Contacts of the strand formed by residues 366 - 374 (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 TYR 366 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B VAL* 3.5 5.5 - - - +
338B SER* 2.9 47.4 + - - -
340B LEU* 5.7 5.4 - - + -
364B ALA* 3.6 29.8 - - + +
365B GLY* 1.3 74.0 - - - -
367B PHE* 1.3 59.0 + - - +
368B ASN* 4.1 11.1 + - - +
386B ALA* 4.4 20.0 - - + -
387B ILE 3.4 9.9 - - - +
388B GLY* 4.4 2.7 - - - -
389B MET* 3.6 7.0 - - - +
392B ASP 4.9 0.5 + - - -
393B ALA* 3.7 21.0 - - + +
394B PRO* 3.2 31.8 - - + +
397B THR* 5.1 2.5 - - - -
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Residues in contact with PHE 367 (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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367A PHE* 4.5 9.4 - + - -
335B PHE* 4.5 15.3 - + + -
336B SER 3.5 22.4 - - - -
337B VAL* 4.6 0.7 - - - +
366B TYR* 1.3 73.9 - - - +
368B ASN* 1.3 62.6 + - - +
369B VAL* 4.0 25.1 + - + -
386B ALA* 3.6 0.7 - - - -
387B ILE* 2.9 55.6 + - + +
389B MET* 4.1 9.1 - - + +
367C PHE* 4.3 15.5 - + - -
369C VAL* 4.0 27.4 - - + -
385C LEU* 3.7 24.0 - - + -
387C ILE* 3.8 22.0 - - + -
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Residues in contact with ASN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B SER* 3.7 1.9 + - - +
335B PHE* 3.3 6.9 - - - +
336B SER* 2.8 56.5 + - - +
337B VAL 4.8 0.8 - - - +
338B SER* 4.4 7.7 + - - -
366B TYR* 4.1 18.8 + - - +
367B PHE* 1.3 78.7 - - - +
369B VAL* 1.3 62.8 + - - +
384B ASN* 3.3 27.8 - - - +
385B LEU 3.3 3.8 - - - +
386B ALA* 3.4 16.7 - - - +
501B LDA 6.4 0.2 - - - +
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Residues in contact with VAL 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A PHE* 5.4 3.8 - - + -
367A PHE* 3.9 35.0 - - + -
333B MET* 3.9 19.1 - - + -
334B SER* 3.5 9.4 - - - +
335B PHE* 3.8 22.2 - - + -
367B PHE* 4.0 18.1 + - + -
368B ASN* 1.3 77.6 - - - +
370B GLY* 1.3 60.9 + - - +
384B ASN* 2.9 14.9 + - - -
385B LEU* 2.9 33.3 + - + +
387B ILE* 5.5 0.4 - - + -
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Residues in contact with GLY 370 (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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333B MET* 3.4 5.7 - - - +
334B SER* 2.8 43.2 + - - +
369B VAL* 1.3 76.9 - - - +
371B MET* 1.3 65.7 + - - +
383B PRO 3.5 11.7 - - - -
384B ASN* 3.7 8.7 - - - +
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Residues in contact with MET 371 (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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282A LEU* 4.4 22.0 - - + -
323A VAL* 4.4 24.0 - - + -
98B GLU* 5.6 1.4 - - - +
327B LEU* 4.0 20.4 - - + -
331B MET* 4.5 11.2 - - + -
332B SER* 3.2 20.2 - - - +
333B MET* 4.4 10.1 - - + -
334B SER 4.9 0.2 - - - +
370B GLY* 1.3 80.5 - - - +
372B THR* 1.3 64.7 + - - +
373B ILE* 4.6 15.0 - - + -
382B VAL* 3.6 12.0 - - - +
383B PRO* 3.2 39.4 + - + +
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Residues in contact with THR 372 (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* 4.3 3.6 - - - +
94B ASN* 3.3 44.6 + - + +
95B LEU* 4.1 3.8 - - - +
98B GLU* 4.8 5.5 - - - +
330B ARG 4.9 0.7 - - - +
331B MET* 3.2 6.6 - - - -
332B SER* 2.8 60.5 + - - +
371B MET* 1.3 74.7 + - - +
373B ILE* 1.3 63.0 + - - +
380B THR* 4.0 1.2 - - - +
381B ILE 3.8 3.8 - - - -
382B VAL* 3.7 20.8 - - - +
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Residues in contact with ILE 373 (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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277A PHE* 6.3 0.7 - - + -
282A LEU* 4.4 20.2 - - + -
330B ARG* 3.7 3.4 - - + -
331B MET* 4.3 25.6 - - + -
371B MET* 4.6 12.3 - - + -
372B THR* 1.3 82.5 + - - +
374B ALA* 1.3 65.5 + - - +
375B ALA* 3.4 6.6 + - + +
380B THR* 3.4 5.4 - - - +
381B ILE* 2.8 57.4 + - + +
383B PRO* 4.6 20.2 - - + -
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Residues in contact with ALA 374 (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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90B GLN* 3.2 32.6 - - + +
94B ASN* 3.6 21.2 - - - +
330B ARG* 3.0 43.5 + - + +
373B ILE* 1.3 73.8 - - - +
375B ALA* 1.3 61.2 + - - +
376B SER 3.5 1.9 + - - +
377B GLU 5.2 0.2 - - - +
379B LEU 4.0 6.5 - - - +
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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