Contacts of the helix formed by residues 824 - 833 (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 SER 824 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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823A LEU* 1.3 75.6 - - - +
825A PRO* 1.3 76.6 - - - +
826A SER* 3.3 7.9 + - - -
827A GLU* 2.7 38.7 + - - +
828A LEU* 3.0 23.8 + - - +
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Residues in contact with PRO 825 (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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823A LEU 4.7 0.4 - - - +
824A SER* 1.3 89.6 - - - +
826A SER* 1.3 60.7 + - - +
828A LEU* 3.5 12.1 - - + +
829A ARG* 3.2 23.9 + - - +
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Residues in contact with SER 826 (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 SER* 3.1 6.9 + - - -
825A PRO* 1.3 79.3 - - - +
827A GLU* 1.3 59.8 + - - +
829A ARG* 3.4 30.3 + - - +
830A LYS* 2.8 36.1 + - - +
897A MET* 5.6 1.8 - - - +
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Residues in contact with GLU 827 (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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822A ILE 4.2 3.1 - - - +
823A LEU* 3.3 23.5 - - + +
824A SER* 2.7 40.9 + - - +
826A SER* 1.3 73.7 - - - +
828A LEU* 1.4 60.7 + - - +
830A LYS* 3.2 5.6 + - - +
831A ILE* 2.9 35.6 + - - +
897A MET* 4.3 17.7 - - + -
901A ARG* 3.2 47.4 + - - -
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Residues in contact with LEU 828 (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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814A TYR* 4.1 20.8 - - + +
817A VAL* 4.0 26.7 - - + -
818A SER* 4.5 18.6 - - - +
823A LEU* 4.0 24.1 - - + +
824A SER 3.0 21.0 + - - +
825A PRO* 3.5 13.5 - - + +
827A GLU* 1.4 75.3 - - - +
829A ARG* 1.3 56.5 + - - +
832A PHE* 2.9 49.1 + - + +
833A SER 3.7 0.3 + - - -
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Residues in contact with ARG 829 (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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825A PRO 3.2 10.7 + - - +
826A SER* 3.6 35.0 + - - +
827A GLU 3.2 0.2 - - - -
828A LEU* 1.3 77.8 - - - +
830A LYS* 1.3 73.9 + - + +
833A SER* 3.0 37.7 + - - +
890A ASN* 3.9 1.2 + - - -
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Residues in contact with LYS 830 (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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826A SER* 2.8 25.8 + - - +
827A GLU 3.2 4.2 + - - +
829A ARG* 1.3 89.9 - - + +
831A ILE* 1.4 59.1 + - - +
890A ASN* 3.0 24.8 + - - +
893A PHE* 3.8 45.9 - - + +
894A ALA* 3.2 14.5 + - - +
897A MET* 4.1 30.5 - - + -
988A GLU* 4.5 11.1 + - - +
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Residues in contact with ILE 831 (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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823A LEU* 4.0 24.9 - - + -
827A GLU 2.9 20.1 + - - +
828A LEU 4.1 1.8 - - - +
829A ARG 3.2 0.2 - - - -
830A LYS* 1.4 76.5 - - - +
832A PHE* 1.3 88.4 + - + +
833A SER* 3.8 0.4 + - - -
887A PHE* 5.3 3.8 - - - -
890A ASN* 4.3 1.4 + - - -
894A ALA* 2.9 22.8 - - - +
897A MET* 3.4 29.8 - - + +
898A ILE* 3.6 38.1 - - + +
901A ARG* 4.6 1.3 - - + -
908A PHE* 4.1 12.8 - - + -
926A LEU* 4.6 2.7 - - + -
930A ILE* 4.6 7.4 - - + +
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Residues in contact with PHE 832 (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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809A LEU* 4.8 6.7 - - + -
813A PHE* 4.0 26.2 - - + -
814A TYR* 3.4 49.6 - + + -
817A VAL* 3.9 23.6 - - + -
823A LEU* 4.4 5.2 - - + -
828A LEU* 2.9 21.6 + - + +
831A ILE* 1.3 99.5 - - + +
833A SER* 1.3 75.7 + - - +
834A ASN 3.0 0.5 + - - -
835A LEU* 2.8 36.3 + - + +
887A PHE* 3.9 8.1 - + - -
908A PHE* 6.0 2.7 - + - -
911A PHE* 6.0 1.1 - + - -
926A LEU* 4.5 15.9 - - + -
930A ILE* 5.4 4.9 - - + -
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Residues in contact with SER 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A TYR* 6.0 1.2 - - - -
828A LEU 3.7 2.4 + - - -
829A ARG* 3.0 31.3 + - - +
831A ILE 5.1 0.2 + - - -
832A PHE* 1.3 81.9 + - - +
834A ASN* 1.3 75.7 + - - -
835A LEU* 3.5 1.7 + - - +
836A GLU* 4.8 3.1 + - - +
886A THR* 5.0 7.4 - - - -
887A PHE* 3.6 15.8 - - - -
890A ASN* 3.6 23.7 + - - +
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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