Contacts of the strand formed by residues 875 - 883 (chain B) in PDB entry 4E5W
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 LEU 875 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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870B PHE* 4.8 3.6 - - + -
871B GLU 3.6 4.2 + - - +
872B LYS* 3.1 20.6 + - + +
873B ARG 5.0 1.4 - - - +
874B PHE* 1.3 75.3 - - - +
876B LYS* 1.3 61.2 + - - +
877B ARG 3.9 2.1 + - - -
892B CYS* 3.9 26.9 - - + -
893B ARG 3.7 0.7 - - - -
894B TYR* 3.9 24.7 - - + -
905B VAL* 3.9 18.2 - - + -
907B VAL* 3.9 12.6 - - + -
944B CYS* 4.2 24.0 - - + -
953B LYS* 4.5 6.3 - - + -
955B ILE* 4.0 22.9 - - + -
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Residues in contact with LYS 876 (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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873B ARG 6.1 0.2 - - - +
874B PHE 4.5 6.1 - - - +
875B LEU* 1.3 72.3 - - - +
877B ARG* 1.4 66.0 + - - +
878B ILE* 3.5 5.1 + - + +
892B CYS* 3.1 6.1 - - - -
893B ARG* 2.9 44.7 + - + +
895B ASP* 2.8 36.1 + - + +
898B GLY* 4.2 13.5 + - - -
900B ASN* 4.1 22.0 + - - +
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Residues in contact with ARG 877 (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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875B LEU 3.9 3.8 + - - -
876B LYS* 1.4 72.4 - - - +
878B ILE* 1.3 76.7 + - - +
879B ARG* 4.3 7.4 - - - +
880B ASP* 3.0 35.7 + - - +
890B GLU* 3.2 37.5 + - + +
891B LEU 4.6 2.0 - - - +
892B CYS* 3.8 11.6 - - - -
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Residues in contact with ILE 878 (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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876B LYS* 3.8 9.6 - - + +
877B ARG* 1.3 90.2 + - - +
879B ARG* 1.4 70.0 + - + +
891B LEU* 2.8 35.1 + - + +
893B ARG* 4.0 33.4 - - + +
904B GLN* 3.9 23.3 - - - +
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Residues in contact with ARG 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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877B ARG* 4.3 10.0 - - - +
878B ILE* 1.4 86.4 - - + +
880B ASP* 1.3 67.9 + - - +
881B LEU* 3.6 20.3 - - - +
890B GLU* 3.4 4.3 - - - +
891B LEU* 2.7 52.2 + - + +
958B PHE* 3.9 24.5 - - - -
960B PRO 5.0 6.3 + - - -
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Residues in contact with ASP 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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877B ARG* 3.0 25.7 + - - +
879B ARG* 1.3 87.7 + - - +
881B LEU* 1.3 64.9 + - - +
882B GLY* 4.6 4.9 - - - +
883B GLU* 5.7 3.1 - - + +
888B LYS* 5.1 8.3 - - - +
889B VAL 3.8 5.8 - - - +
890B GLU* 3.3 22.2 - - - +
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Residues in contact with LEU 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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879B ARG* 3.6 27.4 - - - +
880B ASP* 1.3 73.7 - - - +
882B GLY* 1.3 58.2 + - - +
889B VAL* 2.8 14.4 + - + +
890B GLU 3.9 3.4 - - - -
891B LEU* 3.7 33.0 - - + +
906B ALA* 4.1 13.7 - - + -
958B PHE* 3.8 37.7 - - + -
966B GLU* 4.7 7.6 - - - +
1202B 0NT 3.4 55.7 - - + +
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Residues in contact with GLY 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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880B ASP* 3.7 4.8 - - - +
881B LEU* 1.3 81.7 - - - +
883B GLU* 1.3 58.9 + - - -
888B LYS* 3.6 1.9 - - - +
889B VAL* 2.8 33.5 + - - +
1202B 0NT 3.2 31.0 - - - +
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Residues in contact with GLU 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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880B ASP* 5.7 3.6 - - + +
882B GLY* 1.3 70.6 - - - -
884B GLY* 1.3 63.1 + - - +
887B GLY 4.1 3.4 - - - +
888B LYS* 4.3 16.8 - - + +
911B LYS* 4.3 18.5 + - + -
1202B 0NT 2.9 35.7 + - + +
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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