Contacts of the strand formed by residues 845 - 850 (chain C) in PDB entry 1KO6
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 GLN 845 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ARG* 5.3 1.4 - - - +
780A LYS* 2.9 27.8 + - - +
868B LEU 3.4 10.1 + - - -
869B GLN* 4.6 1.2 - - - +
870B ASP* 1.6 54.0 + - - +
844C ALA* 1.3 73.0 - - - +
846C PHE* 1.3 73.8 + - - +
847C LYS* 3.0 14.5 + - - +
858C PHE* 3.0 3.4 - - - -
859C LYS* 2.7 55.9 + - + +
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Residues in contact with PHE 846 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A TYR* 3.4 36.1 - + - -
779A ARG* 3.2 26.9 - - + +
832C GLU* 4.6 7.9 - - + -
835C LEU* 4.8 0.7 - - + -
836C GLU* 3.1 76.1 - - + +
839C SER* 4.2 4.0 - - - -
840C ARG* 5.5 0.4 - - + +
844C ALA 3.8 4.6 + - - -
845C GLN* 1.3 76.9 + - - +
847C LYS* 1.3 60.9 + - - +
848C GLU* 3.2 30.5 - - - -
849C TYR* 3.7 9.6 - - + -
856C TRP* 4.0 15.5 - + - -
857C VAL 3.8 5.8 - - - -
858C PHE* 3.8 7.6 - - - +
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Residues in contact with LYS 847 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A TYR* 3.5 1.6 - - - -
778A ARG* 3.4 18.1 - - + +
779A ARG* 2.9 41.0 + - - +
780A LYS 3.9 6.1 + - - -
781A GLU* 3.0 48.1 + - - +
865B LYS* 5.0 1.8 - - - +
868B LEU 4.3 11.3 + - - -
869B GLN* 5.5 0.4 - - - +
803C GLU* 4.4 2.2 - - - +
845C GLN* 3.0 20.7 + - + +
846C PHE* 1.3 76.8 - - - +
848C GLU* 1.3 64.5 + - - +
857C VAL* 3.0 25.4 + - + +
858C PHE* 4.4 3.8 - - - +
859C LYS* 3.1 43.4 - - + +
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Residues in contact with GLU 848 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724A TYR* 5.0 0.7 + - - -
752A ARG* 2.3 41.4 + - - +
755A TYR* 3.5 5.2 - - + -
778A ARG* 2.8 31.5 + - + +
846C PHE* 3.2 24.0 - - - -
847C LYS* 1.3 81.9 - - - +
849C TYR* 1.3 57.9 + - - +
850C ARG* 3.1 44.3 + - + +
855C SER 3.6 0.4 - - - +
856C TRP* 3.6 1.0 - - - -
857C VAL* 3.0 45.3 + - + +
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Residues in contact with TYR 849 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A ARG* 4.2 7.6 + - - -
755A TYR* 3.1 16.0 + - - +
809C VAL 2.9 28.4 + - - -
810C TRP* 3.1 21.5 + - - -
826C LEU* 4.4 10.6 - - + +
831C TYR* 3.7 21.1 - + + -
832C GLU* 4.2 27.1 - - + +
835C LEU* 3.3 30.7 - - + -
846C PHE* 4.2 10.5 - - + -
848C GLU* 1.3 78.6 - - - +
850C ARG* 1.3 58.7 + - - +
851C PRO* 3.0 38.0 - - + +
854C GLY* 3.4 18.1 - - - -
855C SER 3.1 10.5 - - - -
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Residues in contact with ARG 850 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721A LYS* 5.6 10.3 - - - -
752A ARG* 4.8 3.1 - - - +
778A ARG* 4.9 0.6 - - - +
805C THR* 4.2 8.7 + - - +
807C ASP* 4.4 1.8 + - - -
848C GLU* 3.1 43.0 + - + +
849C TYR* 1.3 71.0 - - - +
851C PRO* 1.3 57.0 - - - +
852C GLU* 3.5 10.3 - - - +
853C THR* 3.4 11.3 + - + +
854C GLY* 2.7 29.9 + - - -
855C SER* 2.8 46.8 + - - +
857C VAL* 3.5 23.4 - - - +
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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
------------------------------------------------------------
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