Contacts of the helix formed by residues 851 - 861 (chain A) in PDB entry 2DO4
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 GLU 851 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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800A LYS* 3.9 37.1 + - + -
801A HIS* 5.0 10.1 - - + +
850A ASN* 1.3 73.4 - - - +
852A SER* 1.3 66.6 - - - +
853A GLN 3.2 1.6 - - - -
854A ALA* 3.2 6.6 + - - +
855A SER* 3.1 22.2 + - - -
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Residues in contact with SER 852 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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850A ASN* 4.4 4.2 - - - +
851A GLU* 1.3 79.2 - - - +
853A GLN* 1.3 62.6 + - - +
855A SER* 3.3 8.6 + - - -
856A GLN* 3.1 22.3 + - - +
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Residues in contact with GLN 853 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A HIS* 4.3 9.2 - - - +
825A GLY* 2.9 14.6 - - - -
826A THR* 2.9 44.6 + - - +
848A TYR* 3.7 12.8 - - + -
849A GLU* 4.1 4.6 - - - +
850A ASN* 3.5 42.1 - - + +
851A GLU 3.2 1.0 - - - +
852A SER* 1.3 78.9 - - - +
854A ALA* 1.3 63.9 + - - +
856A GLN* 3.2 10.2 + - - +
857A ALA* 3.2 20.6 + - - +
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Residues in contact with ALA 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800A LYS 5.2 0.4 - - - +
801A HIS* 3.4 18.2 - - - +
803A LEU* 3.4 29.6 - - + +
848A TYR* 4.1 15.9 - - + -
850A ASN 4.1 7.7 + - - +
851A GLU* 3.2 10.3 + - + +
853A GLN* 1.3 77.5 - - - +
855A SER* 1.3 64.0 + - - +
857A ALA* 3.1 4.4 + - - +
858A VAL* 2.9 28.1 + - - +
875A ILE* 5.3 1.3 - - + -
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Residues in contact with SER 855 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851A GLU 3.1 12.6 + - - -
852A SER* 3.4 13.9 - - - -
853A GLN 3.2 0.2 - - - -
854A ALA* 1.3 75.8 - - - +
856A GLN* 1.3 63.1 + - - +
858A VAL* 2.9 10.9 + - - +
859A MET* 2.9 30.3 + - - +
875A ILE* 5.1 4.9 - - - +
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Residues in contact with GLN 856 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A HIS* 4.6 23.6 + - + +
852A SER* 3.1 9.0 + - - +
853A GLN* 3.2 11.3 + - - +
855A SER* 1.3 78.1 - - - +
857A ALA* 1.3 64.8 + - - +
859A MET* 3.0 20.2 + - + +
860A LYS* 3.0 24.1 + - + +
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Residues in contact with ALA 857 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A LEU* 4.5 4.9 - - + -
824A HIS* 3.2 39.1 - - + -
848A TYR* 3.5 21.5 - - + +
853A GLN 3.2 5.4 + - - +
854A ALA 3.1 9.0 + - - +
856A GLN* 1.3 79.0 - - - +
858A VAL* 1.3 53.4 + - - +
861A MET* 2.7 46.0 + - + +
873A VAL* 5.6 0.2 - - - -
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Residues in contact with VAL 858 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A LEU* 3.1 28.9 - - + -
854A ALA 2.9 24.7 + - - +
855A SER* 2.9 7.8 + - - +
857A ALA* 1.3 75.7 - - - +
859A MET* 1.3 54.9 + - + +
862A ASP* 2.6 44.3 + - + +
873A VAL* 3.8 29.2 - - + +
874A ALA* 4.8 3.8 - - - +
875A ILE* 3.3 27.4 - - + +
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Residues in contact with MET 859 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855A SER* 2.9 18.8 + - - +
856A GLN* 3.0 12.5 + - + +
858A VAL* 1.3 78.2 - - + +
860A LYS* 1.3 63.0 + - + +
862A ASP* 4.2 13.3 - - - +
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Residues in contact with LYS 860 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824A HIS* 3.7 30.5 + - + +
856A GLN* 3.0 25.6 + - + +
859A MET* 1.3 79.3 - - + +
861A MET* 1.3 66.6 + - - +
862A ASP 3.1 10.1 + - - +
863A GLY 4.8 0.3 - - - +
864A MET* 3.9 9.5 - - - +
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Residues in contact with MET 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A LEU* 6.1 3.4 - - - -
805A ILE* 3.4 27.8 - - - -
817A LEU* 3.9 11.9 - - + -
820A ILE* 3.6 30.1 - - + +
821A CYS* 3.8 32.1 - - - +
824A HIS* 4.3 12.1 - - + +
846A VAL* 5.8 0.7 - - - -
848A TYR* 5.3 0.9 - - - +
857A ALA* 2.7 30.2 + - - +
860A LYS* 1.3 74.2 - - - +
862A ASP* 1.3 62.1 + - - +
863A GLY 2.9 4.0 + - - -
864A MET* 3.0 40.9 + - - +
871A ILE* 3.3 6.7 - - + +
873A VAL* 3.2 16.2 - - + -
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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