Contacts of the helix formed by residues 850 - 861 (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 GLU 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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769A LEU 4.3 9.9 - - - +
846A LYS* 2.9 52.9 + - + +
847A GLN 4.6 1.1 - - - -
848A ARG 3.7 0.8 - - - -
849A LYS* 1.3 83.8 - - + +
851A SER* 1.3 65.6 + - - +
852A ARG* 3.1 5.2 - - + +
853A PHE* 3.1 15.5 + - + +
854A GLN* 3.1 21.8 + - - +
771E PRO* 3.5 36.8 - - + +
773E GLU* 3.5 8.5 - - - +
774E GLU* 5.1 0.3 - - - +
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Residues in contact with SER 851 (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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849A LYS 4.0 1.4 + - - -
850A GLU* 1.3 72.1 - - - +
852A ARG* 1.3 65.1 + - - +
854A GLN* 3.6 13.5 + - - +
855A LEU* 2.9 38.0 + - - +
772E ARG* 5.7 2.1 - - - +
773E GLU* 2.9 24.5 + - - -
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Residues in contact with ARG 852 (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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767A GLU* 3.0 26.8 + - - +
768A ASN 3.2 28.7 + - - -
769A LEU* 3.8 23.7 - - + +
850A GLU* 3.1 7.5 - - + +
851A SER* 1.3 82.7 + - - +
853A PHE* 1.3 61.9 + - - +
855A LEU* 3.5 9.8 + - + +
856A PHE* 3.3 20.3 + - - +
768E ASN* 3.2 40.2 + - - +
771E PRO* 6.0 4.3 - - + -
772E ARG* 5.5 17.9 - - + +
773E GLU* 4.5 3.0 + - - +
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Residues in contact with PHE 853 (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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764A MET* 4.9 0.9 - - + -
769A LEU* 3.9 32.1 - - + +
770A MET* 3.7 18.4 - - + -
843A ILE* 3.7 41.5 - - + -
846A LYS* 3.5 40.8 - - + +
847A GLN* 3.6 13.9 - - + -
850A GLU* 3.1 26.2 + - + +
852A ARG* 1.3 76.5 - - - +
854A GLN* 1.3 57.6 + - - +
855A LEU 2.9 10.1 + - - -
856A PHE* 2.9 14.6 + - - +
857A MET* 3.0 39.6 + - + +
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Residues in contact with GLN 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A GLN* 2.8 52.2 + - + +
848A ARG* 4.5 7.1 + - - +
850A GLU 3.1 7.6 + - - +
851A SER* 4.0 13.6 - - - +
853A PHE* 1.3 79.6 - - - +
855A LEU* 1.3 62.1 + - + +
857A MET* 4.0 2.8 - - - +
858A GLN* 3.4 32.8 + - - +
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Residues in contact with LEU 855 (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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851A SER* 2.9 33.8 + - - +
852A ARG* 3.9 9.0 - - + +
853A PHE 3.0 1.2 - - - -
854A GLN* 1.3 78.1 - - + +
856A PHE* 1.3 67.9 + - - +
857A MET 3.2 0.2 - - - -
858A GLN* 3.3 24.7 + - - +
859A GLU* 2.9 25.9 + - - +
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Residues in contact with PHE 856 (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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759A ILE 4.0 10.1 - - - -
760A PHE* 4.4 1.8 - + - -
763A ARG* 3.7 49.1 - - + -
764A MET* 3.5 27.4 - - + -
767A GLU* 4.2 9.0 - - - -
769A LEU* 3.6 42.4 - - + -
852A ARG 3.3 5.0 + - - +
853A PHE* 2.9 7.6 + + - +
855A LEU* 1.3 79.2 - - - +
857A MET* 1.3 84.9 + - + +
859A GLU* 3.1 8.7 + - - +
860A ALA* 2.9 35.4 + - + +
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Residues in contact with MET 857 (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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760A PHE* 4.2 14.6 - - + -
764A MET* 3.1 36.1 - - + -
843A ILE* 4.9 5.4 - - + -
847A GLN* 3.1 37.9 - - + +
853A PHE* 3.0 36.5 + - + +
854A GLN 4.0 5.8 - - - +
856A PHE* 1.3 102.5 - - + +
858A GLN* 1.3 58.9 + - + +
860A ALA* 3.4 2.0 + - - +
861A GLU* 3.1 45.1 + - - +
871A LEU* 4.5 9.2 - - + -
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Residues in contact with GLN 858 (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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854A GLN* 3.4 29.1 + - - +
855A LEU* 3.3 28.5 + - - +
857A MET* 1.3 78.5 - - + +
859A GLU* 1.3 61.7 + - + +
861A GLU* 4.4 8.5 - - - +
862A SER* 3.4 18.2 + - - -
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Residues in contact with GLU 859 (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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763A ARG* 3.0 28.3 + - - +
855A LEU 2.9 18.0 + - - +
856A PHE* 3.1 6.6 + - - +
858A GLN* 1.3 79.8 - - - +
860A ALA* 1.3 62.0 + - - +
862A SER* 2.8 23.8 + - - +
863A HIS* 3.8 3.1 + - - +
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Residues in contact with ALA 860 (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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759A ILE* 3.5 30.6 - - + +
760A PHE* 3.7 18.8 - - + -
763A ARG* 3.7 19.3 - - - +
856A PHE* 2.9 20.0 + - + +
857A MET 4.0 1.1 - - - +
859A GLU* 1.3 74.0 - - - +
861A GLU* 1.3 55.8 + - - +
862A SER 3.0 4.9 - - - -
863A HIS* 3.0 27.9 + - - +
866A CYS* 3.5 3.0 - - - -
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Residues in contact with GLU 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A PHE* 4.1 10.8 - - + -
847A GLN* 4.4 5.4 + - - -
857A MET* 3.1 31.6 + - - +
858A GLN* 4.7 5.8 - - - +
860A ALA* 1.3 75.0 - - - +
862A SER* 1.3 61.7 + - - +
863A HIS 3.2 5.6 - - - +
866A CYS* 4.0 13.9 - - - +
868A ARG* 4.8 8.8 - - - -
869A LEU 3.9 7.5 - - - +
870A GLN* 3.5 48.0 + - + +
871A LEU* 3.1 27.0 + - - +
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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