Contacts of the helix formed by residues 850 - 862 (chain E) 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 GLU 850 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771A PRO* 3.3 39.2 - - + +
773A GLU* 3.8 7.6 - - + +
774A GLU* 4.9 1.6 - - - +
769E LEU 4.3 8.8 - - - +
846E LYS* 2.8 60.1 + - + +
847E GLN 3.6 8.3 - - - +
849E LYS* 1.3 79.3 - - + +
851E SER* 1.3 63.4 + - - +
852E ARG* 4.6 3.1 - - + +
853E PHE* 3.8 16.7 + - + +
854E GLN* 3.4 15.2 + - - +
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Residues in contact with SER 851 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772A ARG* 5.0 7.8 - - - +
773A GLU* 2.9 22.9 + - - -
850E GLU* 1.3 70.2 - - - +
852E ARG* 1.3 73.2 + - - +
853E PHE 3.1 1.6 - - - -
854E GLN* 3.4 11.3 + - - +
855E LEU* 3.1 32.7 + - - +
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Residues in contact with ARG 852 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A ASN* 3.4 43.8 + - - +
771A PRO* 6.1 4.0 - - + -
772A ARG* 5.1 21.7 - - + +
773A GLU* 5.1 1.0 + - - +
767E GLU* 2.6 36.5 + - - +
768E ASN 3.2 25.3 + - - -
769E LEU* 3.8 21.7 - - + +
850E GLU* 3.5 3.5 - - + +
851E SER* 1.3 85.0 + - - +
853E PHE* 1.3 60.2 + - - +
855E LEU* 3.8 5.8 - - - +
856E PHE* 3.3 21.7 + - - +
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Residues in contact with PHE 853 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764E MET* 3.9 21.8 - - + -
769E LEU* 4.2 27.8 - - + +
770E MET* 3.8 29.4 - - + -
843E ILE* 3.8 20.0 - - + -
846E LYS* 3.6 24.9 - - + +
847E GLN* 3.7 29.4 - - + -
850E GLU* 3.8 27.3 + - + +
851E SER 3.1 0.6 - - - -
852E ARG* 1.3 76.6 - - - +
854E GLN* 1.3 63.3 + - - +
855E LEU 3.0 5.4 + - - -
856E PHE* 3.0 10.5 + + - +
857E MET* 3.0 37.8 + - + +
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Residues in contact with GLN 854 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847E GLN* 3.2 44.3 + - + +
850E GLU 3.4 9.2 + - - +
851E SER* 3.4 11.3 + - - +
853E PHE* 1.3 78.9 - - - +
855E LEU* 1.3 67.0 + - - +
857E MET* 3.7 9.4 - - - +
858E GLN* 2.8 51.7 + - + +
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Residues in contact with LEU 855 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851E SER* 3.1 22.2 + - - +
852E ARG* 3.8 6.7 - - - +
853E PHE 3.0 0.8 + - - -
854E GLN* 1.3 88.1 - - - +
856E PHE* 1.3 63.6 + - - +
857E MET 3.2 0.2 - - - -
858E GLN* 3.5 14.1 + - - +
859E GLU* 3.3 25.0 + - - +
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Residues in contact with PHE 856 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759E ILE 4.1 10.5 - - - -
760E PHE* 4.4 1.8 - - - -
763E ARG* 3.8 51.1 - - + -
764E MET* 3.6 27.8 - - + -
767E GLU* 5.1 1.6 - - - -
769E LEU* 3.6 35.9 - - + -
852E ARG* 3.3 12.1 + - + +
853E PHE* 3.0 13.8 + + - +
855E LEU* 1.3 76.8 - - - +
857E MET* 1.3 90.7 + - + +
859E GLU* 3.3 7.2 + - - +
860E ALA* 3.0 27.7 + - + +
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Residues in contact with MET 857 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760E PHE* 3.9 23.6 - - + -
764E MET* 3.2 23.6 - - + -
843E ILE* 5.7 2.9 - - - -
847E GLN* 3.8 32.8 - - - +
853E PHE* 3.0 28.1 + - + +
854E GLN 3.7 9.9 - - - +
856E PHE* 1.3 111.6 - - + +
858E GLN* 1.3 64.7 + - + +
859E GLU 3.0 1.6 - - - -
860E ALA* 4.8 0.4 - - - -
861E GLU* 2.9 46.6 + - - +
871E LEU* 4.8 8.5 - - - -
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Residues in contact with GLN 858 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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847E GLN* 6.1 1.3 - - - +
854E GLN* 2.8 41.0 + - + +
855E LEU* 3.8 17.7 + - - +
856E PHE 3.4 0.4 - - - -
857E MET* 1.3 79.2 - - - +
859E GLU* 1.3 56.8 + - - +
861E GLU* 4.6 4.1 - - - +
862E SER* 3.0 29.3 + - - -
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Residues in contact with GLU 859 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763E ARG* 3.2 32.7 + - - +
855E LEU* 3.3 14.4 + - - +
856E PHE* 3.6 11.0 - - - +
857E MET 3.0 0.6 - - - -
858E GLN* 1.3 78.9 - - - +
860E ALA* 1.3 67.9 + - - +
862E SER* 3.3 17.3 + - - +
863E HIS* 3.3 8.7 + - - +
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Residues in contact with ALA 860 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759E ILE* 3.5 34.5 - - + +
760E PHE* 3.9 16.2 - - + -
763E ARG* 4.4 9.6 - - - +
856E PHE* 3.0 25.4 + - + +
857E MET* 4.1 1.3 - - - +
859E GLU* 1.3 75.9 - - - +
861E GLU* 1.3 59.5 + - - +
863E HIS* 2.8 30.0 + - - +
866E CYS* 3.4 7.5 - - - -
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Residues in contact with GLU 861 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760E PHE* 4.0 18.4 - - + -
847E GLN* 5.1 5.8 + - - +
857E MET* 2.9 32.6 + - - +
858E GLN* 4.6 4.0 - - - +
860E ALA* 1.3 77.6 - - - +
862E SER* 1.3 57.2 + - - +
863E HIS 3.0 10.4 + - - +
866E CYS* 3.6 18.1 - - - +
868E ARG* 5.1 7.1 - - - -
869E LEU 4.2 6.6 - - - +
870E GLN* 3.0 46.0 + - - +
871E LEU* 3.3 20.6 + - - +
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Residues in contact with SER 862 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858E GLN 3.0 21.6 + - - -
859E GLU* 3.3 10.8 + - - +
860E ALA 3.2 0.6 - - - -
861E GLU* 1.3 75.6 - - - +
863E HIS* 1.3 64.2 + - - +
864E PRO* 3.7 3.5 - - - +
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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