Contacts of the helix formed by residues 819 - 835 (chain A) in PDB entry 3T06
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 GLY 819 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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818A ASP* 1.3 79.4 + - - +
820A PRO* 1.3 71.6 - - - +
822A ARG* 3.2 10.0 + - - +
823A GLU* 3.2 26.5 + - - +
908A ARG* 5.4 1.3 - - - +
912A GLN* 5.0 1.6 + - - -
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Residues in contact with PRO 820 (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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818A ASP 3.8 3.6 - - - +
819A GLY* 1.3 79.8 - - - +
821A ALA* 1.3 58.9 + - + +
822A ARG 3.1 1.1 - - - -
823A GLU* 2.9 14.6 + - + +
824A GLU* 2.8 34.9 + - - +
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Residues in contact with ALA 821 (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 LEU 4.2 0.2 - - - +
815A ALA* 3.3 34.1 - - - +
816A ARG* 3.1 35.3 + - - +
818A ASP 3.5 12.3 - - - +
820A PRO* 1.3 80.2 - - + +
822A ARG* 1.3 59.6 + - - +
824A GLU* 3.5 6.4 + - - -
825A LEU* 3.1 10.6 + - - +
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Residues in contact with ARG 822 (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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816A ARG 4.0 2.8 + - - -
817A PHE 3.5 18.8 - - - +
818A ASP 3.6 3.2 + - - -
819A GLY 3.2 17.3 + - - +
820A PRO 3.1 0.8 - - - -
821A ALA* 1.3 75.9 - - - +
823A GLU* 1.3 69.6 + - - +
825A LEU* 3.2 2.3 + - - +
826A GLN* 2.8 60.1 + - - +
912A GLN* 2.7 45.1 + - - +
915A GLU* 3.3 38.3 + - - +
916A ILE* 3.4 24.8 - - + +
919A TYR* 5.0 2.2 - - - +
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Residues in contact with GLU 823 (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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819A GLY 3.4 15.1 - - - +
820A PRO* 2.9 12.9 + - + +
822A ARG* 1.3 84.7 + - - +
824A GLU* 1.3 69.7 + - - +
826A GLN* 3.7 21.4 + - - +
827A GLN* 3.1 39.7 + - - +
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Residues in contact with GLU 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788A ILE* 3.9 18.8 - - + +
816A ARG* 3.6 21.3 + - - +
820A PRO 2.8 15.7 + - - +
821A ALA* 3.7 8.0 - - - +
823A GLU* 1.3 76.7 - - - +
825A LEU* 1.3 62.2 + - - +
827A GLN* 3.7 6.5 - - - +
828A VAL* 3.0 34.4 + - + +
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Residues in contact with LEU 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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785A LEU* 5.8 1.6 - - + -
788A ILE* 3.6 31.2 - - + -
789A HIS* 4.8 9.9 - - + +
816A ARG* 3.9 15.9 - - + +
817A PHE* 4.0 22.2 - - + -
821A ALA 3.1 14.8 + - - +
822A ARG 3.2 2.4 + - - +
824A GLU* 1.3 80.4 - - - +
826A GLN* 1.3 56.2 + - - +
828A VAL* 3.9 3.8 - - + +
829A ALA* 2.8 33.6 + - + +
878A GLU* 4.9 4.5 - - - +
882A LEU* 4.1 22.9 - - + -
885A TYR* 6.1 0.2 - - + -
916A ILE* 3.5 29.8 - - + -
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Residues in contact with GLN 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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822A ARG* 2.8 61.5 + - - +
823A GLU* 3.7 24.1 + - - +
825A LEU* 1.3 74.4 - - - +
827A GLN* 1.3 60.6 + - + +
830A ALA* 2.9 32.2 + - - +
916A ILE* 3.8 24.5 - - + +
919A TYR* 3.1 55.1 - - + +
920A VAL* 4.3 3.7 - - + +
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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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823A GLU* 3.1 34.2 + - - +
824A GLU* 3.7 5.8 + - - +
826A GLN* 1.3 78.8 - - + +
828A VAL* 1.3 63.9 + - + +
830A ALA* 3.4 2.4 + - - +
831A GLN* 3.2 26.2 + - - +
919A TYR* 4.3 17.9 - - + +
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Residues in contact with VAL 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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781A ASN* 3.2 28.2 + - - +
784A GLU* 4.3 12.3 - - + -
785A LEU* 3.8 38.4 - - + +
788A ILE* 4.1 22.4 - - + -
824A GLU* 3.0 28.5 + - + +
825A LEU* 3.9 3.1 - - + +
827A GLN* 1.3 78.5 - - + +
829A ALA* 1.3 60.1 + - - +
831A GLN* 5.3 0.4 - - - -
832A PHE* 3.6 10.7 + - - +
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Residues in contact with ALA 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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785A LEU* 4.7 4.7 - - + -
825A LEU* 2.8 24.3 + - + +
826A GLN* 4.9 0.2 - - - -
828A VAL* 1.3 73.4 - - - +
830A ALA* 1.3 65.9 + - - +
832A PHE* 3.5 4.4 + - - +
833A CYS* 3.2 28.7 + - - +
878A GLU* 4.6 9.4 - - + +
882A LEU* 3.7 29.8 - - + -
916A ILE* 5.9 0.4 - - + -
920A VAL* 4.3 13.7 - - + +
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Residues in contact with ALA 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A GLN 2.9 21.2 + - - +
827A GLN* 3.8 4.3 - - - +
828A VAL 3.3 0.4 - - - -
829A ALA* 1.3 79.6 - - - +
831A GLN* 1.3 57.2 + - - +
834A SER* 2.9 36.4 + - - -
919A TYR* 3.7 20.9 - - + +
920A VAL* 4.4 8.9 - - + +
923A ALA* 3.7 20.6 - - + -
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Residues in contact with GLN 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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780A PRO* 3.3 39.0 + - + +
781A ASN* 2.8 28.1 + - - +
827A GLN 3.2 11.8 + - - +
828A VAL* 5.3 0.3 - - - -
829A ALA 3.3 0.2 - - - -
830A ALA* 1.3 80.1 - - - +
832A PHE* 1.3 61.0 + - - +
834A SER* 3.6 13.6 + - - +
835A TYR* 4.6 3.5 + - - +
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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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753A LEU* 5.5 1.1 - - + -
756A LEU* 4.6 7.4 - - + -
777A ARG 5.6 0.3 - - - +
778A LEU 4.8 3.9 - - - +
779A PHE* 4.3 19.3 - + - -
780A PRO* 4.0 18.1 - - + +
781A ASN* 3.2 25.1 + - - +
782A LEU* 3.9 26.7 - - + -
785A LEU* 3.7 32.8 - - + -
828A VAL 3.6 10.8 + - - +
829A ALA* 3.5 6.7 + - - +
830A ALA 3.3 0.6 - - - -
831A GLN* 1.3 79.9 - - - +
833A CYS* 1.3 67.5 + - - +
835A TYR* 4.7 0.5 + - - +
836A GLN* 3.2 39.7 + - - +
875A ILE* 3.9 21.5 - - + -
878A GLU* 4.3 7.9 - - + -
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Residues in contact with CYS 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 ALA* 3.2 20.6 + - - +
832A PHE* 1.3 92.1 - - - +
834A SER* 1.3 67.4 + - - +
835A TYR 2.8 5.6 + - - -
836A GLN* 3.1 28.6 + - - +
837A SER 4.5 1.0 + - - -
878A GLU* 4.5 6.7 - - - -
879A MET* 4.0 36.6 - - + -
882A LEU* 5.7 0.4 - - - -
920A VAL* 4.4 17.0 - - + -
924A VAL* 3.9 12.2 - - + +
69B LEU* 6.1 0.4 - - + -
72B LEU* 4.9 5.4 - - + +
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Residues in contact with SER 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A ALA* 2.9 21.1 + - - +
831A GLN* 3.6 12.5 + - - +
833A CYS* 1.3 75.5 - - - +
835A TYR* 1.3 62.6 + - - +
837A SER* 5.0 1.0 + - - -
838A ILE* 5.4 0.5 - - - +
923A ALA* 4.0 12.1 - - - +
924A VAL* 3.8 22.3 - - - +
927A THR* 3.2 39.8 + - - +
928A GLU* 4.6 9.0 + - - +
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Residues in contact with TYR 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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777A ARG* 3.6 64.3 + - + +
780A PRO* 5.7 1.3 - - + -
831A GLN 4.6 5.9 + - - +
832A PHE 4.7 0.9 + - - +
833A CYS 3.0 0.4 - - - -
834A SER* 1.3 85.0 + - - +
836A GLN* 1.3 65.7 + - - +
837A SER 3.2 2.7 - - - -
838A ILE* 2.8 55.8 + - + +
839A ALA* 3.4 11.3 + - + -
842A LEU* 5.9 1.8 - - + +
927A THR* 3.6 20.6 - - + -
931A HIS* 3.9 17.7 - + + -
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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
------------------------------------------------------------
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