Contacts of the strand formed by residues 870 - 875 (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 ILE 870 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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807A GLY* 3.8 4.5 - - - +
863A GLY* 4.6 13.9 - - - +
864A MET 3.5 6.7 - - - +
865A THR* 4.2 23.8 - - + +
868A GLU* 5.6 3.1 - - - +
869A ASN* 1.3 80.4 + - - +
871A ILE* 1.3 67.9 + - - +
872A LYS* 4.2 1.7 + - + +
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Residues in contact with ILE 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A ILE* 3.3 26.2 - - + -
806A SER 3.8 3.8 - - - +
807A GLY 2.9 24.7 - - - +
808A LEU* 3.3 24.9 - - + -
809A PRO* 4.3 1.1 - - + -
861A MET* 3.3 18.6 - - + +
863A GLY* 3.0 18.9 + - - -
864A MET* 2.8 36.2 + - + +
866A ILE* 3.8 14.6 - - + -
869A ASN 3.3 14.1 - - - +
870A ILE* 1.3 74.4 - - - +
872A LYS* 1.3 63.3 + - - +
873A VAL* 3.7 7.6 - - + -
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Residues in contact with LYS 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A ILE* 3.4 5.0 - - - +
806A SER* 3.0 45.3 + - - +
862A ASP* 4.2 12.9 + - - +
863A GLY* 3.9 6.5 - - - +
870A ILE* 4.2 2.4 + - + +
871A ILE* 1.3 73.7 - - - +
873A VAL* 1.3 80.6 + - - +
874A ALA* 4.8 8.1 - - - -
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Residues in contact with VAL 873 (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* 4.8 4.0 - - + -
804A PHE* 3.4 13.7 - - - +
805A ILE* 4.2 13.5 - - + -
858A VAL* 3.8 32.0 - - + +
861A MET* 3.2 24.9 - - + +
862A ASP* 3.1 44.7 - - + +
871A ILE* 3.7 7.2 - - + -
872A LYS* 1.3 95.9 + - - +
874A ALA* 1.3 76.0 + - - +
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Residues in contact with ALA 874 (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* 5.0 0.2 - - - -
804A PHE* 2.7 60.9 + - + +
858A VAL* 5.1 2.2 - - - -
872A LYS* 4.8 9.4 - - + -
873A VAL* 1.3 83.5 - - - +
875A ILE* 1.3 63.4 + - - +
876A SER 3.1 0.3 + - - -
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Residues in contact with ILE 875 (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* 3.4 49.8 - - + +
802A LYS 4.2 1.3 - - - -
803A LEU* 3.6 12.8 - - + +
804A PHE* 5.0 0.2 - - - -
854A ALA* 5.1 1.3 - - + +
855A SER* 5.1 6.7 - - - -
858A VAL* 3.3 39.6 - - + +
874A ALA* 1.3 70.7 - - - +
876A SER* 1.3 53.6 + - - +
877A ASN* 2.5 27.2 + - + +
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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