Contacts of the helix formed by residues 876 - 885 (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 876 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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873A MET* 5.5 0.2 - - - +
874A PRO* 3.2 30.3 + - - +
875A VAL* 1.3 76.1 - - - +
877A SER* 1.3 63.2 + - - +
878A LYS* 3.6 29.4 + - - +
879A PHE* 2.9 21.7 + - - +
880A TYR* 3.0 23.1 + - - -
575B GLN* 3.8 23.1 - - - +
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Residues in contact with SER 877 (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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876A ASP* 1.3 74.8 - - - +
878A LYS* 1.3 65.4 + - - +
880A TYR* 3.9 2.8 - - - +
881A LYS* 3.0 32.4 + - - +
575B GLN* 3.3 48.3 + - - +
577B PRO* 5.5 0.5 - - - +
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Residues in contact with LYS 878 (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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873A MET* 3.8 15.0 - - + +
876A ASP* 3.0 24.0 + - - +
877A SER* 1.3 87.1 + - - +
879A PHE* 1.3 61.1 + - - +
881A LYS* 4.1 5.6 - - + +
882A MET* 3.3 23.7 + - - +
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Residues in contact with PHE 879 (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* 3.8 24.9 - - + -
834A LYS* 4.2 18.8 - - + -
836A MET 6.0 0.7 - - - -
841A ILE* 5.1 3.6 - - + -
870A TYR* 3.4 42.2 - + + -
873A MET* 3.9 22.1 - - - +
874A PRO 3.5 19.1 - - - +
875A VAL* 3.9 15.7 - - + -
876A ASP* 2.9 10.3 + - - +
878A LYS* 1.3 78.7 - - - +
880A TYR* 1.3 81.8 + + - +
882A MET* 3.3 10.5 - - + +
883A ILE* 3.2 44.1 + - + +
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Residues in contact with TYR 880 (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* 3.8 19.5 - - + +
841A ILE* 3.7 27.4 - - + -
842A PHE* 3.6 22.1 - + + -
875A VAL* 3.3 24.8 - - + +
876A ASP* 3.0 27.3 + - - -
877A SER 3.4 4.7 + - - +
879A PHE* 1.3 85.9 - + - +
881A LYS* 1.3 58.3 + - - +
883A ILE* 3.3 6.4 + - + +
884A LYS 3.0 22.7 + - - -
570B PTR 4.2 1.4 + - - -
571B ILE* 3.4 32.5 - - + +
572B ASP 4.1 5.0 + - - -
575B GLN* 3.9 25.4 - - + +
576B LEU* 3.7 19.5 - - + -
577B PRO* 3.7 10.0 - - + +
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Residues in contact with LYS 881 (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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877A SER 3.0 18.3 + - - +
878A LYS* 4.1 5.8 - - + +
880A TYR* 1.3 77.3 - - - +
882A MET* 1.3 58.6 + - - +
884A LYS* 4.0 0.4 - - + +
885A GLU* 3.0 61.7 + - + +
577B PRO* 4.0 23.3 - - + +
579B ASP* 4.2 31.8 + - + +
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Residues in contact with MET 882 (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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870A TYR* 4.7 15.3 - - + -
873A MET* 3.7 31.2 - - + +
878A LYS 3.3 14.3 + - - +
879A PHE* 3.3 23.3 - - - +
881A LYS* 1.3 79.9 - - - +
883A ILE* 1.3 64.5 + - - +
885A GLU* 4.9 0.7 - - - -
886A GLY 3.4 0.5 + - - -
887A PHE* 2.8 63.3 + - + +
888A ARG 6.4 0.2 - - - -
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Residues in contact with ILE 883 (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 5.4 0.9 - - - +
838A PRO* 3.7 34.7 - - + +
841A ILE* 4.8 7.0 - - + -
842A PHE* 4.5 4.5 - - + -
853A TRP* 4.4 16.2 - - + -
870A TYR* 3.7 30.3 - - + +
879A PHE* 3.2 35.6 + - + +
880A TYR* 3.6 9.6 - - - +
882A MET* 1.3 77.5 - - - +
884A LYS* 1.3 68.4 + - - +
886A GLY* 3.0 9.7 + - - -
887A PHE 3.9 15.3 - - - +
888A ARG* 3.0 19.9 + - - +
909A ALA* 6.0 0.2 - - - +
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Residues in contact with LYS 884 (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* 5.5 3.4 - - + -
842A PHE* 4.2 29.5 - - + +
843A ASN* 5.4 5.3 - - - +
880A TYR 3.0 16.2 + - - +
881A LYS* 3.5 2.9 + - + +
883A ILE* 1.3 74.3 - - - +
885A GLU* 1.3 62.1 + - + +
886A GLY* 2.9 12.1 + - - -
909A ALA* 5.5 6.2 - - - +
577B PRO* 3.8 31.4 - - + +
661B THR* 4.8 16.8 + - - -
662B ILE* 6.3 0.6 - - - +
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Residues in contact with GLU 885 (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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881A LYS* 3.0 53.7 + - + +
882A MET* 4.9 0.5 - - - -
884A LYS* 1.3 77.7 - - + +
886A GLY* 1.3 57.9 + - - +
887A PHE* 3.6 31.3 + - + -
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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