Contacts of the helix formed by residues 424 - 429 (chain M) in PDB entry 2O5J
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 GLY 424 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423M ALA* 1.4 73.5 - - - +
425M PHE* 1.4 62.1 + - - +
426M ASP* 3.4 6.3 - - - -
427M VAL* 3.3 17.3 + - - +
428M ARG* 3.1 40.3 + - - +
451M LEU* 5.2 1.7 - - - +
4Z C 5.3 4.4 + - - -
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Residues in contact with PHE 425 (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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424M GLY* 1.4 72.4 - - - +
426M ASP* 1.3 64.6 + - - +
427M VAL 3.6 0.2 + - - -
428M ARG* 3.8 7.9 + - + +
429M ASP* 3.7 25.2 + - - +
1079N LYS* 3.7 59.2 - - + -
1082N ALA* 4.5 18.6 - - + -
1083N ASP* 5.6 5.2 - - + -
1087N ARG* 5.7 7.0 - - - -
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Residues in contact with ASP 426 (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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324M ASP* 6.1 0.4 - - - +
325M ILE* 5.3 9.5 - - - +
326M ASP* 2.6 32.4 - - - +
424M GLY* 4.4 2.1 - - - -
425M PHE* 1.3 80.3 + - - +
427M VAL* 1.3 69.8 + - - +
429M ASP* 4.1 15.7 + - - +
431M HIS* 6.0 0.7 + - - +
4Z C 5.6 2.4 + - - -
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Residues in contact with VAL 427 (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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140M ILE* 5.3 4.0 - - + -
325M ILE* 5.4 4.0 - - + -
326M ASP* 3.0 21.3 - - - +
331M ARG* 2.9 31.3 + - - +
412M ALA* 5.5 5.8 - - + -
423M ALA 5.5 0.9 - - - +
424M GLY* 3.6 19.1 - - - +
426M ASP* 1.3 87.5 - - - +
428M ARG* 1.3 65.2 + - + +
429M ASP 3.2 9.5 - - - +
434M HIS* 4.8 5.9 - - - -
450M GLY 4.9 6.5 - - - +
451M LEU* 5.4 11.4 - - + -
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Residues in contact with ARG 428 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421M GLU 4.2 12.7 + - - -
423M ALA 5.5 1.0 + - - +
424M GLY* 3.1 28.1 + - - +
425M PHE* 4.0 9.6 - - + +
427M VAL* 1.3 75.5 - - - +
429M ASP* 1.3 56.1 + - - +
447M ALA 4.1 7.7 + - - -
448M ASN* 6.0 0.2 - - - +
449M ILE* 3.2 43.0 + - + +
450M GLY* 4.0 11.5 - - - +
451M LEU* 3.3 41.4 - - + +
1078N ARG* 2.6 47.5 + - - +
1082N ALA* 3.9 28.6 - - + +
1085N ALA* 5.7 3.4 - - - +
1086N LEU* 6.2 1.2 - - - +
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Residues in contact with ASP 429 (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* 3.7 19.0 + - - +
426M ASP* 4.2 13.5 - - - +
427M VAL 3.2 11.7 - - - +
428M ARG* 1.3 83.4 - - - +
430M VAL* 1.3 60.9 + - - +
431M HIS* 3.3 7.4 + - - +
434M HIS* 3.5 5.4 - - - -
1048N PRO* 3.6 38.3 - - + +
1075N HIS* 3.4 23.6 - - - +
1078N ARG* 3.4 8.3 + - - +
1079N LYS* 3.7 23.9 + - - +
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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