Contacts of the strand formed by residues 904 - 911 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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900A THR* 3.9 3.1 - - - -
901A GLN* 2.5 48.0 + - - +
902A LEU 3.6 0.6 - - - -
903A THR* 1.3 84.6 + - - +
905A GLY* 1.3 60.9 + - - +
920A GLN* 6.0 1.3 - - - -
921A ALA 3.4 15.0 - - - -
922A GLY* 4.2 6.7 - - - -
923A VAL* 4.1 6.2 - - - +
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Residues in contact with GLY 905 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A ALA 3.7 8.3 - - - -
900A THR* 4.0 10.3 - - - -
901A GLN* 3.2 8.4 + - - -
904A SER* 1.3 79.7 - - - +
906A ALA* 1.3 62.2 + - - +
907A VAL* 5.7 1.1 - - - -
920A GLN* 3.7 5.4 - - - +
921A ALA* 2.9 35.5 + - - +
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Residues in contact with ALA 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898A TRP* 3.2 6.2 - - - +
899A ALA* 3.0 38.9 + - + +
900A THR* 5.0 1.4 - - - +
901A GLN* 4.9 4.7 - - - +
905A GLY* 1.3 75.5 - - - +
907A VAL* 1.3 64.9 + - - +
918A VAL* 5.3 5.2 - - + -
919A VAL 3.3 6.7 - - - +
920A GLN* 3.8 28.0 - - + +
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Residues in contact with VAL 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896A VAL* 5.9 1.6 - - + -
897A GLY 3.7 8.7 - - - +
898A TRP* 4.0 21.5 - - + -
900A THR* 6.2 2.2 - - + -
905A GLY 5.7 0.4 - - - -
906A ALA* 1.3 79.4 - - - +
908A TRP* 1.3 61.8 + - - +
909A VAL* 3.9 22.0 - - + -
917A LEU 3.6 1.7 - - - +
918A VAL* 3.4 5.6 - - - +
919A VAL* 2.9 46.6 + - + +
955B LEU* 4.2 12.6 - - + -
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Residues in contact with TRP 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895A ASN* 4.2 16.2 - - + -
896A VAL* 3.4 8.7 - - - -
897A GLY* 2.7 52.0 + - - +
898A TRP* 4.6 0.2 - - - +
906A ALA 4.3 0.4 - - - -
907A VAL* 1.3 72.4 - - - +
909A VAL* 1.3 75.5 + - - +
910A GLN* 4.0 29.6 - - + -
916A GLN* 2.9 29.1 + - - -
917A LEU 3.6 2.0 - - - -
918A VAL* 3.9 25.6 - - + +
960A LEU* 4.0 21.3 - - + -
962A PHE* 4.9 10.5 - + - -
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Residues in contact with VAL 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A VAL* 3.7 26.0 - - + -
895A ASN 3.5 3.6 - - - -
896A VAL* 3.8 12.6 - - + -
907A VAL* 3.9 10.3 - - + -
908A TRP* 1.3 85.3 + - - +
910A GLN* 1.3 64.4 + - - +
911A PHE* 3.9 24.5 - - + -
916A GLN* 3.3 5.7 - - - +
917A LEU* 2.9 40.6 + - + +
919A VAL* 6.5 0.9 - - + -
955B LEU* 3.5 35.0 - - + -
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Residues in contact with GLN 910 (chain A).
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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893A VAL* 4.0 1.7 - - - +
894A LYS* 2.9 32.6 + - - +
895A ASN* 2.8 49.3 + - + +
908A TRP* 4.0 24.2 - - + -
909A VAL* 1.3 75.9 - - - +
911A PHE* 1.3 70.3 + - - +
914A GLY* 4.5 9.6 + - - +
915A SER 3.6 9.6 - - - +
916A GLN* 4.0 22.7 - - + +
962A PHE* 5.7 0.2 - - - -
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Residues in contact with PHE 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A VAL* 3.8 15.5 - - + -
892A PHE 3.2 23.8 - - - +
893A VAL* 4.1 20.4 - - + -
894A LYS* 3.7 16.3 + - - +
909A VAL* 3.9 14.6 - - + -
910A GLN* 1.3 77.9 - - - +
912A ASN* 1.3 69.6 + - - +
913A ASP* 3.3 18.6 - - - +
914A GLY* 3.2 11.7 + - - -
915A SER* 2.9 31.4 + - - +
916A GLN 4.7 0.4 - - - -
917A LEU* 3.6 36.8 - - + -
951B LYS* 3.6 34.5 - - + -
954B CYS* 4.2 7.4 - - + -
955B LEU* 4.2 2.2 - - + -
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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