Contacts of the strand formed by residues 786 - 795 (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 VAL 786 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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740K ILE* 3.3 8.7 - - - +
741K GLU* 2.8 53.4 + - + +
749K THR* 4.5 20.2 - - + +
784K GLU* 3.9 11.4 - - + +
785K GLU* 1.3 80.5 - - - +
787K GLU* 1.3 63.4 + - - +
788K VAL* 3.8 14.4 - - + -
809K GLN* 6.3 3.8 - - + -
810K ASN* 5.1 14.4 - - - +
71L ARG* 6.1 2.9 - - - +
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Residues in contact with GLU 787 (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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382K PHE* 4.9 6.5 - - - -
722K ARG* 3.2 27.9 + - - -
738K SER* 4.7 4.5 - - - -
739K ARG 3.4 5.2 - - - +
740K ILE* 3.9 20.9 - - + +
786K VAL* 1.3 73.9 - - - +
788K VAL* 1.3 62.5 + - - +
789K HIS* 3.4 14.9 + - + +
810K ASN* 5.1 9.0 + - - -
811K GLU 5.0 1.6 - - - +
812K TYR* 3.0 53.0 + - + +
71L ARG* 3.8 21.4 - - - +
74L HIS* 5.8 0.5 - - - -
75L GLN* 4.8 9.0 + - - -
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Residues in contact with VAL 788 (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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738K SER* 3.3 1.4 - - - -
739K ARG* 2.9 54.2 + - + +
741K GLU* 3.6 31.4 - - + +
749K THR* 5.0 1.6 - - - +
786K VAL* 3.8 15.0 - - + -
787K GLU* 1.3 74.5 - - - +
789K HIS* 1.3 64.0 + - - +
790K ASN* 3.8 17.7 + - - +
806K GLN* 4.0 24.0 - - + +
807K PHE 5.6 0.9 - - - +
808K LEU 6.1 2.2 - - - +
809K GLN* 6.6 0.4 - - + -
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Residues in contact with HIS 789 (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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722K ARG* 3.3 32.3 - - - +
736K LEU* 6.3 0.2 - - - +
737K SER 3.3 7.8 + - - +
738K SER* 3.9 10.1 - - - -
787K GLU* 3.4 25.9 + - - +
788K VAL* 1.3 73.4 - - - +
790K ASN* 1.3 72.9 + - - +
806K GLN* 4.0 2.6 - - - +
807K PHE* 3.2 32.6 + - + +
808K LEU 5.5 2.6 + - - -
811K GLU 3.8 16.9 + - - +
812K TYR* 3.2 44.6 - + + -
813K ALA* 3.2 26.6 + - + +
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Residues in contact with ASN 790 (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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719K GLU* 5.3 0.4 + - - +
736K LEU* 3.5 4.5 - - - +
737K SER* 2.9 37.5 + - - +
739K ARG* 3.0 25.0 + - - +
757K SER* 3.6 26.0 - - - +
788K VAL* 3.8 13.7 + - - +
789K HIS* 1.3 91.6 + - - +
791K LEU* 1.3 63.7 + - - +
792K LEU* 4.7 2.0 - - + -
804K ALA* 4.5 4.3 - - - +
805K HIS 3.3 9.2 + - - +
806K GLN* 3.1 31.2 + - - +
807K PHE* 3.6 9.3 - - - -
813K ALA* 5.7 0.2 - - - +
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Residues in contact with LEU 791 (chain K).
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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734K GLY* 4.0 7.4 - - - -
735K VAL 3.2 35.9 - - - +
736K LEU* 4.1 4.0 - - + +
790K ASN* 1.3 72.1 - - - +
792K LEU* 1.3 68.8 + - - +
793K ILE* 4.2 5.4 + - + +
803K HIS* 4.4 0.5 - - - -
804K ALA* 3.4 4.3 - - - -
805K HIS* 2.9 34.1 + - - +
807K PHE* 3.5 16.7 - - + -
816K LEU* 4.0 15.3 - - + -
829K PHE* 4.5 11.0 - - + -
831K VAL* 4.3 19.1 - - + -
851K PHE* 4.7 2.5 - - + -
858K LEU* 3.7 37.0 - - + -
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Residues in contact with LEU 792 (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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717K LEU* 4.7 11.7 - - + -
719K GLU* 3.4 17.5 - - + +
734K GLY* 3.4 4.9 - - - -
735K VAL* 2.8 40.4 + - + +
737K SER* 3.7 19.5 - - - +
756K ALA* 3.6 22.0 - - + +
757K SER* 3.5 36.1 - - - +
790K ASN* 4.7 0.9 - - + -
791K LEU* 1.3 76.3 - - - +
793K ILE* 1.3 61.4 - - - +
794K ILE* 3.3 22.9 - - + +
801K VAL* 4.4 4.3 - - + -
803K HIS 3.4 4.3 - - - +
804K ALA* 4.0 11.9 - - + -
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Residues in contact with ILE 793 (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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732K CYS* 3.9 21.3 - - + -
733K PHE 3.4 5.8 - - - +
734K GLY* 5.5 1.1 - - - -
791K LEU* 5.1 7.0 - - + +
792K LEU* 1.3 75.6 - - - +
794K ILE* 1.3 57.4 + - - +
801K VAL* 3.6 2.8 - - - -
802K LEU* 2.6 44.6 + - + -
803K HIS* 2.8 36.4 + - + +
829K PHE* 5.0 9.0 - - + -
853K TYR* 3.3 42.8 - - + -
858K LEU* 4.0 27.4 - - + +
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Residues in contact with ILE 794 (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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387K LEU* 4.4 15.3 - - + -
715K VAL* 5.9 0.7 - - + -
717K LEU* 5.6 5.4 - - + -
732K CYS* 3.3 4.5 - - - +
733K PHE* 2.9 42.4 + - + +
735K VAL* 3.6 26.5 - - + -
792K LEU* 3.3 44.0 - - + +
793K ILE* 1.3 74.9 - - - +
795K ASP* 1.3 76.1 + - - +
799K PHE* 3.7 31.9 - - + +
800K GLU 3.4 4.9 - - - +
801K VAL* 5.1 7.4 - - + -
802K LEU* 3.6 4.0 - - - -
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Residues in contact with ASP 795 (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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731K GLN 4.6 6.0 - - - +
732K CYS* 5.3 0.7 - - - -
794K ILE* 1.3 75.7 - - - +
796K GLN* 1.3 60.3 + - - +
797K HIS* 2.8 20.1 + - - +
798K THR* 2.6 49.6 + - - +
799K PHE* 2.9 30.1 + - - +
800K GLU 3.0 14.3 + - - +
802K LEU* 3.4 27.9 - - + +
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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