Contacts of the helix formed by residues 678 - 686 (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 LEU 678 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677B ASP* 1.3 69.9 - - - +
679B LEU* 1.3 64.6 + - - +
681B PHE* 4.3 13.7 - - + -
682B LEU* 3.0 39.0 + - + +
772B PHE* 3.7 43.5 - - + -
795B ALA* 3.1 14.6 + - + +
798B ILE* 2.7 40.1 + - + +
800B LEU* 4.5 15.5 - - + +
806B THR* 5.0 1.6 - - + -
858B PHE* 3.6 27.1 - - + -
862B LEU* 4.4 2.2 - - + -
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Residues in contact with LEU 679 (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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677B ASP* 3.3 8.5 + - - +
678B LEU* 1.3 76.4 - - - +
680B ASN* 1.3 67.1 + - - +
682B LEU* 3.8 2.5 - - - +
683B ARG* 3.2 58.4 + - - +
795B ALA* 2.9 14.7 + - + -
796B ARG* 3.7 28.9 - - + +
835B TRP* 6.4 0.7 - - + -
861B GLU* 3.4 29.2 - - + +
866B GLY* 3.7 24.9 - - - +
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Residues in contact with ASN 680 (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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677B ASP* 2.9 34.9 + - - +
679B LEU* 1.3 88.4 - - - +
681B PHE* 1.3 58.3 + - - +
682B LEU 3.3 0.4 - - - -
683B ARG* 3.9 14.7 - - - +
684B ARG* 2.9 50.4 + - - +
796B ARG* 5.8 0.2 - - - +
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Residues in contact with PHE 681 (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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675B TYR* 4.4 17.7 - + + +
677B ASP 3.0 18.5 + - - +
678B LEU* 4.0 17.7 - - + +
679B LEU 3.4 0.2 - - - -
680B ASN* 1.3 73.3 - - - +
682B LEU* 1.3 64.8 + - + +
684B ARG* 3.5 16.3 - - - +
685B LYS* 2.8 67.8 + - + +
764B LEU* 3.7 30.3 - - + -
768B ASP* 4.7 0.2 - - - -
772B PHE* 4.1 7.9 - + - -
800B LEU* 3.9 25.8 - - + -
804B ARG* 3.5 35.0 - - - -
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Residues in contact with LEU 682 (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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678B LEU* 3.0 34.5 + - + +
679B LEU* 3.8 3.8 - - - +
681B PHE* 1.3 79.5 - - + +
683B ARG* 1.3 58.3 + - - +
685B LYS 3.0 1.6 + - - -
686B ARG* 2.7 37.9 + - - -
764B LEU* 3.8 20.0 - - + -
769B LEU* 4.1 14.8 - - + -
772B PHE* 5.4 1.1 - - + -
795B ALA* 4.7 7.0 - - + -
861B GLU 3.8 23.1 - - - +
862B LEU* 3.8 20.2 - - + +
865B LEU* 3.8 36.1 - - + -
866B GLY* 4.0 5.2 - - - +
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Residues in contact with ARG 683 (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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679B LEU* 3.2 47.7 + - - +
680B ASN* 4.1 15.5 - - - +
682B LEU* 1.3 78.2 - - - +
684B ARG* 1.3 59.5 + - - +
686B ARG* 4.1 23.4 + - - +
861B GLU* 5.3 0.4 + - - -
865B LEU 4.3 4.9 + - - -
866B GLY* 2.6 33.2 + - - +
867B SER 4.8 0.2 - - - -
868B SER* 4.4 19.5 + - - +
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Residues in contact with ARG 684 (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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675B TYR 4.1 17.4 + - - -
676B GLY* 5.3 3.6 - - - -
677B ASP 4.5 1.0 + - - +
680B ASN* 2.9 47.4 + - - +
681B PHE* 3.5 19.2 - - - +
683B ARG* 1.3 79.1 - - - +
685B LYS* 1.3 70.7 + - + +
686B ARG* 3.3 4.9 + - - +
687B ASP* 4.6 5.4 + - - +
688B SER 5.4 0.2 + - - -
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Residues in contact with LYS 685 (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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681B PHE* 2.8 57.1 + - + +
682B LEU 3.4 2.0 - - - -
684B ARG* 1.3 86.2 + - + +
686B ARG* 1.3 62.0 + - - +
687B ASP 3.4 2.5 - - - -
688B SER* 3.0 46.2 + - - +
689B PHE 3.3 5.2 + - - -
764B LEU* 3.7 17.0 - - + +
804B ARG* 5.5 2.7 - - - +
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Residues in contact with ARG 686 (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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682B LEU 2.7 19.9 + - - +
683B ARG* 4.1 22.4 + - - +
684B ARG 3.3 2.4 - - - +
685B LYS* 1.3 73.1 - - - +
687B ASP* 1.3 71.4 + - - +
689B PHE* 3.2 25.1 + - - +
764B LEU* 4.9 1.1 - - - -
864B SER 4.6 3.6 + - - -
865B LEU* 2.6 54.0 + - + +
866B GLY 3.9 13.9 + - - -
867B SER* 4.4 5.9 + - - +
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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