Contacts of the strand formed by residues 348 - 359 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340G ARG* 2.8 38.3 + - + -
341G ILE 3.7 6.3 - - - +
342G TYR* 4.0 18.9 + - + -
346G ARG 3.8 3.0 + - - -
347G VAL* 1.3 79.0 - - - +
349G ARG* 1.3 58.9 + - - +
350G PHE 3.8 13.0 - - - +
351G ASN* 3.3 19.3 - - + +
387G PHE* 3.6 23.3 - - + -
389G ARG* 4.5 2.4 - - - +
137H ARG* 3.3 28.9 + - - +
141H THR* 5.2 0.8 - - - +
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Residues in contact with ARG 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279G PHE* 5.3 2.0 - - - -
341G ILE* 2.9 11.8 + - + +
343G ASP* 3.6 32.9 + - + +
347G VAL* 3.1 25.4 - - + +
348G GLU* 1.3 74.8 - - - +
350G PHE* 1.3 60.4 + - - +
387G PHE* 4.3 2.5 - - - -
388G TRP* 3.4 6.6 - - - -
389G ARG* 2.6 64.7 + - + +
390G ILE 3.2 19.8 + - - -
391G ASN* 3.8 8.7 - - - +
392G ASP* 5.1 1.7 + - - +
601G C8E 3.4 63.5 + - - +
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Residues in contact with PHE 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339G SER* 4.9 3.8 - - - -
340G ARG* 3.7 1.4 - - - -
341G ILE* 3.1 52.2 + - + -
348G GLU* 3.8 7.4 - - - +
349G ARG* 1.3 79.8 - - - +
351G ASN* 1.3 75.9 + - - +
352G VAL* 3.8 34.8 - - + -
386G THR* 4.2 11.0 - - - -
387G PHE* 3.4 17.3 - - - -
388G TRP* 3.9 17.5 - + + -
601G C8E 3.8 48.0 - - - +
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Residues in contact with ASN 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G THR* 3.7 16.8 - - - +
339G SER 3.6 7.9 + - - -
340G ARG* 3.3 22.6 - - + +
348G GLU* 3.3 17.7 - - - +
350G PHE* 1.3 82.6 - - - +
352G VAL* 1.3 69.5 + - - +
353G SER* 3.9 6.6 + - - -
385G ASP* 4.5 11.3 - - - +
386G THR* 3.2 10.0 + - - -
387G PHE* 2.8 56.1 + - + +
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Residues in contact with VAL 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G LEU 3.8 0.9 - - - +
338G THR* 3.4 1.2 - - - +
339G SER* 3.0 53.0 + - - +
350G PHE* 3.8 23.6 - - + -
351G ASN* 1.3 77.5 - - - +
353G SER* 1.3 75.2 + - - +
354G VAL* 4.8 9.6 - - + -
385G ASP 3.6 9.0 - - - +
386G THR* 4.6 7.0 - - - +
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Residues in contact with SER 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G TYR* 3.6 20.0 - - - -
337G LEU 3.3 4.5 - - - -
338G THR* 3.1 28.4 + - - +
340G ARG* 5.3 0.5 + - - -
351G ASN* 3.9 6.6 + - - -
352G VAL* 1.3 77.6 + - - +
354G VAL* 1.3 66.7 + - - +
384G GLY* 3.1 23.2 - - - -
385G ASP* 3.0 31.3 + - - +
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Residues in contact with VAL 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312G TYR* 3.7 3.8 - - - -
336G GLY* 3.3 1.0 - - - -
337G LEU* 2.8 36.2 + - + +
352G VAL* 4.8 11.7 - - + -
353G SER* 1.3 80.1 - - - +
355G GLY* 1.3 61.9 + - - +
382G TRP* 4.0 28.3 - - + -
383G ALA 3.7 5.8 - - - +
384G GLY* 5.1 3.1 - - - -
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Residues in contact with GLY 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312G TYR* 3.7 5.7 - - - -
315G LEU* 3.5 18.8 - - - -
335G THR 3.1 12.6 - - - -
354G VAL* 1.3 76.4 - - - +
356G GLN* 1.3 64.3 + - - +
382G TRP* 3.4 10.5 - - - -
383G ALA 2.9 31.5 + - - +
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Residues in contact with GLN 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315G LEU* 3.8 4.9 - - - +
333G VAL 5.2 1.1 - - - -
334G SER* 3.3 5.2 - - - -
335G THR* 2.8 54.6 + - - +
355G GLY* 1.3 75.9 - - - +
357G ILE* 1.3 85.3 + - - +
358G TYR* 3.4 13.0 + - - +
379G SER* 2.9 26.7 + - - -
381G VAL 3.1 13.2 - - - +
382G TRP* 3.7 31.5 - - + -
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Residues in contact with ILE 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310G SER* 6.0 2.5 - - - -
314G GLY 5.3 1.6 - - - +
315G LEU* 3.6 42.4 - - + +
332G GLN* 4.1 21.3 - - + +
333G VAL 3.7 2.2 - - - +
334G SER* 3.6 16.2 - - - +
356G GLN* 1.3 82.6 - - - +
358G TYR* 1.3 62.3 + - - +
359G TYR* 3.5 44.9 - - + +
378G GLY 3.5 0.9 - - - +
379G SER* 3.4 1.9 - - - -
380G LEU 3.0 26.7 + - - -
381G VAL* 2.9 22.2 + - + -
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Residues in contact with TYR 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332G GLN* 3.2 5.6 - - - +
333G VAL* 2.9 42.6 + - + +
356G GLN* 3.4 14.3 + - - +
357G ILE* 1.3 71.3 - - - +
359G TYR* 1.3 71.2 + - - +
360G PHE* 3.4 42.3 + + - -
378G GLY* 3.5 9.6 - - - -
379G SER* 3.4 29.2 - - - -
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Residues in contact with TYR 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331G ASN 4.0 2.9 - - - -
332G GLN* 3.1 35.2 + - + -
357G ILE* 3.5 37.6 - - + +
358G TYR* 1.3 77.5 - - - +
360G PHE* 1.3 61.8 + - - +
361G SER 3.7 15.9 - - - +
363G SER* 3.8 20.2 - - - -
377G THR* 3.7 8.7 + - + -
378G GLY* 2.9 48.2 + - - +
380G LEU* 3.9 26.2 - - + -
381G VAL* 3.9 13.8 - - + +
405G ARG* 3.9 16.1 + - - -
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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