Contacts of the helix formed by residues 884 - 893 (chain E) in PDB entry 6V3O
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 ASP 884 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135E GLY 4.6 6.4 - - - +
136E SER* 4.3 23.1 + - - -
651E PRO* 6.1 0.5 - - - +
881E LEU* 3.0 28.8 + - + +
883E GLY* 1.3 78.3 - - - +
885E PRO* 1.3 62.9 - - - +
886E PHE* 3.7 7.8 + - - +
887E LEU* 3.0 46.0 + - + +
888E LYS* 3.1 15.9 + - - +
1004E FLC 5.3 2.1 - - - +
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Residues in contact with PRO 885 (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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28E VAL* 4.1 18.7 - - + +
881E LEU 4.0 2.7 - - - +
882E GLU 4.2 7.6 - - - +
883E GLY 3.5 8.7 - - - +
884E ASP* 1.3 88.7 - - - +
886E PHE* 1.3 75.1 + - + +
888E LYS* 3.8 11.2 - - + +
889E GLN* 2.9 31.0 + - - +
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Residues in contact with PHE 886 (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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28E VAL* 3.3 48.0 - - + -
29E SER* 3.9 13.0 - - - -
120E ARG* 3.5 35.0 - - - +
126E LEU* 4.3 24.5 - - + -
136E SER* 5.3 3.1 - - - +
138E THR* 3.9 33.4 - - + -
884E ASP* 3.2 6.2 - - - +
885E PRO* 1.3 91.1 - - + +
887E LEU* 1.3 63.0 + - - +
889E GLN* 3.3 8.0 + - - +
890E GLY* 3.0 19.8 + - - -
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Residues in contact with LEU 887 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E GLU* 6.1 0.7 - - - +
647E ARG* 4.2 11.4 - - - +
651E PRO* 6.0 0.7 - - + -
831E MET* 4.2 15.5 - - + -
881E LEU* 3.7 30.3 - - + -
884E ASP* 3.0 34.7 + - + +
886E PHE* 1.3 75.1 - - - +
888E LYS* 1.3 62.9 + - - +
890E GLY* 3.2 3.5 + - - -
891E LEU* 3.0 51.5 + - + +
1004E FLC 4.2 32.1 - - + +
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Residues in contact with LYS 888 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834E ALA* 5.6 2.9 - - + -
879E ASP* 4.6 11.2 + - - +
880E ILE* 2.9 38.5 + - + +
881E LEU* 4.0 27.7 + - + -
882E GLU* 4.6 5.9 - - - +
884E ASP 3.1 14.7 + - - +
885E PRO* 3.9 9.4 - - + +
886E PHE 3.3 0.2 - - - -
887E LEU* 1.3 78.0 - - - +
889E GLN* 1.3 62.6 + - - +
891E LEU* 4.1 3.5 - - + +
892E VAL* 3.1 31.3 + - + +
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Residues in contact with GLN 889 (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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24E VAL* 3.7 26.0 - - + +
26E GLY 4.0 2.3 - - - +
28E VAL* 3.6 29.0 - - + +
32E ASP* 2.9 32.9 + - - +
34E LEU* 3.5 24.0 - - - +
35E ILE* 5.1 5.2 - - - +
120E ARG* 4.2 5.7 - - - +
885E PRO 2.9 18.4 + - - +
886E PHE* 3.8 4.9 + - - +
888E LYS* 1.3 78.5 - - - +
890E GLY* 1.3 62.0 + - - +
891E LEU 3.4 0.2 + - - -
892E VAL* 3.7 5.1 - - - +
893E LEU* 3.2 39.1 + - + +
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Residues in contact with GLY 890 (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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34E LEU* 4.6 11.0 - - - -
113E GLU* 3.8 25.5 - - - +
886E PHE 3.0 14.5 + - - -
887E LEU* 3.2 3.8 + - - -
889E GLN* 1.3 78.4 - - - +
891E LEU* 1.3 64.4 + - - +
893E LEU* 3.9 5.5 + - - +
894E ARG* 3.5 22.2 + - - +
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Residues in contact with LEU 891 (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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831E MET* 4.3 4.9 - - + +
834E ALA* 4.2 25.1 - - + +
835E LYS* 3.8 35.7 - - + -
881E LEU* 4.3 3.1 - - + -
887E LEU* 3.0 42.2 + - + +
888E LYS* 4.1 3.6 - - + +
889E GLN 3.3 0.2 - - - -
890E GLY* 1.3 75.1 - - - +
892E VAL* 1.3 66.3 + - - +
893E LEU 3.2 0.2 - - - -
894E ARG* 3.0 51.5 + - - +
895E ASN* 3.6 10.8 + - - +
1004E FLC 3.6 11.9 - - - +
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Residues in contact with VAL 892 (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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23E LEU* 3.9 30.5 - - + +
24E VAL* 4.1 23.1 - - + -
72E GLU* 4.7 6.7 - - + +
888E LYS* 3.1 28.6 + - + +
889E GLN* 3.7 8.1 - - - +
891E LEU* 1.3 77.7 - - - +
893E LEU* 1.3 64.9 + - + +
895E ASN* 3.2 29.9 + - - +
896E PRO* 3.4 10.0 - - - +
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Residues in contact with LEU 893 (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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20E LEU* 3.9 25.5 - - + +
23E LEU* 4.6 4.9 - - + -
24E VAL* 3.7 17.0 - - + -
34E LEU* 3.7 33.2 - - + -
35E ILE* 3.7 30.1 - - + -
38E ASP* 4.0 17.9 - - - +
109E ALA* 5.0 2.0 - - - +
889E GLN* 3.2 29.3 + - + +
890E GLY 4.3 4.0 - - - +
891E LEU 3.2 1.0 - - - -
892E VAL* 1.3 76.3 - - + +
894E ARG* 1.3 59.3 + - - +
895E ASN 3.5 0.2 - - - -
896E PRO* 3.8 7.8 - - - +
897E TYR* 3.4 19.2 - - - -
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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