Contacts of the strand formed by residues 904 - 911 (chain E) in PDB entry 5LHY
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 SER 904 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900E THR* 3.8 3.5 - - - -
901E GLN* 2.5 47.8 + - - +
902E LEU 3.6 0.8 - - - -
903E THR* 1.3 83.9 + - - +
905E GLY* 1.3 59.5 + - - +
920E GLN* 6.1 1.1 - - - -
921E ALA 3.5 15.5 - - - -
922E GLY* 4.3 5.6 - - - -
923E VAL* 4.1 4.9 - - - +
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Residues in contact with GLY 905 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899E ALA 3.6 11.0 - - - -
900E THR* 3.9 11.7 - - - -
901E GLN* 3.3 6.7 + - - -
904E SER* 1.3 80.7 - - - +
906E ALA* 1.3 61.8 + - - +
907E VAL* 5.6 1.8 - - - -
920E GLN* 3.8 6.2 - - - +
921E ALA* 2.9 34.8 + - - +
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Residues in contact with ALA 906 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898E TRP* 3.2 5.9 - - - +
899E ALA* 3.0 36.7 + - + +
900E THR* 4.9 0.8 - - - +
901E GLN* 5.3 4.0 - - - +
905E GLY* 1.3 76.0 - - - +
907E VAL* 1.3 64.3 + - - +
908E TRP 4.3 0.2 - - - -
918E VAL* 5.4 5.6 - - + -
919E VAL 3.3 9.9 - - - +
920E GLN* 4.1 22.7 - - - +
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Residues in contact with VAL 907 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896E VAL* 5.8 1.3 - - + -
897E GLY 3.7 7.9 - - - +
898E TRP* 3.9 25.4 - - + -
900E THR* 5.8 3.8 - - + -
905E GLY 5.6 0.9 - - - -
906E ALA* 1.3 81.0 - - - +
908E TRP* 1.3 62.8 - - - +
909E VAL* 3.9 21.5 - - + +
917E LEU 3.6 1.9 - - - +
918E VAL* 3.4 5.4 - - - +
919E VAL* 2.9 45.0 + - + +
921E ALA* 6.3 2.7 - - + -
955F LEU* 4.6 10.8 - - + -
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Residues in contact with TRP 908 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895E ASN* 4.2 8.7 - - + -
896E VAL* 3.2 22.8 - - - -
897E GLY* 2.6 54.1 + - - +
906E ALA 4.3 0.2 - - - -
907E VAL* 1.3 72.8 - - - +
909E VAL* 1.3 71.6 + - - +
910E GLN* 4.0 24.7 - - + -
916E GLN* 3.2 25.1 + - + -
917E LEU 3.6 2.0 - - - -
918E VAL* 4.1 22.9 - - + +
960E LEU* 3.9 15.7 - - + -
962E PHE* 4.2 20.9 - + - -
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Residues in contact with VAL 909 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893E VAL* 3.7 24.7 - - + -
895E ASN 3.4 2.9 - - - -
896E VAL* 3.8 13.5 - - + -
907E VAL* 3.9 12.1 - - + +
908E TRP* 1.3 84.9 - - - +
910E GLN* 1.3 63.6 + - - +
911E PHE* 3.7 26.5 - - + -
916E GLN* 3.3 5.7 - - - +
917E LEU* 2.8 46.0 + - + +
955F LEU* 3.7 32.1 - - + -
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Residues in contact with GLN 910 (chain E).
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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893E VAL* 4.1 1.6 - - - +
894E LYS* 2.9 32.8 + - - +
895E ASN* 2.7 49.9 + - + +
908E TRP* 4.0 21.3 - - + -
909E VAL* 1.3 76.1 - - - +
911E PHE* 1.3 69.5 + - - +
914E GLY* 4.6 9.0 + - - +
915E SER 3.6 9.6 - - - +
916E GLN* 3.9 26.0 - - + +
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Residues in contact with PHE 911 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891E VAL* 4.0 10.8 - - + -
892E PHE 3.2 24.0 - - - +
893E VAL* 3.8 23.3 - - + -
894E LYS* 3.7 15.7 + - - +
909E VAL* 3.7 14.6 - - + -
910E GLN* 1.3 77.0 - - - +
912E ASN* 1.3 68.4 + - - +
913E ASP* 3.3 18.4 - - - +
914E GLY* 3.2 12.4 + - - -
915E SER* 2.9 30.8 + - - +
916E GLN 4.5 0.7 - - - -
917E LEU* 3.6 44.6 - - + -
928F TYR* 5.8 0.2 - + - -
951F LYS* 3.7 29.2 - - + -
954F CYS* 4.4 7.0 - - + -
955F LEU* 5.2 1.6 - - + -
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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