Contacts of the helix formed by residues 923 - 930 (chain X) in PDB entry 2OO8
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 923 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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919X VAL* 2.5 27.6 + - + +
922X THR* 1.3 81.6 - - + +
924X PRO* 1.3 68.6 - - - +
925X ALA* 3.9 8.1 + - - +
926X PHE* 3.1 29.7 + - - +
927X ALA 3.0 17.5 + - - -
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Residues in contact with PRO 924 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919X VAL 3.4 2.0 - - - +
920X LEU* 3.4 24.9 - - + +
921X GLU 4.0 5.6 - - - +
922X THR 3.9 3.8 - - - +
923X ASP* 1.3 89.7 - - - +
925X ALA* 1.3 55.5 + - - +
927X ALA* 4.1 4.5 - - + -
928X ILE* 2.8 52.9 + - + +
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Residues in contact with ALA 925 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923X ASP* 3.2 8.2 - - - +
924X PRO* 1.3 78.0 - - - +
926X PHE* 1.3 63.2 + - - +
928X ILE* 4.5 3.1 - - - +
929X ALA* 3.2 26.5 + - - +
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Residues in contact with PHE 926 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919X VAL* 3.6 19.3 - - + -
923X ASP* 3.1 29.7 + - - +
925X ALA* 1.3 79.3 - - - +
927X ALA* 1.3 66.3 + - - +
929X ALA* 4.7 1.1 - - - -
930X ASN* 2.9 54.6 + - + +
932X THR* 4.0 20.4 - - + -
935X THR* 4.5 15.5 - - + -
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Residues in contact with ALA 927 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919X VAL* 3.5 8.1 - - + -
920X LEU* 3.5 37.9 - - + +
923X ASP 3.0 5.8 + - - +
924X PRO* 3.7 4.9 - - + +
926X PHE* 1.3 82.8 - - - +
928X ILE* 1.3 52.4 + - - +
930X ASN* 3.3 1.6 + - - +
931X SER* 2.8 30.1 + - - -
932X THR* 3.0 32.1 + - - +
1107X LEU* 3.6 2.0 - - - +
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Residues in contact with ILE 928 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920X LEU* 4.1 17.9 - - + -
924X PRO* 2.8 35.7 + - + +
925X ALA* 4.5 3.1 - - - +
927X ALA* 1.3 66.1 - - - +
929X ALA* 1.3 68.8 + - - +
930X ASN 3.0 2.6 + - - -
931X SER* 3.0 15.4 + - - -
1107X LEU* 4.1 9.2 - - + -
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Residues in contact with ALA 929 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925X ALA 3.2 20.1 + - - +
926X PHE* 3.8 4.7 - - - +
928X ILE* 1.3 80.7 - - - +
930X ASN* 1.3 65.2 + - - +
931X SER* 4.8 1.7 + - - -
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Residues in contact with ASN 930 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926X PHE* 2.9 55.2 + - + +
928X ILE 3.0 0.6 - - - -
929X ALA* 1.3 85.5 - - - +
931X SER* 1.3 70.2 + - - +
932X THR* 3.2 19.8 + - + -
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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