Contacts of the strand formed by residues 857 - 865 (chain A) in PDB entry 3K72
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 ILE 857 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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786A VAL 4.1 0.7 - - - +
787A MET* 3.6 1.2 - - - -
788A VAL* 3.2 45.5 + - + +
825A LEU* 5.1 9.9 - - + -
846A ILE* 3.7 30.3 - - + -
851A PHE* 3.7 28.9 - - + -
855A ALA* 5.0 2.9 - - + -
856A GLN* 1.3 82.4 - - - +
858A THR* 1.3 64.6 + - - +
859A PHE* 4.4 5.1 - - + -
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Residues in contact with THR 858 (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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785A GLU* 5.4 13.9 - - + +
786A VAL 3.4 6.3 - - - +
787A MET* 3.3 43.7 - - + +
821A GLN 4.4 12.5 + - - -
822A LEU* 4.4 11.6 - - - +
823A ARG* 4.0 16.6 + - - -
856A GLN* 6.0 1.8 - - + -
857A ILE* 1.3 75.6 - - - +
859A PHE* 1.3 61.9 + - - +
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Residues in contact with PHE 859 (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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784A ALA 4.0 0.2 - - - +
785A GLU* 4.1 3.8 - - - +
786A VAL* 3.0 67.0 + - + +
788A VAL* 5.3 10.1 - - + -
800A ILE* 3.9 32.5 - - + -
802A PHE* 4.8 5.2 - + - -
822A LEU* 5.1 4.3 - - - -
823A ARG* 3.9 15.7 - - + -
825A LEU* 3.5 30.1 - - + -
827A LEU* 4.0 20.9 - - + -
844A CYS* 5.9 2.7 - - + -
846A ILE* 5.2 7.0 - - + -
857A ILE* 5.0 8.5 - - + -
858A THR* 1.3 77.4 - - - +
860A LEU* 1.3 66.7 + - - +
861A ALA* 4.2 15.5 - - + -
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Residues in contact with LEU 860 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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783A ASN* 4.6 14.1 - - + +
784A ALA 3.5 18.2 - - - +
785A GLU* 5.1 4.7 - - + +
810A TYR* 4.5 1.4 + - - -
813A VAL* 3.4 24.6 - - + +
819A GLN* 5.8 4.9 - - - +
822A LEU* 5.1 17.7 - - + -
823A ARG* 3.3 37.5 + - + +
827A LEU* 5.6 0.2 - - - +
859A PHE* 1.3 77.8 - - - +
861A ALA* 1.3 65.1 + - - +
862A THR* 3.2 28.0 - - - +
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Residues in contact with ALA 861 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782A LEU 3.8 1.0 - - - +
784A ALA* 3.2 36.1 + - + +
786A VAL* 5.3 1.3 - - + +
802A PHE* 4.7 13.5 - - + -
810A TYR* 3.6 22.2 - - + -
827A LEU* 6.3 0.9 - - + -
844A CYS* 6.2 1.8 - - - -
859A PHE* 4.2 19.9 + - + -
860A LEU* 1.3 74.9 - - - +
862A THR* 1.3 62.3 + - - +
863A PHE* 3.9 13.6 - - + -
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Residues in contact with THR 862 (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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781A GLU* 3.9 18.4 - - + +
782A LEU 3.3 22.9 + - - +
783A ASN* 3.1 19.0 + - - +
810A TYR* 3.3 10.9 - - - -
811A ARG* 3.0 46.2 + - - +
813A VAL* 4.2 11.4 - - - +
860A LEU* 3.2 18.0 - - - +
861A ALA* 1.3 70.6 - - - +
863A PHE* 1.3 69.3 + - - +
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Residues in contact with PHE 863 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768A PHE* 6.4 0.7 - + - -
780A LEU 3.6 0.2 - - - +
782A LEU* 3.0 45.2 + - + +
784A ALA* 5.2 6.1 - - + -
802A PHE* 3.9 29.2 - + + -
804A HIS* 3.8 11.2 - + + -
808A LEU* 3.3 33.2 - - + +
809A SER 3.1 16.6 - - - +
810A TYR* 3.8 16.8 - + + -
842A THR* 3.4 26.0 - - - -
844A CYS* 6.3 0.9 - - - -
861A ALA* 3.9 27.6 - - + -
862A THR* 1.3 77.8 - - - +
864A ASP* 1.3 65.0 + - - +
865A VAL* 3.5 3.1 + - - +
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Residues in contact with ASP 864 (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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780A LEU* 3.7 22.8 - - + +
781A GLU* 4.0 5.2 - - - -
808A LEU* 3.0 26.7 - - - +
809A SER 3.1 12.5 + - - +
811A ARG* 3.0 55.0 + - + +
862A THR* 4.1 1.4 + - - +
863A PHE* 1.3 70.9 - - - +
865A VAL* 1.3 60.1 + - - +
866A SER 4.4 0.2 + - - -
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Residues in contact with VAL 865 (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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774A LEU* 5.3 10.1 - - + -
776A VAL* 5.5 9.4 - - + -
777A GLY 5.7 1.6 - - - +
778A SER 5.2 1.6 - - - +
779A ASN 3.5 16.2 - - - +
780A LEU* 2.9 46.3 + - - +
782A LEU* 5.7 5.6 - - + -
807A GLY 3.2 19.7 - - - +
808A LEU* 4.3 14.1 - - + -
863A PHE 4.5 2.7 - - - +
864A ASP* 1.3 75.5 - - - +
866A SER* 1.3 66.2 + - - +
867A PRO* 3.8 1.0 - - - +
869A ALA* 3.9 16.8 - - + -
871A LEU* 5.0 6.3 - - + -
875A LEU* 6.3 1.8 - - + -
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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