Contacts of the helix formed by residues 882 - 891 (chain B) in PDB entry 6FF7
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 882 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A TYR* 5.4 11.7 - - - -
880B SER 3.1 2.6 + - - -
881B PHE* 1.3 73.7 - - - +
883B PHE* 1.3 64.3 + - - +
884B GLU 3.6 1.3 - - - -
885B THR* 4.0 14.5 - - - -
886B ASP* 3.3 24.9 + - - +
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Residues in contact with PHE 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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879B ASP 4.8 3.4 - - - +
880B SER* 3.3 29.1 + - - +
881B PHE 4.6 0.2 - - - -
882B GLY* 1.3 75.3 - - - +
884B GLU* 1.3 62.2 + - - +
886B ASP* 4.2 1.1 - - - +
887B LEU* 2.9 31.4 + - - +
897B SER* 5.8 0.9 - - - -
899B SER* 6.3 3.1 - - - -
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Residues in contact with GLU 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882B GLY 3.6 0.2 - - - -
883B PHE* 1.3 78.1 - - - +
885B THR* 1.3 57.6 + - - +
887B LEU* 3.7 5.8 - - - +
888B ARG* 2.9 31.2 + - - +
897B SER* 4.2 29.4 - - - +
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Residues in contact with THR 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLU* 5.0 9.0 - - - -
312A TYR* 5.4 4.5 - - - -
315A ALA* 4.4 22.9 - - - -
882B GLY* 4.0 15.8 - - - -
883B PHE 3.2 0.8 - - - -
884B GLU* 1.3 80.4 - - - +
886B ASP* 1.3 57.1 + - - +
888B ARG* 3.8 3.6 - - - +
889B THR* 2.9 28.3 + - - -
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Residues in contact with ASP 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU* 6.5 0.4 - - - -
849B VAL* 6.0 5.8 - - + -
882B GLY 3.3 16.9 + - - +
883B PHE* 4.3 1.6 - - - +
885B THR* 1.3 79.3 - - - +
887B LEU* 1.3 57.7 + - - +
889B THR* 3.4 8.9 - - - -
890B HIS* 3.0 30.1 + - - +
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Residues in contact with LEU 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845B ALA* 5.8 0.5 - - - +
846B VAL* 6.1 7.6 - - + +
849B VAL* 5.6 10.1 - - + +
883B PHE 2.9 21.6 + - - +
884B GLU* 3.7 8.1 - - - +
885B THR 3.2 0.2 - - - -
886B ASP* 1.3 77.4 - - - +
888B ARG* 1.3 61.0 + - - +
890B HIS* 3.7 3.4 + - - +
891B THR* 3.3 24.8 + - - -
895B ALA* 4.7 7.9 - - + +
896B PHE* 6.3 1.1 - - - -
897B SER* 5.0 12.3 - - - +
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Residues in contact with ARG 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A TYR* 5.3 14.3 - - + +
884B GLU 2.9 18.1 + - - +
885B THR* 3.9 4.3 - - - +
887B LEU* 1.3 74.7 - - - +
889B THR* 1.3 61.4 + - - +
891B THR* 4.8 1.6 - - - -
892B GLN* 3.3 3.3 + - - -
893B GLY* 3.1 34.4 + - - +
895B ALA 4.4 18.6 + - - +
896B PHE* 6.0 0.9 - - - -
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Residues in contact with THR 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A GLU* 6.0 6.7 - - - -
885B THR 2.9 17.5 + - - -
886B ASP* 3.4 11.4 - - - -
887B LEU 3.2 0.4 - - - -
888B ARG* 1.3 79.7 - - - +
890B HIS* 1.3 60.2 + - - +
892B GLN* 3.5 9.4 + - - +
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Residues in contact with HIS 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B CYS* 5.6 0.5 - - - +
845B ALA* 4.1 26.1 - - + +
849B VAL* 6.1 3.6 - - + -
886B ASP 3.0 15.5 + - - +
887B LEU* 4.4 3.1 - - - +
889B THR* 1.3 77.4 - - - +
891B THR* 1.3 58.3 + - - +
892B GLN* 3.3 4.7 + - - +
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Residues in contact with THR 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B CYS* 4.5 25.3 - - - +
845B ALA* 4.9 7.9 - - - -
887B LEU 3.3 17.5 + - - -
888B ARG* 3.6 1.5 + - - -
889B THR 3.3 0.2 - - - -
890B HIS* 1.3 76.5 - - - +
892B GLN* 1.3 60.7 + - - +
893B GLY 3.0 8.0 + - - -
894B GLN* 3.0 17.0 + - - +
895B ALA* 3.8 28.5 - - - -
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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