Contacts of the strand formed by residues 926 - 929 (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 ILE 926 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902A LEU 5.8 0.4 - - - +
903A THR* 6.3 2.9 - - + -
923A VAL* 3.7 22.0 - - + -
925A SER* 1.3 79.6 - - - +
927A SER* 1.3 64.3 + - - +
928A TYR* 5.1 1.1 - - + +
937A ARG* 3.5 4.5 - - - +
938A TYR* 2.8 56.3 + - + +
939A GLY 5.6 4.9 - - - +
944A LEU* 5.1 9.6 - - + -
948A ILE* 5.2 7.9 - - + -
952A LEU* 3.6 29.4 - - + -
917B LEU* 3.8 26.5 - - + -
918B VAL 3.6 4.7 - - - +
919B VAL* 4.9 8.5 - - + -
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Residues in contact with SER 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ILE* 1.3 74.3 - - - +
928A TYR* 1.3 62.3 + - - +
929A THR* 4.2 4.6 - - - +
935A THR* 4.1 13.5 + - - -
936A THR 3.7 5.0 + - - -
937A ARG* 4.5 13.2 - - - +
916B GLN 3.9 0.2 - - - +
917B LEU* 3.4 7.8 - - - +
918B VAL* 2.7 63.4 + - - +
920B GLN* 6.5 0.4 - - - -
920Q GLN* 5.2 6.1 + - - -
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Residues in contact with TYR 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ILE* 5.4 0.7 - - + -
927A SER* 1.3 75.5 + - - +
929A THR* 1.3 63.9 + - - +
930A SER* 4.2 18.3 + - - -
931A PRO* 3.9 9.7 - - - +
934A GLN 3.8 1.6 - - - +
935A THR* 3.6 0.9 - - - -
936A THR* 2.9 47.8 + - - +
938A TYR* 4.7 11.7 - + + -
947A TYR* 4.5 17.5 - + - -
948A ILE* 3.6 33.4 - - + -
951A LYS* 3.1 30.2 + - + -
911B PHE* 5.9 0.2 - + - -
915B SER* 3.5 27.1 - - - -
916B GLN 3.1 21.1 - - - -
917B LEU* 4.4 15.0 - - + -
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Residues in contact with THR 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A SER* 4.2 7.2 - - - +
928A TYR* 1.3 75.9 - - - +
930A SER* 1.3 66.9 + - - +
933A GLY* 5.2 4.9 - - - +
934A GLN 3.6 7.0 - - - -
935A THR* 3.3 25.6 - - - +
915B SER* 3.8 2.1 - - - -
916B GLN* 3.1 56.7 + - + +
918B VAL* 5.9 4.7 - - + -
901Q GLN* 5.4 8.7 - - - +
920Q GLN* 5.1 13.5 - - - +
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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
------------------------------------------------------------
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