Contacts of the strand formed by residues 857 - 866 (chain K) in PDB entry 6R90
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 LYS 857 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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762K SER* 4.6 7.0 - - - +
803K HIS* 3.6 19.5 - - + +
852K GLN 3.5 1.4 - - - +
853K TYR* 3.3 12.5 - - - -
854K SER 3.2 32.5 + - - +
855K ASP* 3.3 26.8 + - - +
856K GLY* 1.3 83.7 - - - +
858K LEU* 1.3 66.6 + - - +
859K GLN* 3.9 19.9 + - + +
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Residues in contact with LEU 858 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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764K SER* 5.3 6.1 - - - -
791K LEU* 3.7 23.8 - - + +
793K ILE* 4.0 22.7 - - + -
803K HIS* 3.8 14.9 + - + +
805K HIS* 3.3 39.5 + - + +
829K PHE* 4.1 19.7 - - + -
851K PHE* 3.4 41.7 - - + -
852K GLN 3.4 7.0 - - - +
853K TYR* 4.6 0.7 - - + -
857K LYS* 1.3 80.5 - - - +
859K GLN* 1.3 62.6 + - - +
860K THR 4.3 0.3 + - - -
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Residues in contact with GLN 859 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851K PHE* 3.3 4.8 - - - -
852K GLN* 2.8 54.0 + - + +
854K SER* 5.3 12.2 - - - +
857K LYS* 4.5 23.5 + - - +
858K LEU* 1.3 77.0 - - - +
860K THR* 1.3 66.8 + - - +
861K VAL* 3.1 4.6 + - + +
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Residues in contact with THR 860 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805K HIS* 5.0 4.3 - - - -
849K VAL* 4.9 6.7 - - + -
850K VAL 4.0 3.6 - - - +
851K PHE* 3.7 18.9 - - - -
858K LEU 4.2 0.4 + - - -
859K GLN* 1.3 69.6 - - - +
861K VAL* 1.3 63.2 + - - +
862K ALA 4.2 6.1 - - - +
863K GLU* 3.5 36.1 - - + +
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Residues in contact with VAL 861 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828K TYR* 3.8 13.7 - - + +
850K VAL* 2.7 19.5 + - + +
852K GLN* 3.5 33.4 - - + +
859K GLN* 3.5 15.9 - - + +
860K THR* 1.3 75.9 - - - +
862K ALA* 1.3 58.4 + - - +
893K TRP* 3.9 21.3 - - + -
897K LYS* 3.8 34.6 - - + +
898K GLU* 5.8 0.2 - - - +
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Residues in contact with ALA 862 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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849K VAL* 3.7 1.7 - - - +
850K VAL* 2.9 35.1 + - + +
860K THR* 3.7 2.0 - - - +
861K VAL* 1.3 77.2 - - - +
863K GLU* 1.3 72.0 + - - +
893K TRP* 3.4 23.1 - - + -
897K LYS 3.2 25.6 - - - +
898K GLU* 3.9 8.7 - - - +
899K LEU* 5.6 0.9 - - + +
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Residues in contact with GLU 863 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768K SER* 2.1 42.3 + - - -
770K LEU* 3.3 17.0 - - + +
847K ARG* 4.2 11.1 + - - -
848K ILE 3.3 8.3 - - - +
849K VAL* 4.5 8.9 - - + +
850K VAL* 6.0 0.2 - - - -
860K THR* 3.5 24.1 - - + +
862K ALA* 1.3 82.2 - - - +
864K LYS* 1.3 66.9 + - - +
865K GLU 4.4 0.2 - - - -
898K GLU* 3.7 15.4 + - - +
899K LEU* 5.7 0.8 + - - -
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Residues in contact with LYS 864 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770K LEU* 5.3 1.1 - - - -
847K ARG* 3.5 4.3 - - - -
848K ILE* 2.9 36.4 + - + +
863K GLU* 1.3 79.4 - - - +
865K GLU* 1.3 73.4 + - - +
866K VAL* 3.8 3.1 + - + +
891K TYR* 4.6 18.6 - - + +
898K GLU* 5.6 3.3 - - + +
899K LEU* 3.9 49.0 + - + +
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Residues in contact with GLU 865 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770K LEU* 3.2 60.3 - - + +
773K SER* 5.1 5.2 + - - -
845K GLN* 4.7 12.4 - - + +
846K GLY 3.6 10.3 - - - +
847K ARG* 4.7 1.1 - - - +
864K LYS* 1.3 83.5 - - - +
866K VAL* 1.3 71.4 + - - +
889K ARG* 5.4 0.5 + - - -
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Residues in contact with VAL 866 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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845K GLN* 3.4 4.2 - - - +
846K GLY 2.9 38.3 + - - +
847K ARG* 4.5 1.3 - - - +
848K ILE* 5.0 6.1 - - + -
864K LYS* 4.5 9.4 - - + +
865K GLU* 1.3 83.5 - - - +
867K LYS* 1.3 62.6 + - - +
868K GLY 3.5 21.1 - - - +
870K VAL* 4.2 8.7 - - + -
884K ILE* 4.1 24.9 - - + -
889K ARG* 3.8 16.2 - - - +
891K TYR* 3.6 25.1 - - + +
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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