Contacts of the helix formed by residues 864 - 873 (chain A) in PDB entry 1TXD
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 864 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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788A ARG* 4.8 0.9 - - - +
792A ILE* 4.0 21.8 - - + -
795A LEU* 5.0 2.0 - - + -
796A PHE* 3.8 33.2 - - + -
852A VAL* 4.4 10.1 - - + -
861A ILE* 4.7 1.6 - - + -
862A ASP 4.5 4.5 - - - +
863A GLN* 1.3 74.1 - - - +
865A GLY* 1.3 66.8 + - - +
866A GLU 3.1 3.4 - - - -
867A ASP* 3.0 30.8 + - + +
868A LEU* 3.0 40.3 + - + +
871A TRP* 4.4 2.9 - - + -
947A ILE* 4.4 17.5 - - + -
956A GLU* 2.8 16.1 + - - +
960A VAL* 4.5 1.1 - - + -
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Residues in contact with GLY 865 (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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863A GLN* 5.2 0.2 - - - +
864A ILE* 1.3 76.5 - - - +
866A GLU* 1.3 56.7 + - - +
868A LEU* 3.2 6.7 + - - +
869A LEU* 2.9 31.2 + - - +
956A GLU* 3.0 21.0 + - - -
959A LYS* 3.8 22.0 - - - +
960A VAL* 4.0 15.0 - - - -
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Residues in contact with GLU 866 (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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863A GLN* 5.6 0.8 - - + +
864A ILE 3.1 1.2 - - - +
865A GLY* 1.3 75.6 - - - +
867A ASP* 1.3 61.7 + - - +
869A LEU* 3.3 22.4 + - - +
870A THR* 3.0 33.0 + - - +
956A GLU* 4.7 0.6 + - - -
959A LYS* 2.8 38.7 + - + +
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Residues in contact with ASP 867 (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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852A VAL* 3.8 9.6 - - - +
855A ARG* 2.9 40.6 + - - -
863A GLN 3.7 0.7 - - - +
864A ILE* 3.0 22.9 + - + +
866A GLU* 1.3 77.9 - - - +
868A LEU* 1.3 60.1 + - - +
870A THR* 3.0 8.7 + - - -
871A TRP* 2.9 61.0 + - + +
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Residues in contact with LEU 868 (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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795A LEU* 3.9 19.5 - - + -
864A ILE* 3.0 35.9 + - + +
865A GLY* 3.4 6.7 - - - +
867A ASP* 1.3 75.3 - - - +
869A LEU* 1.3 57.6 + - - +
871A TRP* 3.6 29.8 - - + -
872A PHE* 3.0 37.7 + - + +
944A LEU* 4.2 21.1 - - + -
947A ILE* 4.7 5.4 - - + -
960A VAL* 4.0 31.4 - - + -
963A ALA* 3.7 14.8 - - + +
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Residues in contact with LEU 869 (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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865A GLY 2.9 13.4 + - - +
866A GLU* 3.5 24.0 - - - +
868A LEU* 1.3 77.1 - - - +
870A THR* 1.3 57.1 + - - +
873A SER* 2.2 53.1 + - - +
959A LYS* 3.8 35.7 - - + +
962A LYS* 3.9 28.9 - - + -
963A ALA* 3.7 30.3 - - + +
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Residues in contact with THR 870 (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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848A GLN* 4.9 9.6 - - - +
866A GLU* 3.0 17.8 + - - +
867A ASP* 3.4 11.6 - - - -
869A LEU* 1.3 78.4 - - - +
871A TRP* 1.3 68.3 + - + +
873A SER 3.9 3.4 - - - +
876A GLY* 3.7 16.6 + - - -
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Residues in contact with TRP 871 (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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796A PHE* 4.1 12.6 - + - -
845A LEU* 3.6 23.6 - - + +
848A GLN* 3.4 62.4 + - + +
849A MET* 3.5 30.5 - - + -
852A VAL* 3.9 12.6 - - + -
864A ILE* 4.4 2.7 - - + -
867A ASP* 2.9 38.6 + - + +
868A LEU* 3.6 32.3 - - + -
870A THR* 1.3 82.9 - - - +
872A PHE* 1.3 83.3 + + + +
873A SER 3.8 0.2 - - - -
876A GLY* 3.4 21.5 - - - +
880A LEU* 5.1 2.1 - - - +
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Residues in contact with PHE 872 (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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795A LEU* 5.1 4.7 - - + -
845A LEU* 4.3 15.3 - - + -
849A MET* 5.1 0.2 - - + -
868A LEU* 3.0 27.8 + - + +
869A LEU 4.1 0.2 - - - -
871A TRP* 1.3 107.3 - + + +
873A SER* 1.3 57.7 + - - +
877A GLU* 3.4 16.4 - - - +
880A LEU* 3.8 28.5 - - + -
940A TYR* 3.8 31.6 - + - -
944A LEU* 3.8 31.4 - - + -
963A ALA* 4.3 7.9 - - + +
966A HIS* 3.0 22.0 - - - +
967A CYS* 3.5 22.7 - - - -
970A ILE* 4.0 5.3 - - + +
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Residues in contact with SER 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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869A LEU* 2.2 47.1 + - - +
870A THR* 3.9 3.3 - - - +
872A PHE* 1.3 76.9 - - - +
874A GLY* 1.3 72.0 + - - +
875A PRO* 3.4 1.7 - - - +
876A GLY* 3.2 12.6 + - - -
877A GLU* 3.5 8.3 - - - -
962A LYS* 4.8 3.0 + - - -
966A HIS* 3.5 30.5 - - - -
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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