Contacts of the helix formed by residues 837 - 843 (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 ALA 837 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835A TRP 4.0 0.2 + - - -
836A MET* 1.3 74.7 - - - +
838A PRO* 1.3 76.2 - - + +
839A GLU* 3.6 6.1 - - - +
840A SER* 3.0 15.2 + - - -
841A ILE* 3.3 8.0 + - - +
850A SER* 3.2 27.9 + - - +
853A TRP* 3.4 30.7 - - + +
914A ARG* 3.6 12.8 - - - +
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Residues in contact with PRO 838 (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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836A MET 3.8 0.6 - - - -
837A ALA* 1.3 84.2 - - + +
839A GLU* 1.3 69.9 + - - +
840A SER 3.0 0.5 + - - -
841A ILE* 3.0 9.6 + - + -
842A PHE* 2.9 52.7 + - + -
853A TRP* 3.1 37.5 - - + -
883A ILE* 3.7 13.9 - - + +
884A LYS* 5.5 2.5 - - + -
888A ARG* 5.0 2.0 - - - +
909A ALA* 4.5 13.9 - - + +
914A ARG* 4.3 3.4 - - - +
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Residues in contact with GLU 839 (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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837A ALA* 3.6 7.8 - - - +
838A PRO* 1.3 80.3 - - - +
840A SER* 1.3 57.3 + - - +
843A ASN* 3.1 34.8 + - - +
845A VAL* 3.2 38.6 + - + +
847A THR* 3.9 10.5 + - - +
850A SER* 3.4 18.4 + - - -
909A ALA 4.2 0.7 - - - +
911A PRO* 3.5 21.8 - - + +
914A ARG* 3.0 43.1 + - - -
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Residues in contact with SER 840 (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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825A VAL* 4.9 1.0 - - - +
836A MET* 4.2 13.5 - - - +
837A ALA 3.0 12.2 + - - -
839A GLU* 1.3 77.7 - - - +
841A ILE* 1.3 65.8 + - - +
844A CYS* 3.2 18.4 - - - -
845A VAL 2.6 25.8 + - - +
846A TYR* 3.7 30.3 + - - -
850A SER* 3.0 23.0 + - - -
571B ILE* 4.7 2.6 - - - +
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Residues in contact with ILE 841 (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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833A VAL* 4.3 17.0 - - + +
836A MET* 3.4 44.9 - - + +
837A ALA 3.5 8.7 - - - +
838A PRO* 3.0 13.4 + - + +
840A SER* 1.3 80.9 - - - +
842A PHE* 1.3 81.4 + - + +
844A CYS* 4.4 3.6 + - - +
879A PHE* 5.1 4.3 - - + -
880A TYR* 3.7 27.4 - - + -
883A ILE* 4.8 10.3 - - + -
571B ILE* 3.8 34.1 - - + +
576B LEU* 4.0 4.4 - - + +
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Residues in contact with PHE 842 (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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838A PRO* 2.9 47.2 + - + +
839A GLU* 5.1 0.2 - - - -
841A ILE* 1.3 95.4 - - + +
843A ASN* 1.3 68.5 + - - +
844A CYS* 3.5 2.5 - - - -
880A TYR* 3.6 29.6 - + + -
883A ILE* 4.5 5.8 - - + -
884A LYS* 4.2 28.7 - - + +
576B LEU* 3.7 21.9 - - + +
577B PRO* 3.0 33.9 - - + -
661B THR 5.4 0.2 - - - +
662B ILE* 3.3 16.9 - - + +
663B GLY* 2.6 33.4 + - - -
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Residues in contact with ASN 843 (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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824A VAL* 4.7 3.6 - - - +
839A GLU* 3.1 25.9 + - - +
842A PHE* 1.3 86.6 - - - +
844A CYS* 1.3 74.6 + - - +
845A VAL* 3.1 17.5 + - + +
884A LYS* 5.4 6.1 - - - +
661B THR 3.2 18.5 + - - +
662B ILE* 3.9 0.3 - - - -
664B GLY* 2.7 44.2 + - - +
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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