Contacts of the strand formed by residues 827 - 835 (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 THR 827 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727K GLN* 3.7 19.1 - - + +
729K VAL* 3.7 30.6 - - + +
818K SER* 3.6 22.2 - - - +
819K CYS* 3.4 20.4 - - - +
820K LYS* 3.4 19.8 + - + +
825K PRO 3.8 1.9 + - - -
826K ASN* 1.3 73.8 - - - +
828K TYR* 1.3 71.6 + - - +
852K GLN* 4.1 12.8 + - - +
853K TYR 4.9 1.6 + - - +
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Residues in contact with TYR 828 (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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727K GLN* 3.5 7.0 + - - +
817K VAL 3.8 0.5 - - - +
818K SER* 3.3 4.7 - - - -
819K CYS 3.1 32.9 + - - +
821K LEU* 4.8 11.2 - - + -
824K ASP* 2.8 23.6 + - + -
826K ASN* 3.6 24.8 + - + -
827K THR* 1.3 79.1 - - - +
829K PHE* 1.3 61.5 + - - +
830K ILE* 4.5 7.3 - - + +
850K VAL* 3.6 21.8 - - + -
851K PHE 3.2 15.7 - - - +
852K GLN* 3.6 31.4 - - + +
853K TYR 5.8 0.2 - - - +
861K VAL* 3.8 18.4 - - + -
893K TRP* 3.6 29.2 - + - -
897K LYS* 3.6 20.3 + - - +
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Residues in contact with PHE 829 (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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725K CYS* 4.0 17.3 - - - -
727K GLN* 3.1 51.8 - - + -
730K SER* 6.0 0.2 - - - -
732K CYS* 5.0 2.7 - - + -
733K PHE 4.6 2.7 - - - -
734K GLY* 4.0 25.8 - - - -
791K LEU* 4.5 10.8 - - + -
793K ILE* 5.0 9.6 - - + -
816K LEU* 4.4 13.9 - - + -
817K VAL 3.5 2.2 - - - -
818K SER* 3.7 17.3 - - - -
828K TYR* 1.3 72.1 - - - +
830K ILE* 1.3 60.5 + - - +
831K VAL* 5.1 0.2 - - - -
849K VAL 3.6 2.1 - - - +
850K VAL* 3.6 1.2 - - - -
851K PHE* 2.9 44.9 + - + +
853K TYR* 4.1 19.7 - + + -
858K LEU* 4.1 17.5 - - + -
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Residues in contact with ILE 830 (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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815K SER 4.0 0.3 - - - +
816K LEU* 3.2 5.4 - - - +
817K VAL* 2.7 44.5 + - + +
819K CYS* 3.6 29.4 - - - -
821K LEU* 3.8 23.8 - - + -
828K TYR* 4.5 6.3 - - + +
829K PHE* 1.3 76.5 - - - +
831K VAL* 1.3 63.9 + - - +
848K ILE* 3.9 18.8 - - + -
849K VAL 3.3 4.9 - - - +
850K VAL* 4.2 16.4 - - + -
873K MET* 3.9 28.2 - - + +
880K LEU* 4.2 17.7 - - + -
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Residues in contact with VAL 831 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736K LEU* 4.1 6.1 - - + -
791K LEU* 4.3 9.9 - - + -
807K PHE* 3.7 39.3 - - + -
813K ALA* 3.9 8.3 - - + -
815K SER 3.4 9.6 - - - +
816K LEU* 3.3 27.4 - - + -
830K ILE* 1.3 76.0 - - - +
832K GLY* 1.3 64.4 + - - +
833K THR* 3.8 12.8 - - + -
847K ARG 3.6 0.9 - - - +
848K ILE* 3.5 4.5 - - - +
849K VAL* 2.9 39.2 + - + +
851K PHE* 4.6 7.9 - - + -
873K MET* 4.7 0.7 - - - -
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Residues in contact with GLY 832 (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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813K ALA* 3.6 0.7 - - - -
814K LEU* 2.9 24.9 + - - -
815K SER* 3.0 27.4 + - - +
831K VAL* 1.3 72.3 - - - +
833K THR* 1.3 65.6 + - - +
847K ARG 3.3 7.0 - - - -
870K VAL* 3.9 18.8 - - - -
873K MET* 4.5 4.3 - - - -
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Residues in contact with THR 833 (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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807K PHE* 4.4 10.5 - - + -
811K GLU* 2.5 35.2 + - + +
812K TYR 3.2 11.7 - - - -
813K ALA* 4.0 9.9 - - + -
814K LEU* 4.6 2.7 - - - +
831K VAL* 3.8 20.0 - - + +
832K GLY* 1.3 80.0 - - - +
834K ALA* 1.3 63.9 + - - +
846K GLY* 3.5 14.0 - - - -
847K ARG* 3.0 29.5 + - - +
849K VAL* 4.9 2.2 - - + -
869K ALA* 4.0 0.2 - - - -
870K VAL* 3.6 16.8 + - - +
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Residues in contact with ALA 834 (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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811K GLU* 3.3 5.9 - - - -
812K TYR* 2.9 32.8 + - + +
814K LEU* 4.6 8.3 - - + -
833K THR* 1.3 78.4 - - - +
835K MET* 1.3 64.4 + - - +
836K VAL* 3.7 8.5 + - + +
843K PRO* 4.3 10.3 - - + -
845K GLN 3.6 11.7 - - - +
846K GLY* 4.2 0.9 - - - -
869K ALA* 3.8 24.7 - - + -
70L VAL* 5.5 2.5 - - + -
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Residues in contact with MET 835 (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* 6.5 0.4 - - + -
771K PHE* 3.9 40.6 - - + +
808K LEU* 4.2 3.1 - - + -
809K GLN 3.7 22.2 - - - +
810K ASN* 3.9 4.9 - - + +
811K GLU* 3.7 36.1 - - + +
834K ALA* 1.3 76.1 - - - +
836K VAL* 1.3 61.6 + - - +
837K TYR* 4.0 12.3 + - + +
840K GLU* 4.5 9.9 - - - +
843K PRO* 4.8 6.6 - - - +
844K LYS 5.5 0.2 + - - -
845K GLN* 3.1 56.4 + - + +
846K GLY* 5.2 2.0 - - - +
847K ARG* 6.0 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