Contacts of the helix formed by residues 506 - 511 (chain M) in PDB entry 2JA7
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 ALA 506 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457M ALA* 3.3 13.7 - - + +
501M LEU 3.0 5.2 + - - +
502M SER* 3.6 26.9 - - - +
504M LEU 3.6 1.6 - - - -
505M CYS* 1.3 76.8 - - - +
507M VAL* 1.3 56.2 + - - +
508M PRO* 3.7 13.5 - - + -
509M LEU* 2.7 43.4 + - + +
510M GLN 3.5 2.1 + - - -
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Residues in contact with VAL 507 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M LEU* 3.7 30.3 - - + +
362M ASP* 4.2 5.8 - - - -
456M MET* 3.4 30.1 - - + -
457M ALA 3.0 7.8 + - - +
458M HIS* 3.1 36.8 - - + +
474M VAL* 3.8 7.2 - - + -
505M CYS 3.2 1.2 + - - -
506M ALA* 1.3 69.2 - - - +
508M PRO* 1.3 69.7 - - + +
510M GLN* 3.0 12.5 + - - -
511M ILE* 3.4 8.5 + - - +
521M MET* 3.7 20.6 - - + +
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Residues in contact with PRO 508 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M LEU* 5.0 0.4 - - + -
362M ASP* 3.5 33.9 - - + +
506M ALA* 3.1 15.3 - - + -
507M VAL* 1.3 96.1 - - + +
509M LEU* 1.3 62.4 + - + +
511M ILE* 3.1 31.1 - - + +
634M THR* 5.5 0.5 - - - +
639M PRO* 3.7 25.6 - - + +
640M GLN* 4.6 10.8 - - + +
643M ALA* 4.0 18.8 - - + -
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Residues in contact with LEU 509 (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 SER 4.1 10.3 - - - +
503M GLN* 3.7 32.1 - - - +
504M LEU* 4.2 5.6 - - - +
506M ALA* 2.7 27.2 + - + +
508M PRO* 1.3 75.6 - - + +
510M GLN* 1.3 71.5 + - - +
511M ILE* 3.1 3.2 + - - +
512M VAL 4.2 8.8 + - - +
639M PRO* 4.2 21.5 - - + +
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Residues in contact with GLN 510 (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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452M LYS* 3.5 21.4 + - - +
453M MET* 4.0 18.3 - - + +
456M MET* 3.6 40.6 - - + -
504M LEU 3.1 26.5 + - - -
505M CYS* 4.2 2.6 - - - +
506M ALA 3.5 4.7 + - - +
507M VAL 3.0 4.1 + - - +
509M LEU* 1.3 83.1 - - - +
511M ILE* 1.3 64.0 + - - +
512M VAL 3.1 11.2 + - - +
513M SER* 4.1 1.2 + - - -
514M PRO* 5.6 3.8 - - - +
520M CYS* 3.2 15.9 - - - -
521M MET* 3.9 4.7 - - + -
1141N HIS* 3.4 20.5 - - + -
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Residues in contact with ILE 511 (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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361M LEU* 4.2 10.5 - - + -
507M VAL 3.4 9.2 + - - +
508M PRO* 3.1 22.0 - - + +
509M LEU 3.1 1.4 - - - +
510M GLN* 1.3 75.4 - - - +
512M VAL* 1.3 54.0 + - - +
519M PRO* 3.0 6.6 - - + +
520M CYS* 2.6 32.4 + - - -
521M MET* 4.1 13.9 + - + +
630M ILE* 3.9 16.4 - - + -
634M THR* 3.4 27.4 - - + +
639M PRO 4.2 2.2 - - - +
642M CYS* 3.6 24.7 - - + -
643M ALA* 4.0 17.0 - - - +
646M PHE* 4.0 15.3 - - + -
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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