Contacts of the strand formed by residues 870 - 876 (chain K) in PDB entry 6R92
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 870 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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814K LEU* 3.6 13.4 - - - +
815K SER* 2.9 17.3 + - - -
832K GLY* 3.7 17.9 - - - -
833K THR 3.2 17.2 + - - +
847K ARG 3.7 16.6 - - - +
848K ILE* 4.2 9.6 - - + -
866K VAL* 3.8 27.6 - - + -
869K ALA* 1.3 69.0 - - - +
871K TYR* 1.3 58.0 + - - +
872K SER 4.2 0.9 - - - +
873K MET* 3.8 31.2 - - + -
882K ALA* 4.3 6.3 - - + -
883K SER 3.3 11.0 - - - +
884K ILE* 4.0 5.2 - - + -
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Residues in contact with TYR 871 (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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723K LYS* 5.5 3.5 + - - -
814K LEU* 4.1 19.8 - - + +
815K SER* 3.5 10.5 - - - -
843K PRO* 3.9 14.4 - - - +
869K ALA* 3.2 24.8 + - + +
870K VAL* 1.3 73.6 - - - +
872K SER* 1.3 60.8 + - - +
883K SER* 2.9 6.0 + - - +
885K ASN* 3.3 34.5 + - - -
910K MET* 3.7 30.9 - - + +
911K ALA 3.6 20.0 - - - +
912K LEU* 3.3 37.6 - - + +
69L ILE* 3.9 7.8 - - - +
70L VAL* 3.4 24.9 - - + -
73L LEU* 4.6 3.4 - - + -
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Residues in contact with SER 872 (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* 3.8 5.2 - - - -
870K VAL 3.4 1.0 - - - -
871K TYR* 1.3 78.7 - - - +
873K MET* 1.3 74.8 + - - +
882K ALA* 3.8 0.2 - - - +
883K SER* 2.8 41.4 + - - +
912K LEU 3.5 15.7 + - - -
913K TYR* 4.3 0.3 - - - -
914K LEU* 3.3 36.1 + - - +
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Residues in contact with MET 873 (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* 3.6 20.4 - - - +
816K LEU* 4.2 2.7 - - - +
817K VAL* 3.2 23.4 - - + +
830K ILE* 3.5 39.7 - - + +
831K VAL* 3.5 2.9 - - - -
832K GLY 3.2 27.1 - - - +
848K ILE* 4.1 15.5 - - - -
870K VAL* 3.8 20.0 - - + -
872K SER* 1.3 87.5 + - - +
874K VAL* 1.3 62.8 + - - +
880K LEU* 4.1 10.3 - - + -
881K LEU 3.2 9.2 - - - +
882K ALA* 3.8 7.4 - - + -
914K LEU* 4.8 1.6 - - - +
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Residues in contact with VAL 874 (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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817K VAL* 4.3 3.4 - - - -
873K MET* 1.3 76.6 - - - +
875K GLU* 1.3 82.0 + - - +
880K LEU* 3.3 5.9 - - - +
881K LEU* 2.9 47.3 + - + +
914K LEU* 4.3 20.0 - - + +
915K LYS* 5.0 6.3 - - + -
916K THR* 3.3 41.1 - - + +
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Residues in contact with GLU 875 (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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817K VAL* 3.0 28.5 - - - +
818K SER 3.9 7.0 - - - +
819K CYS* 3.9 24.5 - - + -
820K LYS 5.3 3.4 - - - +
821K LEU* 5.7 0.4 - - + -
874K VAL* 1.3 90.9 - - - +
876K PHE* 1.3 58.8 + - - +
877K ASN 4.2 0.9 - - - -
878K GLY* 5.9 1.6 - - - +
879K LYS 3.8 6.1 - - - +
880K LEU* 3.9 5.9 - - - +
916K THR* 3.8 7.3 + - - -
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Residues in contact with PHE 876 (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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874K VAL 3.5 6.7 + - - +
875K GLU* 1.3 73.6 - - - +
877K ASN* 1.3 76.9 + - + +
878K GLY 3.2 1.7 - - - +
879K LYS* 2.6 39.3 + - + +
881K LEU* 4.1 14.8 - - + +
890K LEU* 4.1 22.9 - - + -
916K THR* 3.9 21.3 - - + -
918K GLY 3.0 22.0 - - - -
919K ASP* 3.5 23.8 - - - -
920K PHE 4.0 3.1 - - - -
921K ILE* 3.8 24.7 - - + -
935K TYR* 3.6 30.5 - + + -
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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