Contacts of the strand formed by residues 348 - 359 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A ARG* 2.8 40.4 + - + +
341A ILE 3.7 6.1 - - - +
342A TYR* 3.8 23.6 + - + -
346A ARG 3.9 1.2 + - - -
347A VAL* 1.3 78.0 - - - +
349A ARG* 1.3 59.7 + - - +
350A PHE 3.9 13.5 - - - +
351A ASN* 3.3 20.1 - - + +
387A PHE* 3.8 19.4 - - + -
389A ARG* 4.5 4.3 + - - +
137B ARG* 4.2 14.7 + - - -
141B THR* 5.3 2.2 - - - +
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Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A PHE* 5.3 0.8 - - - -
341A ILE* 2.9 10.7 + - + +
343A ASP* 3.6 35.3 + - + +
347A VAL* 3.2 24.5 - - + +
348A GLU* 1.3 75.3 - - - +
350A PHE* 1.3 59.2 + - - +
387A PHE* 4.5 2.9 - - - -
388A TRP* 3.4 5.7 - - - -
389A ARG* 2.6 65.7 + - + +
390A ILE 3.2 10.5 + - - -
391A ASN* 3.6 5.9 - - - +
392A ASP* 5.8 0.4 + - - -
602A C8E 3.1 85.5 + - - +
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Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A SER* 4.9 2.7 - - - -
340A ARG* 3.6 1.2 - - - -
341A ILE* 3.0 55.0 + - + +
348A GLU* 3.9 6.0 - - - +
349A ARG* 1.3 79.3 - - - +
351A ASN* 1.3 74.3 + - - +
352A VAL* 3.7 36.6 - - + -
386A THR* 4.0 11.9 - - - -
387A PHE* 3.4 18.4 - - - -
388A TRP* 3.9 21.5 - + + -
602A C8E 3.7 46.0 - - - +
604A C8E 5.9 6.1 - - + -
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Residues in contact with ASN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A THR* 3.8 18.2 - - - +
339A SER 3.5 8.9 + - - +
340A ARG* 3.6 20.5 - - + +
348A GLU* 3.3 17.3 - - - +
350A PHE* 1.3 81.1 - - - +
352A VAL* 1.3 69.8 + - - +
353A SER* 3.8 5.9 + - - -
385A ASP* 4.0 14.7 - - - +
386A THR* 3.3 4.9 + - - -
387A PHE* 2.8 58.2 + - + +
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A LEU 3.8 1.1 - - - +
338A THR* 3.4 1.0 - - - +
339A SER* 2.9 49.2 + - - +
350A PHE* 3.7 26.2 - - + -
351A ASN* 1.3 76.8 - - - +
353A SER* 1.3 74.1 + - - +
354A VAL* 4.7 9.9 - - + -
385A ASP 3.6 9.2 - - - +
386A THR* 4.5 7.6 - - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TYR* 3.7 17.3 - - - -
337A LEU 3.3 4.3 - - - -
338A THR* 3.2 29.9 + - - +
351A ASN* 3.8 6.6 + - - -
352A VAL* 1.3 77.5 + - - +
354A VAL* 1.3 65.9 + - - +
384A GLY* 3.1 4.2 - - - -
385A ASP* 2.9 54.9 + - - +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TYR* 3.6 4.0 - - - -
336A GLY* 3.4 0.7 - - - -
337A LEU* 2.8 40.3 + - + +
352A VAL* 4.7 12.3 - - + -
353A SER* 1.3 78.8 - - - +
355A GLY* 1.3 61.2 + - - +
382A TRP* 4.2 26.9 - - + -
383A ALA 3.7 7.0 - - - +
384A GLY* 4.8 4.3 - - - -
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TYR* 3.5 6.3 - - - -
315A LEU* 3.5 19.3 - - - -
335A THR 3.2 11.4 - - - -
336A GLY* 3.8 0.2 - - - -
354A VAL* 1.3 75.5 - - - +
356A GLN* 1.3 63.1 + - - +
382A TRP* 3.5 10.1 - - - -
383A ALA 2.8 31.5 + - - +
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Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU* 3.8 4.4 - - - +
333A VAL 4.4 1.4 - - - +
334A SER* 3.3 4.5 - - - -
335A THR* 2.7 65.9 + - - +
355A GLY* 1.3 76.8 - - - +
357A ILE* 1.3 69.5 + - - +
358A TYR* 3.3 29.2 + - - +
379A SER* 3.0 39.4 + - - +
381A VAL 3.2 8.1 - - - +
382A TRP* 3.6 30.7 - - + -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLY 5.3 1.1 - - - +
315A LEU* 3.7 42.2 - - + +
332A GLN* 4.2 22.9 - - + +
333A VAL 3.6 2.2 - - - +
334A SER* 3.4 20.2 - - - +
356A GLN* 1.3 80.2 - - - +
358A TYR* 1.3 61.4 + - - +
359A TYR* 3.6 32.7 - - + +
378A GLY 3.6 0.9 - - - +
379A SER* 3.4 1.6 - - - -
380A LEU 3.0 26.2 + - - -
381A VAL* 2.8 28.9 + - + -
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A GLN* 3.3 5.1 - - - +
333A VAL* 2.9 46.5 + - + +
356A GLN* 3.3 15.5 - - - +
357A ILE* 1.3 71.3 - - - +
359A TYR* 1.3 71.1 + - - +
360A PHE* 3.5 39.2 - + - -
378A GLY* 3.5 20.8 - - - -
379A SER* 3.4 20.4 - - - -
603A C8E 3.5 43.5 - - + +
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Residues in contact with TYR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ASN 4.1 3.1 - - - -
332A GLN* 3.2 32.8 + - + -
357A ILE* 3.6 33.3 - - + +
358A TYR* 1.3 79.1 - - - +
360A PHE* 1.3 58.5 + - - +
361A SER 3.4 17.0 - - - +
362A ARG* 6.0 0.2 - - - -
363A SER* 3.4 22.7 - - - -
376A ALA 4.7 1.3 - - - +
377A THR* 3.4 11.2 - - - -
378A GLY* 2.9 46.8 + - - +
380A LEU* 3.9 26.9 - - + -
381A VAL* 4.0 13.2 - - + +
405A ARG* 3.9 21.4 + - - -
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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