Contacts of the strand formed by residues 348 - 359 (chain C) in PDB entry 5IXM
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 GLU 348 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340C ARG* 2.7 43.4 + - + +
341C ILE 3.6 7.0 - - - +
342C TYR* 3.8 22.9 + - + -
346C ARG 3.9 0.4 + - - -
347C VAL* 1.3 78.6 - - - +
349C ARG* 1.3 60.1 + - - +
350C PHE 3.9 13.7 - - - +
351C ASN* 3.6 17.0 - - - +
387C PHE* 3.8 22.0 - - + -
389C ARG* 4.5 3.6 - - - +
137D ARG* 3.9 15.6 + - - -
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Residues in contact with ARG 349 (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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279C PHE* 4.7 2.7 - - + -
341C ILE* 2.9 12.7 + - + +
343C ASP* 3.7 33.1 + - + +
347C VAL* 3.2 22.9 - - + +
348C GLU* 1.3 75.0 - - - +
350C PHE* 1.3 58.8 + - - +
387C PHE* 4.3 3.1 - - - -
388C TRP* 3.5 5.8 - - - -
389C ARG* 2.6 67.4 + - + +
390C ILE 3.3 6.7 + - - -
391C ASN* 3.7 7.9 - - - +
392C ASP* 5.8 1.8 - - - -
602C C8E 3.2 81.1 + - - -
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Residues in contact with PHE 350 (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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601A C8E 5.7 6.7 - - + -
339C SER* 4.9 4.0 - - - -
340C ARG* 3.7 2.3 - - - -
341C ILE* 3.2 51.1 + - + -
348C GLU* 3.9 7.0 - - - +
349C ARG* 1.3 80.2 - - - +
351C ASN* 1.3 79.5 + - - +
352C VAL* 3.8 31.9 - - + -
386C THR* 3.9 15.5 - - - -
387C PHE* 3.4 13.7 - - - -
388C TRP* 3.8 23.1 - + + -
602C C8E 3.8 49.8 - - + +
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Residues in contact with ASN 351 (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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338C THR* 3.8 16.4 - - - +
339C SER 3.5 8.5 + - - +
340C ARG* 4.0 10.8 - - + +
348C GLU* 3.6 17.2 + - - +
350C PHE* 1.3 83.3 - - - +
352C VAL* 1.3 69.8 + - - +
353C SER* 3.6 17.7 + - - -
385C ASP* 4.4 10.4 - - - +
386C THR* 2.9 12.8 + - - -
387C PHE* 2.7 59.4 + - + +
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Residues in contact with VAL 352 (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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601A C8E 5.8 4.0 - - - -
337C LEU 3.8 0.5 - - - +
338C THR* 3.5 0.7 - - - -
339C SER* 3.0 46.5 + - - -
350C PHE* 3.8 26.2 - - + -
351C ASN* 1.3 78.1 + - - +
353C SER* 1.3 72.8 + - - +
354C VAL* 4.6 10.5 - - + -
385C ASP 3.6 9.2 - - - +
386C THR* 4.3 7.4 - - - +
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Residues in contact with SER 353 (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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601A C8E 4.9 0.3 - - - +
312C TYR* 3.7 18.9 - - - -
337C LEU 3.3 5.2 - - - -
338C THR* 3.1 30.0 + - - +
351C ASN* 3.6 7.6 + - - -
352C VAL* 1.3 77.4 + - - +
354C VAL* 1.3 65.6 + - - +
384C GLY* 3.1 4.6 - - - -
385C ASP* 2.8 51.6 + - - +
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Residues in contact with VAL 354 (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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601A C8E 4.1 29.2 - - - -
312C TYR* 3.5 4.9 - - - -
336C GLY* 3.4 0.7 - - - -
337C LEU* 2.9 35.8 + - + +
352C VAL* 4.6 13.2 - - + -
353C SER* 1.3 78.8 - - - +
355C GLY* 1.3 61.9 + - - +
382C TRP* 4.3 26.2 - - + -
383C ALA 3.6 7.0 - - - +
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Residues in contact with GLY 355 (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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312C TYR* 3.5 7.1 - - - -
315C LEU* 3.5 18.4 - - - -
335C THR 3.1 12.1 - - - -
354C VAL* 1.3 75.8 - - - +
356C GLN* 1.3 63.4 + - - +
382C TRP* 3.5 9.6 - - - -
383C ALA 2.9 31.8 + - - +
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Residues in contact with GLN 356 (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 LEU* 3.8 4.7 - - - +
333C VAL 3.5 16.8 + - - -
334C SER* 3.3 5.0 - - - -
335C THR* 2.8 59.9 + - - +
355C GLY* 1.3 75.9 - - - +
357C ILE* 1.3 71.9 + - - +
358C TYR* 3.5 9.7 + - - +
379C SER* 2.8 32.2 + - - -
381C VAL 3.2 12.1 - - - +
382C TRP* 3.7 30.5 - - + -
607C C8E 4.2 18.0 - - + +
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Residues in contact with ILE 357 (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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310C SER* 6.1 2.0 - - - +
314C GLY 5.3 1.3 - - - +
315C LEU* 3.6 41.7 - - + +
332C GLN* 4.1 21.3 - - + +
333C VAL 3.6 3.8 - - - +
334C SER* 3.5 18.2 - - - +
356C GLN* 1.3 81.3 - - - +
358C TYR* 1.3 61.3 + - - +
359C TYR* 3.6 39.9 - - + +
378C GLY 3.5 0.9 - - - +
379C SER* 3.4 1.4 - - - -
380C LEU 3.0 26.2 + - - -
381C VAL* 2.8 23.0 + - + -
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Residues in contact with TYR 358 (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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332C GLN* 3.2 5.1 - - - +
333C VAL* 2.8 44.4 + - + +
356C GLN* 3.5 5.4 - - - +
357C ILE* 1.3 71.7 - - - +
359C TYR* 1.3 72.4 + - - +
360C PHE* 3.5 40.5 + + - -
378C GLY* 3.4 21.5 + - - -
379C SER* 3.3 22.0 - - - +
607C C8E 3.7 47.6 - - + +
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Residues in contact with TYR 359 (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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331C ASN 4.0 2.7 - - - -
332C GLN* 3.3 32.7 + - + -
357C ILE* 3.6 33.1 - - + +
358C TYR* 1.3 80.0 - - - +
360C PHE* 1.3 61.0 + - - +
361C SER 3.3 17.3 - - - +
362C ARG* 5.7 0.2 - - - -
363C SER* 3.4 22.9 - - - -
376C ALA 5.1 0.7 - - - +
377C THR* 3.4 10.2 - - - -
378C GLY 2.9 41.8 + - - +
380C LEU* 3.9 26.9 - - + -
381C VAL* 3.8 14.0 - - + +
405C ARG* 3.8 21.1 + - - -
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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