Contacts of the helix formed by residues 861 - 866 (chain A) in PDB entry 2IVF
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 ASN 861 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASN* 3.4 27.4 + - - +
136A ASN* 3.5 17.0 - - - +
139A GLY* 4.9 1.0 - - - -
141A GLU* 2.8 25.2 + - - +
858A HIS* 3.1 23.4 + - - +
859A LEU 3.4 0.4 - - - -
860A THR* 1.3 77.3 - - - +
862A SER* 1.3 66.5 + - - +
863A HIS* 3.3 12.9 + - - +
864A LEU* 3.0 32.6 + - + +
865A SER* 2.8 30.4 + - - -
113B PHE* 5.3 0.4 - - - -
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Residues in contact with SER 862 (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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141A GLU* 4.8 1.0 + - - -
860A THR 3.7 3.6 + - - -
861A ASN* 1.3 75.8 - - - +
863A HIS* 1.3 63.8 + - - +
865A SER* 3.2 1.9 + - - -
866A ARG* 3.2 51.1 + - - +
97B PHE* 3.4 23.2 + - - +
99B HIS* 3.2 26.3 + - - -
113B PHE* 5.2 0.2 - - - -
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Residues in contact with HIS 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ALA* 3.8 13.4 - - + +
135A ASN* 3.4 36.8 + - + +
861A ASN* 3.3 10.6 + - - +
862A SER* 1.3 80.8 - - - +
864A LEU* 1.3 66.1 + - + +
866A ARG* 3.4 33.3 + - - +
867A LEU* 4.2 6.1 + - + +
36B VAL* 4.5 8.0 - - + +
39B LYS* 3.7 29.6 - - + +
40B ASN* 3.0 30.7 + - - -
44B LYS* 4.0 11.6 - - + +
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Residues in contact with LEU 864 (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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128A GLN* 3.5 24.5 - - + +
129A LYS* 3.8 18.4 - - + +
132A ALA* 3.8 17.0 - - + -
136A ASN* 3.8 11.7 - - - +
852A VAL* 4.4 9.3 - - - +
858A HIS* 3.3 48.2 - - + +
861A ASN* 3.0 18.7 + - + +
863A HIS* 1.3 76.9 - - + +
865A SER* 1.3 60.2 + - - +
867A LEU* 3.1 47.1 + - + +
868A HIS* 3.5 8.1 - - - -
36B VAL* 4.3 2.0 - - + -
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Residues in contact with SER 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A HIS 3.8 5.5 + - - -
859A LEU* 3.7 19.1 + - - -
861A ASN 2.8 23.6 + - - -
862A SER 3.2 0.6 + - - -
864A LEU* 1.3 78.4 - - - +
866A ARG* 1.3 55.7 + - - +
867A LEU 3.2 0.9 - - - -
868A HIS* 3.3 41.5 + - - +
870A GLY* 3.6 13.5 + - - -
95B PHE* 4.9 0.5 - - - -
97B PHE* 3.5 28.4 - - - -
113B PHE* 4.7 1.4 - - - -
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Residues in contact with ARG 866 (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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862A SER* 3.2 30.3 + - - +
863A HIS* 3.5 36.8 + - - +
864A LEU 3.2 1.2 - - - -
865A SER* 1.3 74.9 - - - +
867A LEU* 1.3 59.0 + - + +
868A HIS 3.2 9.6 + - - +
39B LYS* 6.5 1.1 - - - +
49B GLU* 5.6 1.8 - - - +
52B ARG* 3.9 20.7 + - - +
94B ASP* 3.3 24.1 + - - -
95B PHE* 2.8 54.0 + - + +
96B GLN* 4.4 8.1 - - - +
97B PHE* 4.2 0.9 - - + -
128B TYR* 3.4 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