Contacts of the strand formed by residues 878 - 888 (chain B) in PDB entry 6CNB
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 PRO 878 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835B LYS* 4.2 29.4 - - + -
836B VAL 3.7 11.0 - - - +
837B GLN* 4.6 17.0 - - + +
873B TYR* 4.1 0.6 + - - -
876B PRO 4.7 1.1 - - - +
877B GLU* 1.3 101.2 - - + +
879B SER* 1.3 64.4 + - - +
880B HIS* 6.1 1.3 - - - +
902B GLN* 2.9 23.3 - - - +
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Residues in contact with SER 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B LYS* 3.5 2.1 - - - +
836B VAL* 2.9 43.2 + - - +
873B TYR* 3.4 27.9 - - - -
878B PRO* 1.3 78.7 - - - +
880B HIS* 1.3 77.3 + - - +
900B LEU* 3.8 9.5 - - - +
901B ARG 3.5 15.3 - - - -
902B GLN* 4.1 9.0 - - - -
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Residues in contact with HIS 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833B GLY 4.3 5.1 + - - -
834B MET 3.9 4.6 - - - +
835B LYS* 3.2 51.4 + - + -
836B VAL* 4.5 1.8 - - - -
878B PRO* 6.1 1.0 - - - +
879B SER* 1.3 77.9 + - - +
881B ILE* 1.3 64.3 + - - +
882B ASP 3.7 0.2 - - - -
900B LEU* 3.3 5.1 - - - -
901B ARG* 2.8 63.0 + - + +
902B GLN* 5.6 2.5 - - - -
903B ASN* 5.9 1.8 - - - -
95C GLU* 5.0 12.1 - - + +
67L PHE* 3.3 42.3 - + - -
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Residues in contact with ILE 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823B SER 4.9 0.7 - - - +
830B GLY* 4.6 1.1 - - - -
831B GLU* 3.2 32.8 - - - +
832B VAL 3.2 1.0 - - - -
833B GLY* 2.3 38.0 + - - -
834B MET 3.6 7.3 + - - +
836B VAL* 3.7 26.9 - - + -
842B TYR* 3.5 37.2 - - + +
880B HIS* 1.3 72.4 - - - +
882B ASP* 1.3 55.6 + - - +
883B GLN 4.3 3.1 - - - +
884B VAL* 3.6 28.0 - - + -
898B VAL* 4.8 4.9 - - + -
899B LEU 4.0 8.3 - - - +
900B LEU* 4.3 13.0 - - + -
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Residues in contact with ASP 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B PHE 5.6 0.7 - - - +
788B ARG* 2.7 28.3 + - - -
832B VAL* 3.1 26.8 - - - +
833B GLY 4.3 2.0 - - - +
880B HIS 3.6 2.8 + - - -
881B ILE* 1.3 74.3 - - - +
883B GLN* 1.3 87.3 + - - +
899B LEU* 2.7 38.7 + - - +
901B ARG* 3.7 34.8 - - - +
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Residues in contact with GLN 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B PHE 3.8 16.1 + - - +
719B LYS* 4.1 22.1 + - - +
721B ILE* 4.3 21.4 - - + +
832B VAL* 4.4 5.2 - - - -
881B ILE* 3.7 1.2 - - - +
882B ASP* 1.3 101.2 + - - +
884B VAL* 1.3 69.0 + - - +
897B LYS 4.5 0.2 - - - +
898B VAL* 3.7 0.2 - - - -
899B LEU* 3.2 32.3 + - + +
57L LEU* 3.3 44.0 - - + +
58L LYS 5.6 1.3 - - - +
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Residues in contact with VAL 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721B ILE* 5.8 0.4 - - - -
829B LEU* 4.0 16.8 - - + -
830B GLY 4.6 11.9 - - - +
831B GLU 4.9 3.4 - - - -
832B VAL* 4.7 3.1 - - + +
881B ILE* 3.6 20.9 - - + -
883B GLN* 1.3 80.8 - - - +
885B MET* 1.3 63.4 + - - +
886B MET* 5.4 1.1 - - + +
896B ILE* 5.8 0.2 - - + -
897B LYS 3.4 4.9 - - - -
898B VAL* 3.5 27.1 - - + -
57L LEU* 3.4 9.2 - - - +
58L LYS* 3.3 54.7 + - + +
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Residues in contact with MET 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.2 62.8 - - + +
721B ILE* 4.2 12.6 - - + -
884B VAL* 1.3 77.9 - - - +
886B MET* 1.3 61.5 + - - +
887B SER* 3.4 26.0 - - - +
895B LEU* 3.8 4.5 - - + +
896B ILE* 3.3 5.3 - - - +
897B LYS* 2.5 74.6 + - + +
55L ILE* 4.8 4.0 - - + -
56L LEU 3.7 9.6 - - - +
57L LEU* 5.2 6.1 - - + -
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Residues in contact with MET 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806B ILE* 6.0 6.3 - - + -
827B ASP* 4.8 9.4 - - - +
829B LEU* 3.8 31.6 - - + -
884B VAL* 4.2 1.7 - - + +
885B MET* 1.3 72.1 - - - +
887B SER* 1.3 70.0 + - - +
895B LEU 3.5 4.7 - - - +
896B ILE* 4.1 20.2 - - + -
29L TYR* 4.4 30.1 - - - +
40L LEU* 5.3 7.0 - - + -
46L VAL* 4.6 6.7 - - + -
56L LEU* 3.0 41.7 + - + +
57L LEU* 5.1 1.0 - - - +
58L LYS* 6.4 2.0 - - + -
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Residues in contact with SER 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 4.6 4.7 - - - -
885B MET* 3.4 18.7 - - - +
886B MET* 1.3 82.0 + - - +
888B VAL* 1.3 66.5 + - - +
894B ALA* 3.8 2.9 - - - +
895B LEU* 2.9 39.4 + - - +
46L VAL* 3.7 16.4 - - - +
55L ILE* 3.2 37.8 - - - +
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Residues in contact with VAL 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 3.0 25.5 + - - +
887B SER* 1.3 78.2 - - - +
889B SER* 1.3 73.3 + - - +
892B ASP* 3.5 27.8 - - + +
893B GLN 3.7 12.6 - - - +
894B ALA* 4.8 0.9 - - - +
895B LEU* 4.8 2.0 - - - -
46L VAL* 3.9 22.6 - - + +
54L ARG* 3.5 45.9 - - + +
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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