Contacts of the helix formed by residues 465 - 474 (chain B) in PDB entry 2JED
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 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464B GLY* 1.3 75.3 - - - -
466B LEU* 1.3 63.9 + - - +
467B MET* 3.2 16.6 + - - +
468B TYR* 3.0 37.3 + - - +
469B HIS* 3.1 23.6 + - - -
507B LEU 4.3 0.7 - - - +
508B ASP* 3.8 15.5 - - - +
510B ILE 3.1 13.2 - - - +
511B LEU* 3.9 14.0 - - + +
1712B LG8 3.4 24.2 - - - -
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ASP* 1.3 70.0 - - - +
467B MET* 1.3 59.3 + - - +
469B HIS* 3.7 3.8 - - + -
470B ILE* 3.0 32.4 + - - +
476B PHE* 3.6 10.8 - - + -
484B TYR* 3.6 46.7 - - + +
488B ILE* 4.7 2.7 - - + -
507B LEU* 3.6 26.7 + - + +
510B ILE* 2.8 42.8 + - + +
512B LEU* 3.8 25.6 - - + -
518B ILE* 4.9 0.4 - - + -
568B LEU* 5.8 0.2 - - + -
572B MET* 4.1 15.9 - - - -
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Residues in contact with MET 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B ASP* 3.2 11.9 + - - +
466B LEU* 1.3 73.6 - - - +
468B TYR* 1.3 66.3 + - - +
470B ILE* 3.4 3.3 - - + +
471B GLN* 3.1 63.3 + - + +
507B LEU* 3.6 18.3 + - + +
508B ASP* 4.0 34.3 - - - +
1713B MPD 3.3 42.6 - - + -
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Residues in contact with TYR 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B GLY* 4.8 8.3 - - - -
465B ASP* 3.0 27.8 + - - +
467B MET* 1.3 77.2 - - - +
469B HIS* 1.3 94.2 + + - +
471B GLN* 3.3 26.3 + - + +
472B SER* 3.7 17.4 + - - -
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Residues in contact with HIS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B GLY 2.7 29.0 + - - -
464B GLY* 3.7 7.8 - - - -
465B ASP 3.1 26.6 + - - +
466B LEU* 3.4 2.9 + - + +
467B MET 3.3 0.2 - - - -
468B TYR* 1.3 96.4 - + - +
470B ILE* 1.3 60.0 + - - +
471B GLN 3.5 0.2 + - - -
472B SER* 3.5 13.8 + - - -
473B CYS* 3.4 17.0 + - - -
476B PHE* 3.8 11.8 - - + -
480B ARG* 3.6 20.0 + - - +
512B LEU* 3.6 21.1 - - + +
651B PHE* 3.8 28.0 - + - -
653B PRO* 4.5 4.3 - - + -
654B LYS 5.8 0.2 - - - -
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B LEU 3.0 15.3 + - - +
467B MET* 3.4 15.0 - - + +
469B HIS* 1.3 75.1 - - - +
471B GLN* 1.3 59.9 + - - +
472B SER 3.2 0.9 - - - -
473B CYS* 4.1 1.6 - - - -
474B HIS* 2.8 42.0 + - - +
475B LYS* 3.9 15.9 - - - +
476B PHE* 3.7 19.9 - - + -
507B LEU* 4.1 14.6 - - + -
571B GLU 3.3 27.8 - - - +
572B MET* 3.9 17.3 - - - +
1713B MPD 3.4 30.1 - - + +
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Residues in contact with GLN 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467B MET* 3.1 50.0 + - + +
468B TYR* 3.3 21.3 + - + +
469B HIS 3.3 0.8 - - - -
470B ILE* 1.3 79.0 - - - +
472B SER* 1.3 60.8 + - - +
474B HIS* 4.0 13.7 + - - -
1713B MPD 4.2 12.8 - - + +
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Residues in contact with SER 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B TYR* 3.7 24.3 + - - -
469B HIS* 3.5 10.3 + - - -
470B ILE 3.2 0.6 - - - -
471B GLN* 1.3 79.9 - - - +
473B CYS* 1.3 61.2 + - - +
474B HIS* 3.5 12.2 + - - -
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Residues in contact with CYS 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LYS* 4.8 16.6 + - - +
469B HIS 3.4 17.3 - - - -
470B ILE* 4.1 1.8 - - - -
472B SER* 1.3 76.0 - - - +
474B HIS* 1.3 73.2 + - - +
475B LYS* 3.0 37.0 + - - +
476B PHE* 3.7 21.5 - - - -
480B ARG* 3.8 11.9 - - - +
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Residues in contact with HIS 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B ILE* 2.8 22.5 + - - +
471B GLN 4.0 11.2 + - - -
472B SER 4.0 14.3 + - - -
473B CYS* 1.3 80.3 - - - +
475B LYS* 1.3 60.4 + - + +
575B GLY* 3.3 24.4 - - - +
1713B MPD 4.1 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