Contacts of the helix formed by residues 656 - 664 (chain E) in PDB entry 6T8G
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 656 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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654E VAL* 4.0 3.6 - - - +
655E SER* 1.3 84.4 - - - +
657E LYS* 1.3 62.4 + - - +
658E ILE* 3.1 23.3 + - - +
659E ASP* 2.5 47.6 + - - +
660E SER 3.4 11.3 + - - -
670E GLU* 3.9 7.1 - - - +
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Residues in contact with LYS 657 (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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382E SER* 6.4 0.2 - - - -
655E SER 3.8 1.2 + - - -
656E SER* 1.3 71.3 - - - +
658E ILE* 1.3 62.8 + - + +
659E ASP 3.3 0.2 - - - -
660E SER* 3.2 6.7 + - - -
661E ARG* 3.0 47.3 + - - +
667E GLY* 4.2 20.9 - - - -
670E GLU* 3.4 34.4 - - + +
671E GLN* 6.1 0.4 - - - +
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Residues in contact with ILE 658 (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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635E VAL* 6.4 1.6 - - + -
656E SER* 3.1 18.8 + - - +
657E LYS* 1.3 81.6 - - + +
659E ASP* 1.3 54.4 + - - +
661E ARG* 3.3 21.0 + - + +
662E THR* 2.5 38.5 + - - +
7G A 3.3 28.9 - - - +
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Residues in contact with ASP 659 (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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467E THR* 5.6 1.9 - - - +
633E PRO* 4.1 22.7 - - + +
634E SER* 4.1 20.0 - - - -
654E VAL* 3.8 24.3 - - + +
655E SER* 4.7 2.8 + - - -
656E SER* 2.5 29.3 + - - +
658E ILE* 1.3 73.2 - - - +
660E SER* 1.3 59.7 + - - +
662E THR* 2.9 24.1 + - - -
663E ILE* 3.0 22.3 + - - +
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Residues in contact with SER 660 (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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654E VAL* 4.2 0.8 - - - +
656E SER 3.4 4.6 + - - -
657E LYS* 3.2 13.4 + - - -
659E ASP* 1.3 79.2 - - - +
661E ARG* 1.3 56.5 + - - +
663E ILE* 4.7 1.1 - - - -
664E LEU* 3.1 23.0 + - - +
665E ASP 3.2 1.9 + - - -
666E GLN 2.5 36.0 + - - +
667E GLY* 4.1 2.2 - - - -
668E GLY 2.6 15.9 + - - -
669E ALA* 2.8 31.4 + - - +
670E GLU* 3.6 10.5 - - - -
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Residues in contact with ARG 661 (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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643E LYS* 4.7 0.7 + - - -
657E LYS* 3.0 33.9 + - - +
658E ILE* 3.3 40.3 + - + +
660E SER* 1.3 75.0 - - - +
662E THR* 1.3 60.0 + - - +
665E ASP* 2.9 25.2 - - - +
666E GLN* 3.8 10.3 - - - +
667E GLY* 4.3 17.0 - - - +
7G A 3.7 25.7 + - - -
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Residues in contact with THR 662 (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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633E PRO 3.3 26.5 - - - +
634E SER* 4.3 3.7 - - - +
635E VAL* 4.1 28.3 - - + +
638E ILE* 4.9 9.6 - - + +
643E LYS* 3.4 16.8 + - - +
658E ILE* 2.5 26.5 + - - +
659E ASP* 2.9 18.8 + - - -
661E ARG* 1.3 78.3 - - - +
663E ILE* 1.3 59.3 + - - +
665E ASP* 3.1 14.2 - - - +
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Residues in contact with ILE 663 (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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463E LEU* 3.7 30.7 - - + +
465E ALA* 3.7 26.2 - - + -
633E PRO* 4.7 12.6 - - + -
638E ILE* 4.6 14.1 - - + -
643E LYS* 4.8 1.6 - - - -
649E ARG* 2.5 50.0 + - + +
650E ILE 4.0 9.2 - - - +
651E ALA* 4.3 18.8 - - + -
654E VAL* 5.5 3.6 - - + -
659E ASP 3.0 16.9 + - - +
660E SER* 4.6 2.2 - - - +
662E THR* 1.3 77.7 - - - +
664E LEU* 1.3 67.1 + - + +
665E ASP* 3.3 2.0 + - - +
669E ALA* 5.4 1.3 - - + -
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Residues in contact with LEU 664 (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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649E ARG* 4.2 16.8 - - + +
651E ALA* 3.7 32.8 - - + +
660E SER 3.1 12.2 + - - +
663E ILE* 1.3 77.4 - - + +
665E ASP* 1.3 69.2 + - - +
666E GLN* 3.3 17.0 + - + +
668E GLY* 4.9 0.9 - - - +
669E ALA* 3.9 12.8 - - + +
679E LEU* 3.8 31.9 - - + +
681E LEU* 3.7 49.7 - - + +
688E PRO* 4.9 8.7 - - + -
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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