Contacts of the helix formed by residues 866 - 871 (chain B) in PDB entry 3QCF
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 ALA 866 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864B ILE 4.1 1.0 + - - +
865B THR* 1.3 75.6 - - - +
867B GLU* 1.3 65.9 + - - +
868B HIS 3.5 1.6 - - - -
869B SER* 3.6 5.9 - - - -
870B ASN* 3.6 23.3 + - - -
884B LEU* 3.9 28.9 - - + -
885B ALA 3.7 17.7 - - - +
886B TYR* 4.1 11.7 - - + -
887B ASP* 3.4 6.7 - - - -
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Residues in contact with GLU 867 (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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1030A GLY* 5.9 4.2 + - - -
1105A THR* 3.7 39.0 + - + +
1106A GLU 5.6 1.1 - - - +
1107A GLU* 4.6 16.9 - - - +
865B THR* 4.5 9.8 - - - +
866B ALA* 1.3 74.4 + - - +
868B HIS* 1.3 67.7 + - + +
870B ASN* 2.9 21.0 + - - +
871B HIS* 3.0 13.9 + - - +
887B ASP* 2.8 17.6 + - - +
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Residues in contact with HIS 868 (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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867B GLU* 1.3 79.6 - - + +
869B SER* 1.3 63.7 + - - +
870B ASN 3.1 1.0 + - - -
871B HIS* 3.2 11.4 + - - +
874B ASN* 2.8 25.1 + - - +
887B ASP* 3.2 26.9 + - + +
890B ARG* 3.4 44.1 + - - +
903B HIS* 4.4 21.6 - + - -
905B ASP* 4.4 7.6 + - - -
906B TYR* 4.2 9.6 - - + -
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Residues in contact with SER 869 (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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866B ALA 3.6 12.6 + - - -
867B GLU 3.2 0.4 - - - -
868B HIS* 1.3 78.5 - - - +
870B ASN* 1.3 60.7 + - - +
871B HIS 3.7 1.9 + - - +
874B ASN* 4.2 6.2 - - - +
875B LYS* 4.5 1.4 + - - +
878B ASN* 2.8 24.5 + - - -
884B LEU* 3.6 24.2 - - - -
885B ALA 2.7 33.7 + - - -
887B ASP* 4.7 0.4 + - - -
906B TYR* 2.8 27.6 + - - -
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Residues in contact with ASN 870 (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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1029A MET* 5.6 10.5 - - - +
866B ALA 3.6 8.0 + - - +
867B GLU* 2.9 17.6 + - - +
869B SER* 1.3 77.8 - - - +
871B HIS* 1.3 62.3 + - - +
872B PRO* 3.5 2.4 - - - +
875B LYS* 3.0 39.3 + - - +
878B ASN* 5.3 0.5 + - - -
881B ILE 4.3 6.8 + - - +
884B LEU* 3.3 38.6 - - - +
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Residues in contact with HIS 871 (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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845A GLN* 4.6 15.0 + - - -
1106A GLU* 6.0 1.8 + - - -
867B GLU 3.0 9.5 + - - +
868B HIS* 3.2 14.0 + - - +
870B ASN* 1.3 79.2 - - - +
872B PRO* 1.3 78.7 - - + +
873B GLU* 3.1 39.4 + - + +
874B ASN* 2.7 34.2 + - - +
875B LYS* 3.2 9.3 + - - +
903B HIS* 3.2 29.0 + + + -
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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