Contacts of the helix formed by residues 921 - 925 (chain B) in PDB entry 3O33
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 SER 921 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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915B LEU 2.8 27.1 - - - -
916B TYR* 2.9 24.2 + - - -
918B HIS* 3.2 7.8 + - - -
919B GLU 3.4 0.4 - - - -
920B MET* 1.3 75.4 - - - +
922B LEU* 1.3 66.1 + - - +
923B ALA 3.3 2.9 - - - -
924B PHE* 2.9 15.6 + - - +
925B GLN* 3.0 22.0 + - - +
945B LEU* 4.2 5.4 - - - -
993B LEU* 3.9 16.9 - - - +
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Residues in contact with LEU 922 (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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919B GLU 4.8 4.4 + - - +
920B MET 3.5 2.6 - - - -
921B SER* 1.3 78.9 + - - +
923B ALA* 1.3 62.6 + - - +
924B PHE 3.1 1.2 + - - -
925B GLN* 3.4 35.5 + - + +
926B ASP* 4.6 4.7 + - - +
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Residues in contact with ALA 923 (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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920B MET 4.4 2.3 + - - +
921B SER 3.1 1.2 + - - -
922B LEU* 1.3 76.2 - - - +
924B PHE* 1.3 83.3 + - + +
925B GLN 3.7 0.4 - - - -
926B ASP 4.6 6.9 - - - +
928B VAL* 5.1 9.7 - - - +
986B VAL* 4.8 16.2 - - + -
989B ALA* 5.9 2.7 - - + -
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Residues in contact with PHE 924 (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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920B MET 3.7 19.1 - - - -
921B SER 2.9 7.1 + - - +
923B ALA* 1.3 87.9 - - + +
925B GLN* 1.3 59.5 + - - +
926B ASP 3.7 2.2 - - - -
943B MET 6.0 0.2 - - - -
944B ASP* 3.6 8.6 - - - +
945B LEU* 2.9 31.6 + - + +
972B ILE* 3.9 29.3 - - + +
973B PHE* 5.6 2.9 - + - -
976B CYS* 3.5 40.8 - - + -
986B VAL* 3.9 16.2 - - + -
989B ALA* 4.1 6.7 - - + -
990B GLY* 3.6 25.1 - - - -
993B LEU* 3.5 27.1 - - + -
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Residues in contact with GLN 925 (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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831B VAL* 4.7 11.4 + - - +
832B CYS* 6.1 0.6 - - - +
916B TYR* 3.6 41.2 + - + -
921B SER* 3.0 33.1 + - - +
922B LEU* 3.4 33.3 + - + +
924B PHE* 1.3 78.9 - - - +
926B ASP* 1.3 71.9 + - - +
944B ASP* 3.7 0.4 - - - +
945B LEU* 3.6 10.3 + - + -
946B SER* 2.9 34.3 + - - -
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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