Contacts of the strand formed by residues 893 - 900 (chain G) 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 VAL 893 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892G PHE* 1.3 92.5 - - - +
894G LYS* 1.3 63.4 + - - +
895G ASN 3.9 2.7 - - - +
896G VAL* 3.5 31.4 - - + -
909G VAL* 3.6 16.4 - - + -
910G GLN 3.9 4.5 - - - +
911G PHE* 4.0 19.1 - - + -
963G SER* 4.6 2.3 + - - -
954H CYS* 4.0 22.0 - - + +
955H LEU* 4.6 6.1 - - + -
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Residues in contact with LYS 894 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892G PHE* 3.9 4.2 + - + -
893G VAL* 1.3 74.6 - - - +
895G ASN* 1.3 87.0 + - - +
910G GLN* 2.8 38.9 + - - +
911G PHE 3.8 18.4 + - - -
912G ASN* 4.3 16.7 + - + +
914G GLY* 5.4 2.8 - - - -
961G MET* 4.7 3.6 - - - +
962G PHE 4.3 0.3 - - - -
963G SER* 2.5 42.5 + - - +
965G PRO* 6.4 0.9 - - + -
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Residues in contact with ASN 895 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893G VAL* 3.9 0.3 - - - +
894G LYS* 1.3 109.2 - - - +
896G VAL* 1.3 67.5 + - - +
908G TRP* 3.9 9.9 - - + -
910G GLN* 2.8 52.6 + - + +
961G MET* 3.4 4.0 - - - -
962G PHE* 3.3 33.3 - - + +
963G SER 3.0 19.2 + - - +
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Residues in contact with VAL 896 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893G VAL* 3.5 22.2 - - + -
895G ASN* 1.3 79.5 - - - +
897G GLY* 1.3 58.1 + - - +
898G TRP* 5.9 4.7 - - + -
907G VAL* 5.8 2.0 - - + -
908G TRP* 3.4 14.7 - - - +
909G VAL* 4.0 15.3 - - + -
959G LEU* 4.1 12.1 - - + -
960G LEU* 3.8 6.2 - - - +
961G MET* 2.9 57.8 + - + +
955H LEU* 5.4 2.5 - - + -
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Residues in contact with GLY 897 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896G VAL* 1.3 78.3 - - - +
898G TRP* 1.3 61.0 + - - +
907G VAL* 3.6 2.4 - - - +
908G TRP* 2.7 47.4 + - - +
959G LEU* 3.2 19.3 - - - +
960G LEU* 4.2 8.3 - - - -
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Residues in contact with TRP 898 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961F MET* 4.0 10.5 - - + -
896G VAL* 5.9 4.3 - - + -
897G GLY* 1.3 76.7 - - - +
899G ALA* 1.3 63.2 + - - +
900G THR* 4.0 17.6 - - + +
906G ALA 3.2 14.6 - - - +
907G VAL* 3.9 22.4 - - + -
957G SER* 3.4 30.2 + - - -
958G ILE* 3.2 10.2 - - - +
959G LEU* 3.0 78.5 + - + +
898H TRP* 3.5 39.0 - + - -
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Residues in contact with ALA 899 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898G TRP* 1.3 75.5 - - - +
900G THR* 1.3 61.8 + - - +
901G GLN* 3.7 12.7 + - + +
905G GLY* 3.5 2.1 - - - -
906G ALA* 3.0 31.6 + - + +
957G SER 3.6 5.4 - - - -
958G ILE* 3.9 23.3 - - + -
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Residues in contact with THR 900 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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964F ASN* 5.4 3.8 + - - +
898G TRP* 4.0 21.8 - - + +
899G ALA* 1.3 75.6 - - - +
901G GLN* 1.3 64.1 + - - +
904G SER 3.7 7.6 - - - -
905G GLY* 3.9 10.1 - - - -
906G ALA 5.0 1.1 - - - +
907G VAL* 6.0 2.2 - - + -
955G LEU* 3.2 13.7 + - - +
956G SER* 3.3 17.0 - - - -
957G SER* 3.0 28.8 + - - +
958G ILE* 5.0 0.5 - - - +
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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