Contacts of the strand formed by residues 331 - 342 (chain B) in PDB entry 5O65
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 MSE 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* 3.5 52.5 - - + -
280A ALA* 4.2 11.2 - - - -
282A LEU* 3.9 14.6 - - + -
91B SER* 3.5 10.8 - - - -
327B LEU* 2.8 30.7 + - + -
328B ASN* 2.7 29.9 + - - +
330B ARG* 1.3 89.0 - - + +
332B SER* 1.3 61.0 + - - +
371B MSE 4.0 23.3 - - + -
372B THR 3.2 9.0 - - - +
373B ILE* 3.9 21.8 - - + -
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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 6.3 - - - -
95B LEU* 4.0 30.8 - - - +
324B ALA* 5.8 0.2 - - - +
325B PHE 3.1 14.6 - - - -
326B ALA* 4.3 1.8 - - - -
327B LEU* 4.2 4.0 - - - +
331B MSE 1.3 75.8 - - - +
333B MSE 1.3 63.2 + - - +
334B SER* 5.9 0.9 - - - -
371B MSE 3.3 14.2 - - - +
372B THR* 2.9 52.1 + - - +
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Residues in contact with MSE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A VAL* 3.6 26.0 - - + -
325A PHE* 3.9 29.4 - - - -
335A PHE* 3.9 14.8 - - + -
324B ALA* 3.2 3.3 - - - +
325B PHE* 2.8 39.4 + - + +
327B LEU* 4.1 18.4 - - + -
332B SER* 1.3 78.0 - - - +
334B SER* 1.3 64.0 + - - +
335B PHE* 3.8 27.8 - - + -
369B VAL* 3.7 25.8 - - + -
370B GLY 3.4 10.3 - - - +
371B MSE 4.2 8.1 - - + +
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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* 5.9 7.1 - - - +
283B PHE* 3.5 24.1 - - - -
323B VAL 3.6 4.0 - - - -
324B ALA* 4.0 10.5 - - - +
332B SER* 5.9 1.1 - - - -
333B MSE 1.3 76.0 - - - +
335B PHE* 1.3 68.6 + - - +
336B SER* 4.3 3.2 + - - -
368B ASN 4.4 0.4 - - - -
369B VAL* 3.4 8.3 - - - +
370B GLY* 2.8 42.7 + - - +
371B MSE 5.7 0.2 - - - -
384B ASN* 5.9 1.7 + - - -
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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* 4.1 18.2 - + - -
367A PHE* 5.9 0.7 - + - -
322B GLY* 3.2 1.6 - - - -
323B VAL* 2.8 43.5 + - + +
325B PHE* 4.4 19.7 - + - -
333B MSE 3.8 34.3 - - + -
334B SER* 1.3 76.8 + - - +
336B SER* 1.3 61.3 + - - +
367B PHE* 4.3 11.4 - + + -
368B ASN 3.4 5.2 - - - +
369B VAL* 4.2 27.6 - - + -
333C MSE 4.0 23.1 - - + -
335C PHE* 3.8 36.1 - + - -
369C VAL* 5.2 0.4 - - + -
508C C8E 3.9 11.0 - - + +
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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* 3.8 17.6 - - - -
321B VAL 3.4 13.9 - - - -
322B GLY* 3.8 5.8 - - - -
334B SER* 4.3 3.0 + - - -
335B PHE* 1.3 76.3 - - - +
337B VAL* 1.3 62.6 + - - +
367B PHE* 3.4 11.8 - - - -
368B ASN* 2.8 54.7 + - - +
508C C8E 4.4 3.6 - - - +
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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 3.9 - - - -
321B VAL* 2.9 54.5 + - + +
336B SER* 1.3 78.2 - - - +
338B SER* 1.3 65.3 + - - +
366B TYR 3.3 13.7 - - - +
368B ASN* 4.4 2.2 - - - +
389B MSE 3.8 7.9 - - + -
385C LEU* 3.8 27.1 - - + -
398C PHE* 3.4 39.7 - - + -
508C C8E 4.8 9.2 - - + -
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Residues in contact with SER 338 (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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319B PHE* 3.3 13.7 - - - -
320B GLY* 4.0 3.1 - - - -
337B VAL* 1.3 82.6 - - - +
339B ASP* 1.3 62.1 + - - +
364B ALA 4.7 0.2 - - - -
365B GLY* 3.4 1.9 - - - -
366B TYR* 2.8 56.4 + - - +
368B ASN* 4.1 8.4 + - - +
389B MSE 4.2 0.9 - - - +
502B LDA 3.6 27.8 - - - +
398C PHE* 5.0 1.3 - - - -
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Residues in contact with ASP 339 (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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317B PHE 3.9 0.2 - - - +
318B GLN* 3.5 2.9 - - - -
319B PHE* 2.9 60.3 + - + -
338B SER* 1.3 75.1 - - - +
340B LEU* 1.3 59.3 + - - +
341B ILE* 3.9 12.6 - - - +
363B ASN* 2.5 43.0 + - - +
364B ALA 3.2 11.0 - - - +
365B GLY* 3.4 6.8 - - - -
502B LDA 5.2 2.5 - - - -
116C TYR* 4.8 3.5 - - - -
396C PHE* 3.6 16.2 - - - -
398C PHE* 4.3 9.3 - - + -
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Residues in contact with LEU 340 (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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316B SER* 4.0 16.8 - - - +
317B PHE 3.4 2.9 - - - -
318B GLN* 3.5 35.7 - - + +
339B ASP* 1.3 73.8 - - - +
341B ILE* 1.3 64.6 + - - +
342B GLN* 4.1 19.7 - - + +
362B ALA* 5.2 3.1 - - + +
363B ASN* 3.3 4.7 - - - -
364B ALA* 2.8 51.0 + - + +
366B TYR* 5.4 0.7 - - + -
502B LDA 4.3 21.7 - - + +
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Residues in contact with ILE 341 (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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315B ASP 4.1 0.2 - - - +
316B SER* 3.1 2.1 - - - -
317B PHE* 2.8 54.0 + - + +
319B PHE* 4.3 17.7 - - + -
339B ASP* 3.9 13.5 - - - +
340B LEU* 1.3 78.3 - - - +
342B GLN* 1.3 64.2 + - - +
343B ARG* 4.1 20.6 + - - +
362B ALA 3.5 7.0 - - - +
363B ASN* 3.7 20.0 - - + +
116C TYR* 5.7 4.7 - - + +
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Residues in contact with GLN 342 (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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291B ASN* 4.5 5.7 - - - +
313B LEU* 5.0 5.3 - - - +
314B GLY 3.0 27.9 + - - +
315B ASP 3.5 3.6 - - - +
316B SER* 3.9 8.4 - - - -
340B LEU* 4.1 16.4 - - + +
341B ILE* 1.3 78.0 - - - +
343B ARG* 1.3 76.7 + - - +
345B SER* 4.9 3.3 + - - -
360B SER 4.7 8.4 - - - +
361B ASP* 3.4 4.5 - - - +
362B ALA* 2.8 45.5 + - + +
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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