Contacts of the helix formed by residues 824 - 836 (chain A) in PDB entry 1TBF
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 824 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A VIA 4.1 22.9 - - - +
725A LEU* 4.4 18.2 - - + -
728A TYR* 3.7 32.7 + - + -
729A ILE* 4.9 14.6 - - + -
732A ARG* 4.2 9.7 + - - +
765A LEU* 3.6 29.4 - - + -
820A PHE* 3.0 32.6 + - + +
822A ASP 3.4 0.4 - - - -
823A ALA* 1.3 89.7 - - + +
825A CYS* 1.3 64.6 + - - +
826A LEU 3.7 1.6 - - - -
827A GLN* 4.3 4.0 + - - +
828A LEU* 3.8 7.0 + - + +
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Residues in contact with CYS 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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765A LEU* 4.2 11.2 - - - -
768A ILE* 3.8 15.9 - - - -
820A PHE* 3.3 50.0 + - - -
821A ILE* 3.2 10.8 + - + +
824A ILE* 1.3 79.0 - - - +
826A LEU* 1.3 66.0 + - - +
828A LEU* 3.2 4.5 + - - +
829A TYR* 3.1 35.9 + - + -
846A CYS* 3.9 17.9 - - - -
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Residues in contact with LEU 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ILE* 2.9 30.1 + - + +
822A ASP* 4.0 24.2 - - - +
824A ILE 3.7 0.2 - - - -
825A CYS* 1.3 74.2 - - - +
827A GLN* 1.3 60.2 + - - +
829A TYR* 3.3 1.1 + - - -
830A GLU* 2.9 45.3 + - - +
843A LEU* 3.9 16.4 - - + +
846A CYS* 4.1 13.2 - - - -
847A ARG* 3.8 31.6 - - + +
850A ARG* 4.6 8.5 - - - +
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Residues in contact with GLN 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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732A ARG* 6.1 0.3 - - - -
736A PHE* 3.4 47.9 - - + +
822A ASP 5.4 3.8 + - - +
824A ILE 4.3 4.1 + - - +
825A CYS 3.3 0.4 - - - -
826A LEU* 1.3 80.2 - - - +
828A LEU* 1.3 58.4 + - - +
830A GLU* 3.6 17.6 - - + +
831A ALA* 2.9 31.2 + - + +
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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
----------------------------------------------------------
728A TYR* 3.3 31.9 + - + +
735A PHE* 4.7 7.6 - - + -
736A PHE* 4.3 3.6 - - + -
758A MET* 3.9 29.2 - - + +
761A THR* 3.6 30.7 - - + +
762A ALA* 3.6 27.8 - - + +
765A LEU* 4.7 8.3 - - + -
824A ILE 3.8 7.3 + - - +
825A CYS* 3.2 9.8 + - - +
827A GLN* 1.3 79.9 - - - +
829A TYR* 1.3 64.7 + - + +
831A ALA* 3.3 1.7 + - - +
832A LEU* 2.9 28.5 + - + +
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Residues in contact with TYR 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ALA* 2.7 48.0 + - + -
765A LEU* 3.3 10.7 - - + +
766A SER* 3.3 17.5 + - - -
768A ILE* 3.8 13.9 - - + -
769A THR* 3.6 19.7 - - + -
825A CYS* 3.1 33.3 + - + +
828A LEU* 1.3 77.1 - - + +
830A GLU* 1.3 64.9 + - - +
832A LEU* 3.5 6.7 + - + +
833A THR* 3.0 28.6 + - - -
842A LEU* 3.7 33.4 - - + -
843A LEU* 3.8 27.4 - - + +
846A CYS* 4.2 9.2 - - + -
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Residues in contact with GLU 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 LEU* 2.9 41.3 + - - +
827A GLN* 3.6 20.1 - - + +
829A TYR* 1.3 76.6 - - - +
831A ALA* 1.3 62.6 + - - +
833A THR* 3.2 12.6 + - - -
834A HIS* 3.2 25.0 + - + +
843A LEU* 3.8 25.3 - - + +
847A ARG* 5.8 1.4 - - - -
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Residues in contact with ALA 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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735A PHE* 3.6 26.2 - - + -
736A PHE* 3.6 19.7 - - + -
739A ILE* 3.7 17.6 - - + +
827A GLN* 2.9 19.1 + - + +
828A LEU 3.6 2.2 - - - +
830A GLU* 1.3 76.5 - - - +
832A LEU* 1.3 62.9 + - - +
834A HIS* 3.0 21.5 + - - +
835A VAL* 3.3 8.8 + - - +
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Residues in contact with LEU 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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628A ALA* 5.6 0.2 - - + -
634A ILE* 4.2 14.4 - - + -
735A PHE* 4.7 4.1 - - + -
755A PHE* 3.9 31.0 - - + -
759A LEU* 4.4 12.6 - - + -
762A ALA* 4.0 23.6 - - + -
828A LEU* 2.9 19.8 + - + +
829A TYR* 3.9 8.5 - - + +
830A GLU 3.3 0.2 - - - -
831A ALA* 1.3 76.5 - - - +
833A THR* 1.3 57.7 + - - +
835A VAL* 3.1 7.3 + - + +
836A SER 2.9 26.0 + - - +
839A CYS* 3.9 16.8 - - + -
842A LEU* 3.9 28.3 - - + -
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Residues in contact with THR 833 (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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829A TYR 3.0 18.8 + - - -
830A GLU 3.6 5.4 - - - -
831A ALA 3.2 0.2 - - - -
832A LEU* 1.3 76.9 - - - +
834A HIS* 1.3 60.9 + - - +
836A SER 3.2 22.5 - - - -
837A GLU* 3.2 17.6 + - + +
839A CYS* 3.8 5.4 + - - +
840A PHE* 3.6 46.8 + - + -
843A LEU* 3.9 13.3 + - + +
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Residues in contact with HIS 834 (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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739A ILE* 3.5 34.1 - - + +
830A GLU* 3.2 33.1 + - + +
831A ALA* 3.0 11.0 + - - +
833A THR* 1.3 77.4 - - - +
835A VAL* 1.3 61.8 + - - +
836A SER* 4.7 0.2 - - - -
837A GLU 5.1 0.3 + - - -
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Residues in contact with VAL 835 (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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634A ILE* 5.9 0.2 - - + -
637A LYS* 3.6 28.9 + - + -
735A PHE* 4.1 18.6 - - + -
739A ILE* 4.4 4.9 - - + -
744A PHE* 3.8 34.3 - - + -
746A LEU* 4.4 4.5 - - + -
755A PHE* 3.8 28.9 - - + -
831A ALA 3.8 11.2 - - - +
832A LEU* 3.1 7.9 + - + +
834A HIS* 1.3 79.3 - - - +
836A SER* 1.3 59.2 + - - +
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Residues in contact with SER 836 (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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632A GLY 2.7 28.8 + - - -
633A LYS* 4.4 3.6 - - - +
634A ILE* 4.4 7.2 - - - -
637A LYS* 4.2 14.6 + - - +
832A LEU* 2.9 7.6 + - - -
833A THR* 3.2 15.2 - - - +
835A VAL* 1.3 78.8 - - - +
837A GLU* 1.3 64.7 + - - +
838A ASP* 3.5 10.9 + - - -
839A CYS* 2.9 22.0 + - - +
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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