Contacts of the helix formed by residues 907 - 912 (chain B) in PDB entry 1OFD
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 907 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877B LEU* 6.1 2.3 - - + +
882B ARG* 3.8 8.3 + - - +
886B GLU* 5.6 0.4 - - - +
906B GLU* 1.3 75.6 - - - +
908B VAL* 1.3 68.1 + - - +
909B VAL* 3.1 29.5 + - + +
910B ARG* 3.1 28.4 + - + +
911B TYR* 4.1 1.1 - - - -
987B TYR* 2.6 42.6 + - - +
990B MET* 4.7 3.9 - - - +
991B LEU* 3.8 17.8 - - + +
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Residues in contact with VAL 908 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B GLU 4.4 5.6 - - - +
907B ASP* 1.3 69.2 + - - +
909B VAL* 1.3 61.3 + - - +
910B ARG 3.0 7.3 + - - -
911B TYR* 3.0 39.3 + - + +
912B LEU* 4.5 1.7 + - - +
953B THR* 6.2 1.8 - - + -
955B GLU* 3.4 34.1 - - + +
993B ARG* 6.0 3.4 - - - +
1294B ASN* 5.6 4.5 - - - +
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Residues in contact with VAL 909 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882B ARG* 4.0 15.5 - - - +
907B ASP* 3.1 30.3 + - + +
908B VAL* 1.3 77.1 - - - +
910B ARG* 1.3 64.1 + - + +
911B TYR 3.5 0.3 + - - -
912B LEU* 3.8 16.0 + - - +
914B LEU* 5.9 1.2 - - - +
925B THR* 3.9 34.3 - - + +
926B LEU* 4.2 12.4 - - + +
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Residues in contact with ARG 910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877B LEU* 3.2 23.0 - - - +
885B HIS* 2.6 40.5 + - - -
886B GLU* 3.4 29.2 + - + +
889B ALA* 3.7 14.8 - - - +
906B GLU* 3.5 32.0 + - + +
907B ASP* 3.1 21.0 + - + +
908B VAL 3.0 0.4 + - - -
909B VAL* 1.3 81.9 - - + +
911B TYR* 1.3 64.2 + - + +
912B LEU 3.2 7.8 + - - +
926B LEU* 5.2 4.5 - - + -
937B THR* 3.6 4.9 + - - -
938B ALA* 2.7 50.5 + - + +
939B ASN* 3.2 21.0 + - - +
940B SER* 3.8 1.4 + - - -
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Residues in contact with TYR 911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906B GLU* 3.6 31.7 + - + +
907B ASP 4.1 2.0 - - - -
908B VAL* 3.0 43.3 + - + +
910B ARG* 1.3 81.1 - - - +
912B LEU* 1.3 68.7 + - + +
913B THR* 4.1 0.9 + - - -
937B THR* 4.8 1.4 + - - -
939B ASN* 3.1 29.7 + - - +
943B LYS* 3.8 0.7 - - - -
953B THR* 5.7 0.2 - - - +
955B GLU* 3.8 29.8 - - + -
956B TYR* 3.4 33.3 - - - +
959B SER* 3.4 30.2 + - - -
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Residues in contact with LEU 912 (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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908B VAL 4.5 1.3 + - - +
909B VAL 3.8 12.2 + - - +
910B ARG* 3.2 10.2 - - - +
911B TYR* 1.3 92.7 - - + +
913B THR* 1.3 68.9 + - - +
914B LEU* 3.7 7.8 + - - +
937B THR* 4.2 7.4 + - - -
938B ALA 5.1 0.3 + - - -
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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