Contacts of the helix formed by residues 837 - 844 (chain B) in PDB entry 1PKG
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 837 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835B TRP 3.8 0.2 + - - -
836B MET* 1.3 75.9 - - - +
838B PRO* 1.3 73.7 - - + +
839B GLU* 3.0 28.6 + - - +
840B SER* 3.2 14.6 + - - +
841B ILE* 3.2 11.6 + - - +
850B SER* 3.8 17.6 + - - -
853B TRP* 3.6 29.4 - - + +
914B ARG* 3.9 0.9 - - - +
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Residues in contact with PRO 838 (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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836B MET 4.0 0.4 - - - -
837B ALA* 1.3 88.2 - - + +
839B GLU* 1.3 61.0 + - + +
840B SER 3.3 0.2 - - - -
841B ILE* 3.8 8.5 - - + -
842B PHE* 2.9 58.6 + - + +
853B TRP* 3.4 36.6 - - + -
883B ILE* 4.2 13.2 - - + -
884B LYS* 5.2 4.3 - - + -
888B ARG* 5.3 1.6 - - - +
909B ALA* 4.4 14.6 - - + +
914B ARG* 4.0 4.3 - - - +
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Residues in contact with GLU 839 (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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837B ALA* 3.1 16.0 - - - +
838B PRO* 1.3 82.9 - - + +
840B SER* 1.3 61.8 + - - +
843B ASN* 3.0 40.5 + - - +
844B CYS 3.4 2.6 + - - -
845B VAL* 3.6 28.1 + - + +
847B THR* 3.6 13.8 + - - +
850B SER* 3.5 12.9 - - - -
909B ALA 4.9 0.4 - - - +
911B PRO* 3.6 23.9 - - + +
914B ARG* 2.7 40.6 + - - -
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Residues in contact with SER 840 (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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836B MET* 3.7 16.2 - - - +
837B ALA* 3.5 13.7 + - - +
839B GLU* 1.3 76.2 - - - +
841B ILE* 1.3 66.3 + - - +
844B CYS* 3.2 19.9 + - - -
845B VAL 3.2 17.7 + - - +
846B TYR* 3.6 29.6 + - - -
850B SER* 3.4 26.2 - - - -
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Residues in contact with ILE 841 (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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833B VAL* 3.9 26.7 - - + +
836B MET* 3.8 31.0 - - + +
837B ALA 3.2 11.1 + - - +
838B PRO* 3.5 5.4 + - + +
840B SER* 1.3 77.6 - - - +
842B PHE* 1.3 88.0 + - + +
843B ASN 3.7 0.2 + - - -
844B CYS* 4.5 6.2 + - - -
879B PHE* 4.9 5.2 - - + -
880B TYR* 3.7 39.7 - - + +
883B ILE* 5.6 4.5 - - + -
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Residues in contact with PHE 842 (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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838B PRO* 2.9 36.2 + - + +
841B ILE* 1.3 103.5 - - + +
843B ASN* 1.3 75.9 + - - +
844B CYS* 5.6 1.1 - - - -
880B TYR* 3.9 32.5 - + + -
883B ILE* 5.0 3.1 - - + -
884B LYS* 3.5 47.1 - - + -
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Residues in contact with ASN 843 (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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838B PRO 4.6 0.2 + - - -
839B GLU* 3.0 23.7 + - - +
842B PHE* 1.3 97.6 - - - +
844B CYS* 1.3 69.4 + - - +
845B VAL* 3.1 15.3 + - + +
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Residues in contact with CYS 844 (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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839B GLU 3.4 0.6 + - - -
840B SER 3.2 19.7 + - - -
841B ILE 4.9 5.2 - - - -
842B PHE 5.6 0.7 - - - -
843B ASN* 1.3 79.3 - - - +
845B VAL* 1.3 58.5 + - - +
846B TYR* 3.2 30.6 - - + -
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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