Contacts of the helix formed by residues 406 - 419 (chain A) in PDB entry 5MJU
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 ILE 406 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.8 40.8 - - + -
143A LEU* 3.8 28.9 - - + -
391A ILE* 4.4 6.1 - - + -
405A GLN* 1.3 80.2 - - - +
407A ILE* 1.4 54.9 + - - +
408A THR 3.3 1.1 - - - -
409A ILE* 3.0 22.8 + - + -
410A SER* 2.8 35.5 + - - -
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Residues in contact with ILE 407 (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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405A GLN* 3.4 26.0 - - - +
406A ILE* 1.4 78.4 - - - +
408A THR* 1.3 65.8 + - + +
410A SER* 3.2 18.8 + - - +
411A ILE* 3.3 38.2 + - + +
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Residues in contact with THR 408 (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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405A GLN* 2.8 41.9 + - + +
407A ILE* 1.3 78.5 - - + +
409A ILE* 1.4 52.3 + - - +
411A ILE* 4.5 3.0 - - - +
412A THR* 2.9 33.7 + - - +
437A ALA* 4.9 8.0 - - - +
438A VAL* 3.5 29.9 + - - +
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Residues in contact with ILE 409 (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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139A ILE* 4.7 9.6 - - + -
387A ALA* 4.8 7.2 - - - +
390A ALA* 3.8 29.2 - - + -
391A ILE* 4.5 18.6 - - + -
405A GLN 3.5 20.6 - - - +
406A ILE* 3.0 25.9 + - + +
408A THR* 1.4 77.0 - - - +
410A SER* 1.3 57.5 + - - +
411A ILE 3.4 0.7 - - - -
412A THR* 3.0 16.7 + - - +
413A ALA* 3.1 20.1 + - - +
434A VAL* 5.3 6.1 - - + +
438A VAL* 3.8 25.6 - - + -
440A LEU* 5.1 6.5 - - + -
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Residues in contact with SER 410 (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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135A VAL* 3.8 14.9 - - - +
136A VAL* 6.1 3.8 - - - -
139A ILE* 3.8 22.1 - - - +
406A ILE* 2.8 24.2 + - - -
407A ILE* 3.2 18.4 + - - +
409A ILE* 1.3 72.5 - - - +
411A ILE* 1.3 60.9 + - - +
414A THR* 2.7 31.4 + - - -
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Residues in contact with ILE 411 (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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407A ILE* 3.3 41.8 + - + +
408A THR* 5.0 2.5 - - - +
410A SER* 1.3 83.9 + - - +
412A THR* 1.4 61.8 + - + +
414A THR* 3.5 6.0 + - - -
415A ALA* 3.1 28.4 + - + +
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Residues in contact with THR 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A THR 2.9 24.3 + - - +
409A ILE* 3.0 14.0 + - - -
411A ILE* 1.4 76.6 - - + +
413A ALA* 1.4 51.9 + - - +
415A ALA* 3.2 9.1 + - + +
416A ALA* 2.8 33.6 + - - +
433A ILE* 4.8 4.9 - - + +
434A VAL* 3.5 30.2 + - - +
437A ALA* 3.8 26.9 - - + -
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Residues in contact with ALA 413 (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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135A VAL* 3.7 21.1 - - + -
383A ALA* 3.8 12.3 - - - +
386A GLU* 3.9 23.9 - - + +
387A ALA* 4.1 7.9 - - - +
409A ILE* 3.1 18.6 + - + +
411A ILE 3.5 0.2 - - - -
412A THR* 1.4 72.5 + - - +
414A THR* 1.3 60.3 + - - +
416A ALA* 3.6 5.0 + - - +
417A SER* 3.1 23.9 + - - -
434A VAL* 3.9 9.4 - - + +
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Residues in contact with THR 414 (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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128A MET* 4.2 23.3 - - + -
131A THR* 3.8 32.5 - - - +
132A ILE* 4.5 13.7 - - + +
135A VAL* 3.3 18.7 - - - +
383A ALA* 5.0 0.2 - - - -
410A SER 2.7 22.7 + - - -
411A ILE* 3.5 6.5 + - - -
412A THR 3.3 0.4 - - - -
413A ALA* 1.3 76.1 - - - +
415A ALA* 1.4 62.0 + - - +
417A SER* 3.5 18.1 - - - -
418A ILE* 3.4 15.9 - - + +
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Residues in contact with ALA 415 (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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411A ILE* 3.1 17.5 + - + +
412A THR* 3.2 13.7 + - + +
414A THR* 1.4 75.0 - - - +
416A ALA* 1.4 60.5 + - - +
417A SER 3.3 0.2 - - - -
418A ILE* 3.6 15.9 + - + +
419A GLY* 3.4 15.8 + - - -
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Residues in contact with ALA 416 (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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379A MET* 5.4 0.5 - - - +
382A THR* 4.7 6.5 - - - +
386A GLU* 3.8 29.8 - - + +
412A THR 2.8 15.5 + - - +
413A ALA* 3.7 9.4 - - - +
414A THR 3.3 0.2 - - - -
415A ALA* 1.4 74.8 - - - +
417A SER* 1.3 63.2 + - - +
418A ILE 3.4 0.2 - - - -
419A GLY* 3.2 19.9 + - - +
430A THR* 4.2 24.1 + - - +
434A VAL* 5.1 2.7 - - + -
602A 7O9 5.5 0.9 - - - -
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Residues in contact with SER 417 (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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131A THR* 4.1 14.1 - - - -
376A THR 4.1 0.7 - - - +
377A ILE 3.0 14.1 - - - +
379A MET* 3.1 52.7 + - - +
382A THR* 4.2 5.3 - - - +
383A ALA* 3.3 16.3 + - - +
413A ALA 3.1 14.7 + - - -
414A THR 3.5 10.4 + - - -
416A ALA* 1.3 77.7 - - - +
418A ILE* 1.4 58.8 + - - +
419A GLY 3.5 1.2 + - - +
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Residues in contact with ILE 418 (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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128A MET* 4.8 23.3 - - + -
131A THR* 5.8 4.5 - - + +
179A LEU* 5.1 4.8 - - + +
224A LEU* 5.6 5.3 - - + +
376A THR 3.8 10.5 - - - +
377A ILE* 3.8 42.4 - - + +
414A THR* 3.4 21.5 - - + +
415A ALA* 3.6 15.8 + - + +
416A ALA 3.4 0.2 - - - -
417A SER* 1.4 75.1 - - - +
419A GLY* 1.3 62.9 + - - +
420A ALA* 3.6 3.3 + - - +
601A 6Z6 5.0 7.6 - - - -
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Residues in contact with GLY 419 (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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179A LEU* 4.7 9.2 - - - -
376A THR 4.7 0.9 - - - +
415A ALA 3.4 9.4 + - - -
416A ALA* 3.2 17.5 + - - +
417A SER 3.2 5.6 - - - +
418A ILE* 1.3 77.7 - - - +
420A ALA* 1.3 58.0 + - - +
421A ALA* 4.1 0.7 - - - -
430A THR* 5.0 11.1 - - - +
602A 7O9 3.1 21.8 - - - -
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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