Contacts of the helix formed by residues 677 - 685 (chain A) 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 ASP 677 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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595A LEU 4.9 1.6 - - - +
675A TYR 4.1 0.2 + - - -
676A GLY* 1.3 73.0 - - - -
678A LEU* 1.3 69.3 + - - +
679A LEU* 2.8 10.0 + - - +
680A ASN* 2.9 49.7 + - - +
681A PHE* 2.9 19.7 + - - +
684A ARG* 4.8 0.7 + - - +
796A ARG* 3.3 30.7 - - - +
798A ILE 3.1 8.5 - - - +
799A LEU* 4.1 1.8 - - + +
1480A ADP 2.5 33.0 + - - +
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Residues in contact with LEU 678 (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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676A GLY 3.6 2.4 + - - -
677A ASP* 1.3 69.4 - - - +
679A LEU* 1.3 52.9 + - - +
681A PHE* 4.0 14.4 - - + -
682A LEU* 2.6 49.1 + - + +
772A PHE* 3.7 40.4 - - + -
795A ALA* 3.5 12.1 + - + +
798A ILE* 2.7 38.8 + - + +
800A LEU* 4.1 22.2 - - + -
806A THR* 4.4 2.0 - - + -
858A PHE* 4.1 8.3 - - + -
862A LEU* 3.6 27.4 - - + -
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Residues in contact with LEU 679 (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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677A ASP* 2.8 5.2 + - - +
678A LEU* 1.3 81.2 - - - +
680A ASN* 1.3 74.5 + - - +
682A LEU* 3.3 7.6 + - - +
683A ARG* 3.3 66.8 + - - +
795A ALA* 3.2 11.7 + - + -
796A ARG* 3.7 37.7 - - + +
861A GLU* 4.2 15.0 - - - +
866A GLY* 3.5 15.5 - - - +
867A SER 5.0 1.3 - - - +
868A SER* 6.1 0.4 - - - -
566B ASN 6.1 2.9 - - - +
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Residues in contact with ASN 680 (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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595A LEU 5.4 2.6 - - - +
677A ASP* 2.9 35.6 + - - +
679A LEU* 1.3 92.5 - - - +
681A PHE* 1.3 64.3 + - - +
683A ARG* 3.1 23.9 + - - +
684A ARG* 3.1 33.1 + - - +
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Residues in contact with PHE 681 (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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675A TYR* 4.1 24.2 - + + +
676A GLY 5.2 0.4 - - - +
677A ASP 2.9 12.5 + - - +
678A LEU* 3.5 19.3 - - + +
680A ASN* 1.3 77.0 - - - +
682A LEU* 1.3 68.3 + - + +
684A ARG* 3.4 27.8 + - - +
685A LYS* 3.2 53.2 + - + +
763A ALA 5.9 1.3 - - - -
764A LEU* 3.6 32.3 - - + -
772A PHE* 4.2 6.7 - + - -
800A LEU* 3.9 32.3 - - + -
804A ARG* 5.1 14.4 - - - -
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Residues in contact with LEU 682 (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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678A LEU* 2.6 41.9 + - + +
679A LEU* 3.4 7.9 - - - +
681A PHE* 1.3 79.7 - - + +
683A ARG* 1.3 55.5 + - - +
685A LYS 3.4 1.0 + - - -
686A ARG* 2.9 30.7 + - - +
764A LEU* 3.8 25.6 - - + +
769A LEU* 4.1 9.4 - - + -
772A PHE* 5.5 2.2 - - + -
795A ALA* 4.9 4.0 - - + -
861A GLU 3.9 22.0 - - - +
862A LEU* 3.9 30.1 - - + +
865A LEU* 3.7 19.3 - - - +
866A GLY* 4.0 6.3 - - - -
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Residues in contact with ARG 683 (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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679A LEU* 3.4 44.7 - - - +
680A ASN* 3.1 14.6 + - - +
682A LEU* 1.3 75.3 - - - +
684A ARG* 1.3 63.9 + - - +
685A LYS 3.2 0.6 + - - -
686A ARG* 3.8 20.3 + - - +
687A ASP* 3.3 18.4 - - - +
865A LEU 4.2 8.3 - - - +
866A GLY 2.7 28.0 + - - +
867A SER* 4.9 0.4 - - - +
868A SER* 4.1 22.0 - - - +
566B ASN 5.9 1.4 - - - +
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Residues in contact with ARG 684 (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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675A TYR* 2.7 36.6 + - - +
676A GLY* 4.5 3.8 - - - -
677A ASP* 4.3 1.6 + - - -
680A ASN* 3.1 28.5 + - + +
681A PHE* 3.4 39.8 - - - +
683A ARG* 1.3 76.5 - - - +
685A LYS* 1.3 66.2 + - + +
687A ASP* 2.7 19.0 - - - +
688A SER* 5.6 0.7 - - - -
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Residues in contact with LYS 685 (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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681A PHE* 3.2 45.6 + - + +
682A LEU 3.6 1.8 - - - -
683A ARG 3.2 0.2 - - - -
684A ARG* 1.3 86.2 - - + +
686A ARG* 1.3 63.8 + - - +
687A ASP* 3.2 2.6 + - - -
688A SER* 3.5 17.2 + - - -
689A PHE* 3.4 17.5 + - - -
763A ALA* 2.9 34.4 - - - +
764A LEU* 4.1 26.2 - - + +
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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