Contacts of the strand formed by residues 331 - 342 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277B PHE* 3.3 54.1 - - + -
280B ALA* 4.0 18.8 - - - -
282B LEU* 3.8 14.4 - - + -
91C SER* 3.5 11.3 - - - -
327C LEU* 2.8 30.1 + - + -
328C ASN* 2.7 26.2 + - - +
330C ARG* 1.3 88.5 - - + +
332C SER* 1.3 61.6 + - - +
371C MSE 4.0 18.4 - - + -
372C THR 3.2 8.5 - - - +
373C ILE* 3.9 22.2 - - + -
508C C8E 4.4 3.8 - - - +
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Residues in contact with SER 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C SER 4.1 4.9 - - - -
95C LEU* 3.6 29.4 - - - +
325C PHE 3.1 14.6 - - - -
326C ALA* 4.3 1.1 - - - -
327C LEU* 4.2 4.5 - - - +
331C MSE 1.3 73.9 - - - +
333C MSE 1.3 62.8 + - - +
334C SER* 5.9 0.9 - - - -
371C MSE 3.3 14.9 - - - +
372C THR* 2.4 59.6 + - - +
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Residues in contact with MSE 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B VAL* 4.1 20.0 - - + -
325B PHE* 3.8 30.3 - - - -
335B PHE* 4.0 20.6 - - + -
324C ALA* 3.3 3.3 - - - +
325C PHE* 2.8 39.0 + - + +
327C LEU* 4.1 18.4 - - + +
332C SER* 1.3 77.3 - - - +
334C SER* 1.3 64.4 + - - +
335C PHE* 3.7 28.5 - - + -
369C VAL* 3.7 27.1 - - + -
370C GLY 3.4 11.2 - - - +
371C MSE 4.2 5.8 - - + +
508C C8E 4.8 1.1 - - + -
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Residues in contact with SER 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C GLU* 6.3 3.8 - - - -
283C PHE* 3.6 24.1 - - - -
323C VAL 3.6 4.9 - - - -
324C ALA* 4.1 9.6 - - - -
332C SER* 5.9 1.3 - - - -
333C MSE 1.3 76.1 - - - +
335C PHE* 1.3 68.0 + - - +
336C SER* 4.3 3.7 + - - -
368C ASN 4.4 0.4 - - - -
369C VAL* 3.4 7.8 - - - +
370C GLY* 2.8 42.1 + - - +
371C MSE 5.8 0.2 - - - -
384C ASN* 6.0 0.2 - - - -
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Residues in contact with PHE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A MSE 3.9 23.8 - - + -
335A PHE* 3.9 19.3 - + - -
369A VAL* 5.2 0.7 - - + -
335B PHE* 3.8 33.7 - + - -
367B PHE* 5.8 0.2 - + - -
283C PHE* 4.3 0.2 - - - -
322C GLY* 3.2 1.6 - - - -
323C VAL* 2.8 42.8 + - + +
325C PHE* 4.3 20.0 - + - -
333C MSE 3.7 31.6 - - + -
334C SER* 1.3 77.0 + - - +
336C SER* 1.3 60.5 + - - +
367C PHE* 4.4 9.0 - + + -
368C ASN 3.4 4.5 - - - +
369C VAL* 4.0 28.0 - - + -
507C C8E 4.1 12.2 - - + +
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Residues in contact with SER 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 3.9 18.0 - - - -
321C VAL 3.4 13.7 - - - -
322C GLY* 3.8 6.1 - - - -
334C SER* 4.7 3.5 + - - -
335C PHE* 1.3 76.7 - - - +
337C VAL* 1.3 64.0 + - - +
367C PHE* 3.3 8.7 - - - -
368C ASN* 2.8 56.7 + - - +
507C C8E 4.0 7.3 - - - +
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Residues in contact with VAL 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A LEU* 3.9 27.1 - - + -
396A PHE* 6.1 0.4 - - + -
398A PHE* 4.2 19.3 - - + -
320C GLY* 3.2 2.6 - - - -
321C VAL* 2.9 57.0 + - + +
336C SER* 1.3 76.8 - - - +
338C SER* 1.3 69.3 + - - +
339C ASP* 6.2 0.4 - - + -
366C TYR 3.3 13.9 - - - +
368C ASN* 4.4 2.5 - - - +
389C MSE 3.8 20.0 - - + -
507C C8E 4.5 7.2 - - + -
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Residues in contact with SER 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C PHE* 3.3 13.2 - - - -
320C GLY* 4.0 4.0 - - - -
337C VAL* 1.3 83.2 - - - +
339C ASP* 1.3 62.5 + - - +
364C ALA 4.7 0.4 - - - -
365C GLY* 3.4 2.6 - - - -
366C TYR* 2.8 54.9 + - - +
368C ASN* 4.1 9.0 + - - -
389C MSE 4.2 0.5 - - - +
503C LDA 4.0 26.6 - - - +
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Residues in contact with ASP 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 5.4 2.4 - - - -
396A PHE* 3.9 18.8 - - + -
317C PHE 3.9 0.3 - - - +
318C GLN* 3.5 2.6 - - - -
319C PHE* 2.9 58.5 + - + -
337C VAL* 6.2 0.2 - - + -
338C SER* 1.3 76.4 - - - +
340C LEU* 1.3 60.5 + - - +
341C ILE* 3.8 11.9 - - - +
363C ASN* 2.5 42.5 + - - +
364C ALA 3.2 11.3 - - - +
365C GLY* 3.4 7.3 - - - -
389C MSE 5.9 0.7 - - + -
503C LDA 5.0 2.9 - - - -
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Residues in contact with LEU 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316C SER* 4.0 6.1 - - - -
317C PHE 3.4 2.7 - - - -
318C GLN* 3.5 35.7 - - + +
339C ASP* 1.3 74.0 - - - +
341C ILE* 1.3 76.2 + - - +
342C GLN* 4.0 20.2 - - + +
362C ALA* 5.2 2.9 - - + +
363C ASN* 3.3 5.7 - - - -
364C ALA* 2.8 51.1 + - + +
503C LDA 4.3 20.8 - - + +
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Residues in contact with ILE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C ASP 4.1 0.2 - - - +
316C SER* 3.1 2.4 - - - -
317C PHE* 2.8 52.6 + - + +
319C PHE* 4.3 18.4 - - + -
339C ASP* 3.8 13.7 - - - +
340C LEU* 1.3 78.5 - - - +
342C GLN* 1.3 65.0 + - - +
343C ARG* 4.2 4.5 + - + +
362C ALA 3.5 7.0 - - - +
363C ASN* 3.7 20.4 - - + +
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Residues in contact with GLN 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C ASN* 4.4 6.1 - - - +
313C LEU* 5.1 5.7 - - - +
314C GLY 2.9 28.1 + - - +
315C ASP 3.5 3.6 - - - +
316C SER* 3.9 7.6 - - - -
340C LEU* 4.0 16.8 - - + +
341C ILE* 1.3 78.1 - - - +
343C ARG* 1.3 75.6 + - - +
345C SER* 5.0 3.0 + - - -
360C SER 4.7 9.0 - - - +
361C ASP* 3.4 5.0 - - - +
362C ALA* 2.8 44.2 + - + +
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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