Contacts of the helix formed by residues 340 - 357 (chain A) in PDB entry 4XJO
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 ASP 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLN* 1.3 72.0 - - - +
341A TRP* 1.3 60.8 + - - +
342A ARG* 3.7 8.0 + - - +
343A THR* 2.7 37.0 + - - +
344A ARG* 3.2 18.1 + - - +
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Residues in contact with TRP 341 (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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261A GLY* 4.4 12.6 - - - -
264A GLY 3.7 19.7 - - - -
265A ALA* 3.7 6.5 - - - -
266A LEU* 3.2 55.6 - - + +
336A LEU* 3.4 51.4 - - + +
337A LEU* 4.4 13.4 + - + +
339A GLN* 2.9 19.3 + - + -
340A ASP* 1.3 72.3 - - - +
342A ARG* 1.3 108.9 + - + +
344A ARG* 3.4 7.9 - - - +
345A ILE* 2.9 39.9 + - + +
412A TYR* 5.8 0.4 - - + -
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Residues in contact with ARG 342 (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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264A GLY 4.1 22.3 + - - +
265A ALA* 4.7 6.5 - - - +
340A ASP* 3.2 7.2 + - - +
341A TRP* 1.3 119.1 - - + +
343A THR* 1.3 52.9 + - - +
345A ILE* 3.5 2.5 + - - +
346A THR* 2.7 42.7 + - - +
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Residues in contact with THR 343 (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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340A ASP* 2.7 35.1 + - - +
341A TRP 3.3 0.2 - - - -
342A ARG* 1.3 74.9 - - - +
344A ARG* 1.3 59.9 + - - +
346A THR* 3.3 6.9 + - - -
347A GLU* 2.9 51.7 + - + +
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Residues in contact with ARG 344 (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 GLN* 4.4 15.7 - - - +
340A ASP 3.2 12.7 + - - +
341A TRP* 3.2 13.2 + - - +
343A THR* 1.3 77.3 - - - +
345A ILE* 1.3 57.9 + - + +
347A GLU* 3.0 40.6 + - - +
348A LEU* 2.9 44.0 + - + +
412A TYR* 2.8 49.8 + - + +
413A ILE* 5.4 0.7 - - - +
414A CYS 3.0 20.6 + - - -
416A PRO* 4.6 9.1 - - - +
503A EDO 3.3 34.6 + - - -
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Residues in contact with ILE 345 (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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261A GLY* 3.5 16.4 - - - +
264A GLY* 3.6 29.2 - - - -
341A TRP* 2.9 30.6 + - + +
342A ARG* 4.1 4.0 - - - +
344A ARG* 1.3 74.2 - - + +
346A THR* 1.3 56.2 + - - +
348A LEU* 3.2 5.7 + - + +
349A ALA* 2.8 32.4 + - - +
372A GLY* 3.8 3.1 - - - -
373A ALA* 3.7 24.2 - - + +
412A TYR* 3.5 52.0 - - + -
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Residues in contact with THR 346 (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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264A GLY 5.7 0.5 + - - -
342A ARG* 2.7 29.9 + - - +
343A THR* 3.6 8.9 - - - -
345A ILE* 1.3 76.3 - - - +
347A GLU* 1.3 57.3 + - + +
349A ALA* 3.4 6.7 + - - +
350A ALA* 3.0 29.5 + - + +
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Residues in contact with GLU 347 (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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343A THR* 2.9 40.2 + - + +
344A ARG* 3.0 32.6 + - - +
346A THR* 1.3 74.9 - - + +
348A LEU* 1.3 59.4 + - - +
350A ALA* 3.4 7.8 + - - +
351A GLY* 3.0 24.8 + - - -
416A PRO* 5.7 3.0 - - + +
503A EDO 5.0 3.3 - - - -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG* 2.9 39.0 + - - +
345A ILE* 3.5 12.3 - - + +
347A GLU* 1.3 75.7 - - - +
349A ALA* 1.3 57.4 + - - +
351A GLY* 3.2 2.6 + - - -
352A LEU* 2.9 34.9 + - + +
373A ALA* 3.6 28.5 - - + -
410A PRO* 4.2 6.7 - - + +
411A PRO 3.8 18.2 - - - +
412A TYR* 4.0 14.4 - - + +
414A CYS* 3.7 8.1 - - + +
419A ILE* 3.4 39.0 - - + +
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Residues in contact with ALA 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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345A ILE 2.8 18.8 + - - +
346A THR* 3.7 7.2 - - + +
348A LEU* 1.3 71.8 - - - +
350A ALA* 1.3 57.2 + - - +
352A LEU* 3.2 4.0 + - - +
353A THR* 2.8 34.3 + - - -
370A VAL* 3.7 9.2 - - + +
372A GLY* 3.2 36.5 + - - +
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Residues in contact with ALA 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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346A THR* 3.0 18.4 + - + +
347A GLU* 3.6 7.9 - - - +
349A ALA* 1.3 75.8 - - - +
351A GLY* 1.3 58.4 + - - +
353A THR* 3.4 6.1 + - - -
354A ALA* 2.9 31.4 + - - +
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Residues in contact with GLY 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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347A GLU 3.0 13.6 + - - -
348A LEU 3.2 4.4 + - - -
350A ALA* 1.3 73.8 - - - +
352A LEU* 1.3 59.0 + - - +
354A ALA* 3.5 4.8 + - - +
355A GLY* 2.9 26.7 + - - -
416A PRO* 6.1 0.9 - - - -
419A ILE* 3.6 20.3 - - - +
420A THR* 5.2 5.4 + - - -
423A THR* 4.2 0.9 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 2.9 19.5 + - + +
349A ALA 3.6 5.8 - - - +
351A GLY* 1.3 76.0 - - - +
353A THR* 1.3 62.3 + - - +
355A GLY 3.4 0.3 + - - -
356A LEU* 2.9 34.1 + - + +
370A VAL* 4.0 13.5 - - + -
372A GLY 3.8 11.2 - - - +
373A ALA* 3.8 8.7 - - + -
374A ILE 3.7 35.4 - - - +
375A GLY* 3.9 8.5 - - - +
408A ALA* 5.1 7.0 - - + -
410A PRO* 4.3 21.8 - - + -
419A ILE* 4.2 11.2 - - + +
422A ILE* 5.2 2.7 - - + -
423A THR* 3.8 20.0 - - + -
426A MET* 5.3 0.7 - - - -
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Residues in contact with THR 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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349A ALA 2.8 20.6 + - - -
350A ALA* 3.7 7.6 - - - -
352A LEU* 1.3 76.9 - - - +
354A ALA* 1.3 63.8 + - - +
356A LEU* 3.5 1.3 + - - +
357A ASP* 3.2 24.2 + - + +
360A ARG* 5.6 7.6 + - - +
368A VAL* 5.9 0.6 - - - +
370A VAL* 3.6 24.4 - - + +
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Residues in contact with ALA 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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350A ALA 2.9 19.0 + - - +
351A GLY* 3.9 4.9 - - - +
353A THR* 1.3 78.8 - - - +
355A GLY* 1.3 61.2 + - - +
356A LEU 3.5 0.2 + - - -
357A ASP* 3.6 14.0 + - - +
358A THR* 4.9 1.0 + - - +
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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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351A GLY 2.9 15.5 + - - -
354A ALA* 1.3 77.3 - - - +
356A LEU* 1.3 59.4 + - - +
357A ASP 3.4 0.4 + - - -
358A THR* 4.1 7.2 - - - +
420A THR* 5.0 9.2 - - - -
423A THR* 3.3 29.2 + - - +
424A SER* 5.5 0.5 - - - -
427A VAL* 3.7 17.3 - - - +
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Residues in contact with LEU 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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352A LEU* 2.9 24.2 + - + +
353A THR* 4.4 1.6 - - - +
354A ALA 3.3 0.2 - - - -
355A GLY* 1.3 74.5 - - - +
357A ASP* 1.3 65.6 + - - +
358A THR 3.2 2.9 - - - -
359A ALA* 3.0 21.6 + - - +
368A VAL* 3.7 26.2 - - + +
370A VAL* 4.2 8.7 - - + -
375A GLY* 3.9 29.2 - - - -
376A VAL 4.0 9.6 - - - +
377A ILE* 3.8 17.7 - - + -
423A THR* 3.9 24.0 - - + +
426A MET* 3.8 29.8 - - + -
427A VAL* 4.5 2.9 - - + -
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Residues in contact with ASP 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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353A THR* 3.2 17.1 + - + +
354A ALA* 3.8 11.9 - - - +
355A GLY 3.4 1.6 - - - -
356A LEU* 1.3 76.9 - - - +
358A THR* 1.3 63.2 + - - +
359A ALA 3.2 0.9 + - - -
360A ARG* 3.2 46.7 + - - +
361A ALA* 4.6 0.5 + - - +
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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