Contacts of the helix formed by residues 907 - 912 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877A LEU* 6.2 1.5 - - + +
882A ARG* 3.7 9.4 + - - +
886A GLU* 5.5 0.2 - - - +
906A GLU* 1.3 77.9 - - - +
908A VAL* 1.3 68.6 + - - +
909A VAL* 3.1 27.5 + - + +
910A ARG* 3.2 29.4 + - + +
911A TYR* 4.0 2.5 - - - -
987A TYR* 2.7 42.0 + - + +
990A MET* 4.9 8.6 - - - +
991A LEU* 4.4 10.7 - - + +
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Residues in contact with VAL 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A GLU 3.4 4.2 + - - +
907A ASP* 1.3 69.6 + - - +
909A VAL* 1.3 62.7 + - - +
910A ARG 2.9 7.2 + - - -
911A TYR* 3.0 41.2 + - + +
912A LEU* 4.5 2.6 + - - +
953A THR* 6.2 1.3 - - + -
955A GLU* 3.6 32.3 - - + +
993A ARG* 6.3 1.3 - - - +
1294A ASN* 5.5 4.0 - - - +
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Residues in contact with VAL 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ARG* 4.2 14.6 - - - +
907A ASP* 3.1 29.5 + - + +
908A VAL* 1.3 78.2 - - - +
910A ARG* 1.3 64.1 + - + +
911A TYR 3.5 0.5 + - - -
912A LEU* 3.7 18.2 + - - +
914A LEU* 6.1 0.5 - - - +
925A THR* 3.7 34.7 - - + +
926A LEU* 4.2 13.0 - - + +
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Residues in contact with ARG 910 (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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877A LEU* 3.3 21.8 - - - +
885A HIS* 2.7 40.7 + - - -
886A GLU* 3.4 30.2 + - + +
889A ALA* 3.7 13.7 - - - +
906A GLU* 3.5 31.3 + - + +
907A ASP* 3.2 21.0 + - + +
908A VAL 2.9 0.4 + - - -
909A VAL* 1.3 83.1 - - + +
911A TYR* 1.3 63.5 + - + +
912A LEU 3.1 6.7 + - - +
926A LEU* 5.1 5.4 - - + -
937A THR* 3.6 4.2 + - - -
938A ALA* 2.8 51.2 + - + +
939A ASN* 3.1 22.5 + - - +
940A SER* 3.8 1.4 + - - -
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Residues in contact with TYR 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A GLU* 3.6 20.7 + - + +
907A ASP 4.0 8.5 - - - -
908A VAL* 3.0 43.9 + - + +
910A ARG* 1.3 80.2 - - - +
912A LEU* 1.3 68.9 + - + +
913A THR* 4.1 0.9 + - - -
937A THR* 4.6 2.8 + - - -
939A ASN* 3.2 26.9 + - - +
943A LYS* 3.9 5.6 - - - -
955A GLU* 3.8 31.2 - - + -
956A TYR* 3.4 33.3 - - - +
959A SER* 3.5 28.7 + - - -
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Residues in contact with LEU 912 (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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908A VAL 5.5 1.8 - - - +
909A VAL* 3.7 13.7 + - - +
910A ARG* 3.1 9.5 - - - +
911A TYR* 1.3 90.8 - - + +
913A THR* 1.3 69.5 + - - +
914A LEU* 3.7 7.4 + - - +
915A ASP* 6.0 1.6 - - - +
937A THR* 3.9 7.8 + - - -
938A ALA 5.1 0.7 + - - -
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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