Contacts of the helix formed by residues 477 - 488 (chain M) in PDB entry 6M6A
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 THR 477 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475M GLY* 4.9 2.9 - - - -
476M LYS* 1.3 79.9 + - + +
478M GLU* 1.3 50.9 + - - +
479M VAL 3.4 2.0 - - - -
480M ALA* 3.0 12.8 + - - +
481M LEU* 2.5 50.3 + - - +
496M PHE* 6.3 0.2 - - + -
507M HIS* 3.9 27.8 - - + +
510M THR* 3.9 26.3 + - + +
511M PHE* 3.6 23.3 - - + -
596M LEU* 5.5 1.6 - - + -
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Residues in contact with GLU 478 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439M PHE* 3.2 20.1 - - + -
443M LEU* 3.7 34.5 - - + -
447M GLN* 5.6 1.1 - - - +
474M PHE 4.7 0.7 - - - +
475M GLY* 3.5 20.3 + - - +
476M LYS 3.2 2.0 - - - -
477M THR* 1.3 79.4 + - - +
479M VAL* 1.3 57.9 + - - +
481M LEU* 3.3 11.4 - - - +
482M ARG* 3.0 42.4 + - - +
514M ARG* 2.5 50.3 + - - -
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Residues in contact with VAL 479 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443M LEU* 5.5 1.0 - - - +
447M GLN* 4.0 22.6 - - + +
450M ALA 5.3 0.4 - - - -
451M LEU* 3.7 43.7 - - + +
454M VAL* 4.2 15.9 - - + -
468M VAL* 5.8 8.1 - - + -
476M LYS 3.9 15.9 - - - +
478M GLU* 1.3 77.7 - - - +
480M ALA* 1.3 61.9 + - + +
482M ARG 3.5 0.2 + - - -
483M ALA* 2.9 33.1 + - + +
594M LEU* 6.0 7.6 - - + -
596M LEU* 5.0 14.8 - - + -
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Residues in contact with ALA 480 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477M THR* 3.0 18.0 + - - +
479M VAL* 1.3 83.3 - - + +
481M LEU* 1.3 56.6 + - - +
483M ALA* 4.0 1.7 - - - +
484M ALA* 2.8 32.8 + - - +
511M PHE* 5.3 5.4 - - + -
567M LEU* 4.5 1.7 - - - +
569M ILE* 3.7 28.1 - - + +
594M LEU* 3.7 20.9 - - + -
596M LEU* 5.1 5.8 - - + -
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Residues in contact with LEU 481 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435M VAL* 4.5 3.8 - - + -
477M THR* 2.5 39.0 + - - +
478M GLU* 3.2 35.4 + - - +
480M ALA* 1.3 73.6 - - - +
482M ARG* 1.3 58.8 + - - +
484M ALA* 3.3 6.2 + - + +
485M HIS* 2.9 27.7 + - - +
510M THR* 4.7 3.4 - - - +
511M PHE* 3.5 27.1 - - + -
514M ARG* 3.6 27.8 - - + +
515M PHE* 3.6 33.2 - - + -
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Residues in contact with ARG 482 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432M ASP* 2.9 35.2 - - + +
435M VAL* 3.7 23.6 - - + -
436M GLU* 3.5 43.8 + - - +
439M PHE* 3.4 41.0 + - - +
443M LEU* 3.4 23.3 - - - +
448M LYS* 6.2 0.6 - - - +
451M LEU* 3.8 31.8 - - + +
452M GLU* 5.6 0.4 - - - -
455M LEU* 4.6 4.5 - - + -
478M GLU* 3.0 28.2 + - - +
481M LEU* 1.3 72.2 - - - +
483M ALA* 1.3 61.0 + - - +
485M HIS 3.2 0.5 + - - -
486M ARG 3.0 10.2 + - - -
514M ARG* 3.2 5.7 - - - +
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Residues in contact with ALA 483 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454M VAL* 5.6 5.4 - - + -
455M LEU* 3.8 17.8 - - + +
458M LEU* 4.0 16.2 - - + +
479M VAL* 2.9 22.9 + - + +
480M ALA* 4.0 5.2 - - - +
482M ARG* 1.3 76.4 - - - +
484M ALA* 1.3 57.9 + - - +
486M ARG* 3.2 5.4 + - - +
487M VAL* 2.9 30.1 + - - +
567M LEU* 4.0 11.7 - - + -
594M LEU* 5.4 5.4 - - + -
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Residues in contact with ALA 484 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480M ALA 2.8 21.5 + - - +
481M LEU* 3.5 6.5 - - + +
483M ALA* 1.3 77.8 - - - +
485M HIS* 1.3 57.8 + - - +
487M VAL* 3.6 1.5 - - - +
488M VAL* 2.8 31.8 + - - +
494M VAL* 3.7 26.5 - - + +
515M PHE* 5.3 2.9 - - + -
520M VAL* 5.0 1.7 - - - +
548M ILE* 4.2 13.9 - - + -
567M LEU* 3.7 12.5 - - + +
569M ILE* 5.3 1.3 - - + -
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Residues in contact with HIS 485 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431M TRP* 2.5 55.4 + + - +
432M ASP* 3.6 2.5 - - - +
434M LEU* 3.5 24.0 - - + -
435M VAL* 3.3 30.4 - - + +
481M LEU 2.9 16.3 + - - +
482M ARG 3.2 1.5 + - - +
484M ALA* 1.3 73.9 - - - +
486M ARG* 1.3 60.8 + - - +
488M VAL* 3.5 9.6 - - + -
489M GLY* 2.9 21.9 + - - -
515M PHE* 4.6 4.0 - + + -
518M LEU* 4.6 12.6 - - + +
519M PRO* 5.6 3.0 - - - +
520M VAL* 3.5 28.8 - - + +
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Residues in contact with ARG 486 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425M PHE* 3.6 26.5 - - + -
426M PRO 3.7 11.9 - - - +
427M PRO* 3.2 18.9 + - - +
428M LEU* 3.2 20.3 - - + +
432M ASP* 2.8 39.9 + - - +
452M GLU* 6.0 0.2 - - - +
455M LEU* 2.4 60.1 + - - +
458M LEU* 3.8 14.5 - - + +
459M GLU* 2.5 24.7 + - - +
482M ARG 3.0 3.4 + - - +
483M ALA* 3.4 10.8 - - - +
485M HIS* 1.3 78.8 - - - +
487M VAL* 1.3 58.5 + - - +
489M GLY* 2.9 12.3 + - - -
490M HIS 3.3 2.9 + - - -
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Residues in contact with VAL 487 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425M PHE* 3.5 20.2 - - + -
458M LEU* 4.6 13.2 - - + -
483M ALA 2.9 19.1 + - - +
484M ALA* 3.2 7.6 + - - +
486M ARG* 1.3 76.3 - - - +
488M VAL* 1.3 58.2 + - - +
490M HIS 3.3 8.0 + - - -
492M ALA* 2.8 49.5 + - + +
493M GLN 3.4 18.6 - - - +
494M VAL* 3.7 8.1 - - + -
566M GLY* 3.9 9.4 - - - +
567M LEU* 3.8 22.9 - - + -
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Residues in contact with VAL 488 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431M TRP* 4.3 10.8 - - + -
484M ALA 2.8 22.2 + - - +
485M HIS* 3.5 26.0 - - + -
487M VAL* 1.3 71.2 - - - +
489M GLY* 1.3 61.4 + - - +
491M GLY* 2.8 25.2 + - - +
492M ALA 3.5 11.7 - - - +
494M VAL* 5.3 2.0 - - + -
519M PRO 5.1 2.5 - - - +
520M VAL* 3.7 19.1 - - + -
521M ARG* 5.6 0.2 - - - +
547M ASP* 3.5 40.4 - - + +
563M ARG* 6.0 0.2 - - - +
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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