -
449B MET* 5.6 0.6 - - - +
458B VAL 2.8 7.3 + - - +
459B PHE* 3.5 29.6 - - + -
460B LEU* 2.8 27.0 + - - +
461B LEU* 4.6 8.3 - - + -
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Residues in contact with TYR 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU 2.9 8.3 + - - +
347B LEU* 3.3 20.4 - - + -
348B ILE 2.9 25.6 + - - -
365B ASP* 3.5 20.9 - - + +
366B VAL* 4.1 19.5 - - + -
369B LEU* 3.4 29.6 - - + -
409B LEU* 3.9 5.5 - - + +
410B LEU* 1.3 76.7 - - - +
412B TYR* 1.3 61.2 + - - +
413B ALA* 3.5 18.1 - - + +
460B LEU* 3.3 26.2 - - + -
462B ASP* 2.6 42.8 + - + -
511B PHE* 4.2 9.0 - + - -
512B MET* 3.5 24.1 - - + +
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Residues in contact with TYR 412 (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* 3.3 21.5 - - + -
350B ASN* 3.5 19.2 + - - -
353B TYR* 3.0 20.3 + - - -
391B MET* 4.0 9.4 - - + -
410B LEU* 4.8 3.5 - - + +
411B TYR* 1.3 76.0 - - - +
413B ALA* 1.3 65.7 + - - +
414B GLY* 3.7 19.3 - - - -
415B HIS 2.7 29.2 + - - -
425B MET* 3.5 46.0 - - + -
426B VAL 3.0 8.8 + - - -
460B LEU 3.1 6.9 + - - -
461B LEU* 4.5 8.1 - - + -
462B ASP* 2.8 34.2 + - - +
463B MET* 3.7 16.2 - - + -
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Residues in contact with ALA 413 (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 2.9 9.3 + - - +
349B GLY* 3.2 3.2 - - - -
350B ASN 2.9 25.1 + - - +
362B PRO* 3.9 27.2 - - + +
365B ASP* 4.7 2.7 - - - +
366B VAL* 4.8 0.7 - - + -
411B TYR* 3.5 28.7 - - + +
412B TYR* 1.3 77.2 - - - +
414B GLY* 1.3 57.9 + - - +
462B ASP* 3.4 11.2 - - + +
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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