Contacts of the strand formed by residues 331 - 337 (chain B) in PDB entry 5O67
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 MET 331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A PHE* 3.2 57.7 - - + -
280A ALA* 4.2 15.3 - - - -
282A LEU* 3.9 21.3 - - + -
91B SER* 3.6 6.7 - - - -
327B LEU* 3.1 32.8 + - + -
328B ASN* 2.6 32.6 + - - +
330B ARG* 1.3 83.4 - - + +
332B SER* 1.3 61.2 + - - +
371B MET* 4.5 6.3 - - + -
372B THR* 3.2 8.7 - - - +
373B ILE* 4.3 20.2 - - + -
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Residues in contact with SER 332 (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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91B SER* 4.2 4.5 - - - -
95B LEU* 4.0 24.6 - - - +
324B ALA* 5.8 0.7 - - - +
325B PHE 3.2 15.5 - - - -
326B ALA* 4.5 1.3 - - - -
327B LEU* 4.0 4.7 - - - +
331B MET* 1.3 74.7 - - - +
333B MET* 1.3 63.4 + - - +
334B SER* 5.9 0.7 - - - -
371B MET* 3.2 13.3 - - - +
372B THR* 2.8 57.0 + - - +
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Residues in contact with MET 333 (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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323A VAL* 3.7 25.1 - - + -
325A PHE* 3.9 26.7 - - - -
335A PHE* 3.9 15.3 - - + -
324B ALA* 3.4 2.9 - - - +
325B PHE* 3.0 39.2 + - + -
327B LEU* 3.9 19.3 - - + +
332B SER* 1.3 76.7 - - - +
334B SER* 1.3 65.3 + - - +
335B PHE* 3.8 30.1 - - + -
369B VAL* 3.9 17.7 - - + -
370B GLY 3.4 11.0 - - - +
371B MET* 4.3 8.5 - - + +
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Residues in contact with SER 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLU* 6.1 1.2 - - - +
283B PHE* 4.7 11.3 - - - -
323B VAL 3.5 12.1 - - - -
324B ALA* 3.7 11.9 - - - -
332B SER* 5.9 0.9 - - - -
333B MET* 1.3 77.1 - - - +
335B PHE* 1.3 67.9 + - - +
336B SER* 5.5 1.2 - - - -
368B ASN* 4.3 1.6 + - - +
369B VAL* 3.5 9.9 - - - +
370B GLY* 2.8 43.1 + - - +
384B ASN* 5.4 2.3 + - - -
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Residues in contact with PHE 335 (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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335A PHE* 4.0 32.8 - + - -
367A PHE* 6.1 0.4 - + - -
283B PHE* 4.2 0.5 - - - -
322B GLY* 3.2 1.9 - - - -
323B VAL* 2.9 35.7 + - + +
325B PHE* 4.2 23.6 - + - -
333B MET* 3.8 30.5 - - + -
334B SER* 1.3 78.6 - - - +
336B SER* 1.3 61.1 + - - +
367B PHE* 4.5 21.1 - + + -
368B ASN 3.3 5.6 - - - +
369B VAL* 3.8 23.6 - - + -
333C MET* 4.2 24.0 - - + -
335C PHE* 4.0 20.2 - + - -
369C VAL* 5.3 3.8 - - + -
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B PHE* 4.0 15.0 - - - -
321B VAL 3.4 14.1 - - - -
322B GLY* 3.8 5.4 - - - -
334B SER* 5.5 1.6 - - - -
335B PHE* 1.3 77.1 - - - +
337B VAL* 1.3 63.1 + - - +
367B PHE* 3.5 11.0 - - - -
368B ASN* 2.8 55.9 + - - +
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Residues in contact with VAL 337 (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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320B GLY* 3.1 20.8 - - - -
321B VAL* 3.0 33.3 + - + +
336B SER* 1.3 78.2 - - - +
338B SER* 1.3 66.0 + - - +
366B TYR 3.5 12.1 - - - +
367B PHE* 4.8 0.4 - - - -
368B ASN* 4.8 1.1 - - - +
389B MET* 4.0 9.6 - - + -
385C LEU* 3.6 33.7 - - + -
398C PHE* 4.0 31.9 - - + -
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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