Contacts of the helix formed by residues 500 - 515 (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 500 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498M VAL* 3.3 8.9 - - - +
499M PRO* 1.3 79.9 - - + +
501M THR* 1.3 71.6 + - - +
502M LEU* 3.4 23.1 - - + +
503M LEU* 3.6 35.7 - - + +
504M ALA 3.1 17.7 + - - -
552M THR* 3.2 7.0 - - - -
713M ILE* 5.8 5.6 - - + +
31T A 3.6 9.6 + - - -
32T C 2.8 15.4 + - - -
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Residues in contact with THR 501 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500M THR* 1.3 77.7 + - - +
502M LEU* 1.3 59.5 + - - +
504M ALA* 3.4 5.9 + - - +
505M GLU* 2.9 27.9 + - - +
524M VAL* 5.8 0.7 - - - +
526M SER* 3.7 30.5 - - - -
527M ARG* 2.6 38.2 + - - +
528M PHE* 3.3 26.5 - - + -
552M THR* 3.4 10.3 - - + +
32T C 2.9 7.2 + - - +
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Residues in contact with LEU 502 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500M THR* 3.2 22.4 - - + +
501M THR* 1.3 82.0 - - - +
503M LEU* 1.3 59.2 + - + +
505M GLU* 3.3 13.4 + - - +
506M GLN* 2.9 28.0 + - - +
528M PHE* 5.7 4.5 - - + -
713M ILE* 6.1 4.9 - - + -
717M LEU* 6.6 0.2 - - + -
32T C 5.2 1.1 - - - +
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Residues in contact with LEU 503 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498M VAL* 3.6 14.4 - - + -
499M PRO* 3.8 27.1 - - + -
500M THR* 3.4 16.3 + - + +
502M LEU* 1.3 76.2 - - + +
504M ALA* 1.3 60.5 + - - +
506M GLN* 3.7 20.0 - - - +
507M HIS* 2.9 55.8 + - + +
575M ARG* 4.0 14.1 - - - +
744M ARG* 6.3 1.1 - - - +
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Residues in contact with ALA 504 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496M PHE* 4.2 3.6 - - - -
498M VAL* 3.4 23.2 - - + +
500M THR 3.1 13.5 + - - +
501M THR* 3.5 12.1 - - + +
503M LEU* 1.3 77.6 - - - +
505M GLU* 1.3 57.6 + - - +
507M HIS* 3.4 0.3 + - - -
508M GLY* 2.9 25.5 + - - -
524M VAL* 4.7 6.1 - - + +
526M SER* 6.1 0.2 - - - -
550M ILE* 3.3 31.5 - - + +
551M GLY* 4.1 8.3 - - - -
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Residues in contact with GLU 505 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501M THR 2.9 13.9 + - - +
502M LEU* 3.3 16.7 + - - +
504M ALA* 1.3 77.1 - - - +
506M GLN* 1.3 70.1 + - - +
508M GLY 3.5 0.5 + - - -
509M LYS* 2.9 61.8 + - - +
512M ARG* 3.8 9.4 + - - +
524M VAL* 5.1 10.3 - - + +
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Residues in contact with GLN 506 (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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502M LEU 2.9 15.0 + - - +
503M LEU* 3.7 25.8 - - - +
505M GLU* 1.3 85.3 + - - +
507M HIS* 1.3 66.8 + - - +
509M LYS* 3.2 11.1 - - + +
510M THR* 3.0 37.0 + - + +
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Residues in contact with HIS 507 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477M THR* 3.9 20.8 - - + +
496M PHE* 3.4 36.8 - + + -
503M LEU* 2.9 47.9 + - + +
506M GLN* 1.3 86.8 - - - +
508M GLY* 1.3 59.8 + - - +
510M THR* 2.5 23.0 + - - +
511M PHE* 2.8 29.1 + - + -
571M ASP* 4.6 7.4 + - - -
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Residues in contact with GLY 508 (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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504M ALA 2.9 16.2 + - - -
505M GLU 3.8 0.9 - - - -
507M HIS* 1.3 73.0 - - - +
509M LYS* 1.3 58.7 + - - +
511M PHE* 3.6 15.4 - - - +
512M ARG* 2.9 41.4 + - - +
522M VAL* 4.0 1.2 - - - +
524M VAL* 4.9 4.5 - - - -
550M ILE* 3.8 17.9 - - - +
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Residues in contact with LYS 509 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505M GLU* 2.9 40.5 + - - +
506M GLN* 3.2 11.0 - - + +
508M GLY* 1.3 77.2 - - - +
510M THR* 1.3 59.2 + - + +
512M ARG* 3.2 26.9 + - - +
513M GLU* 2.9 49.0 + - - +
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Residues in contact with THR 510 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477M THR* 3.9 23.3 + - + +
481M LEU* 4.7 3.0 - - - +
506M GLN* 3.0 20.0 + - + +
507M HIS* 2.5 29.4 + - - +
509M LYS* 1.3 74.3 - - + +
511M PHE* 1.3 58.5 + - - +
513M GLU* 3.3 20.8 - - - +
514M ARG* 2.9 28.9 + - - +
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Residues in contact with PHE 511 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477M THR* 3.6 28.9 - - + -
480M ALA* 5.3 5.2 - - + -
481M LEU* 3.5 25.8 - - + -
496M PHE* 4.1 35.9 - + + -
507M HIS* 2.8 38.4 + - + +
508M GLY* 3.6 14.1 - - - +
510M THR* 1.3 76.6 - - - +
512M ARG* 1.3 55.5 + - - +
514M ARG 3.2 0.9 + - - -
515M PHE* 2.7 44.6 + - + -
522M VAL* 3.7 17.5 - - + -
548M ILE* 4.4 16.2 - - + -
550M ILE* 4.2 11.4 - - + -
569M ILE* 4.9 9.2 - - + -
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Residues in contact with ARG 512 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505M GLU* 3.8 12.9 + - - +
508M GLY 2.9 20.9 + - - +
509M LYS* 3.2 45.0 + - - +
511M PHE* 1.3 76.2 - - - +
513M GLU* 1.3 57.2 + - + +
515M PHE* 3.1 6.1 - - - +
516M GLN* 2.9 42.2 + - - +
522M VAL* 3.7 20.1 - - + +
524M VAL* 5.5 9.1 - - - +
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Residues in contact with GLU 513 (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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509M LYS* 2.9 49.1 + - - +
510M THR* 3.3 23.5 + - - +
511M PHE 3.3 0.2 - - - -
512M ARG* 1.3 75.5 - - + +
514M ARG* 1.3 61.5 + - - +
516M GLN* 3.3 25.5 + - - +
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Residues in contact with ARG 514 (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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435M VAL* 2.4 47.1 + - + +
438M GLY* 3.2 11.3 - - - -
439M PHE* 3.1 33.4 - - - +
478M GLU* 2.5 46.9 + - - -
481M LEU* 3.6 26.1 - - + +
482M ARG* 3.2 15.0 - - - +
510M THR 2.9 17.6 + - - +
511M PHE 3.2 5.1 + - - +
513M GLU* 1.3 76.5 - - - +
515M PHE* 1.3 68.3 + - + +
516M GLN 3.6 1.1 + - - -
517M GLY 5.4 0.2 + - - -
518M LEU* 3.3 14.8 - - - +
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Residues in contact with PHE 515 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435M VAL* 3.6 24.9 - - + -
481M LEU* 3.6 42.4 - - + -
484M ALA* 5.3 0.7 - - + -
485M HIS* 4.6 5.4 - + + -
511M PHE* 2.7 23.2 + - + +
512M ARG* 3.1 8.0 + - - +
514M ARG* 1.3 86.6 - - + +
516M GLN* 1.3 64.0 + - - +
517M GLY 3.6 0.4 - - - -
518M LEU* 3.1 38.6 - - + +
520M VAL* 3.6 50.7 - - + +
522M VAL* 4.1 5.4 - - + -
548M ILE* 4.2 11.2 - - + -
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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