Contacts of the helix formed by residues 832 - 836 (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 PRO 832 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791A ARG 3.8 13.0 - - - +
792A ASP* 3.3 36.3 - - - +
796A ARG* 3.4 14.6 - - - +
813A LEU* 4.0 13.7 - - + -
831A LEU* 1.3 90.8 - - + +
833A VAL* 1.3 51.7 + - - +
834A LYS 3.4 2.5 - - - -
835A TRP* 2.8 40.7 + - + +
836A MET* 3.5 12.6 + - + +
846A TYR* 6.3 0.2 - - + -
567B ASN 4.1 10.8 - - - +
568B PTR 3.8 8.3 - - + -
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Residues in contact with VAL 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A LEU* 2.8 17.3 + - + +
832A PRO* 1.3 70.1 - - - +
834A LYS* 1.3 56.2 + - - +
835A TRP 3.0 0.2 - - - -
836A MET* 2.7 42.3 + - + +
841A ILE* 4.3 8.7 - - + +
875A VAL* 4.0 13.7 - - + -
879A PHE* 3.8 26.0 - - + -
880A TYR* 3.8 17.9 - - + +
567B ASN 4.4 3.0 + - - +
569B VAL* 3.9 19.5 - - + +
571B ILE* 3.5 30.5 - - + -
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Residues in contact with LYS 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A PRO 3.2 1.0 + - - -
833A VAL* 1.3 73.9 - - - +
835A TRP* 1.3 75.4 + - + +
836A MET 3.4 0.7 - - - -
853A TRP* 5.0 1.2 + - - -
857A ILE* 3.6 19.9 - - - +
868A SER* 5.6 0.2 + - - -
869A PRO* 3.4 14.5 + - + +
870A TYR* 2.8 60.2 + - + +
872A GLY 5.0 0.6 - - - +
873A MET 2.4 32.3 + - - +
874A PRO 4.7 0.2 - - - -
875A VAL* 3.6 27.8 - - + +
879A PHE* 4.2 12.8 - - + -
566B ASN* 4.5 16.7 - - + +
567B ASN 5.3 3.0 + - - +
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Residues in contact with TRP 835 (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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792A ASP* 5.3 1.1 - - - +
793A LEU 3.4 26.9 - - - +
794A ALA* 3.3 6.8 - - + +
796A ARG* 3.2 30.1 - - - -
832A PRO* 2.8 27.5 + - + +
834A LYS* 1.3 87.8 - - + +
836A MET* 1.3 60.0 + - - +
853A TRP* 3.5 4.9 - - - -
854A SER* 2.7 38.8 + - - -
857A ILE* 3.3 25.2 - - + +
861A GLU* 2.5 33.6 + - - -
869A PRO* 3.6 24.7 - - + -
566B ASN* 3.1 51.8 - - + -
567B ASN 4.5 4.3 - - - -
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Residues in contact with MET 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A ARG 5.6 2.5 - - - +
831A LEU* 3.5 25.1 - - + -
832A PRO* 3.8 12.1 - - + +
833A VAL* 2.7 33.3 + - - +
834A LYS 3.4 0.9 - - - -
835A TRP* 1.3 79.6 - - - +
837A ALA* 1.3 63.9 + - - +
838A PRO 3.8 0.3 - - - -
840A SER* 4.2 11.4 - - - +
841A ILE* 3.4 23.2 - - + +
846A TYR* 3.4 39.3 - - + +
853A TRP* 3.2 15.6 + - - -
854A SER* 4.8 0.9 - - - +
879A PHE* 6.0 0.9 - - - -
883A ILE* 5.4 1.4 - - - +
571B ILE* 3.7 27.4 - - + -
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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