Contacts of the strand formed by residues 916 - 922 (chain I) 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 GLN 916 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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908I TRP* 3.0 27.0 + - + +
909I VAL 3.2 7.6 - - - +
910I GLN* 3.9 27.7 - - + +
911I PHE* 4.8 1.1 - - - -
914I GLY 4.0 6.1 + - - +
915I SER* 1.3 79.7 - - - +
917I LEU* 1.3 61.8 + - - +
918I VAL* 5.4 4.4 - - + +
927J SER 3.9 0.4 - - - +
928J TYR* 3.2 22.2 - - - -
929J THR* 3.1 39.0 + - + +
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Residues in contact with LEU 917 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907I VAL 3.6 1.7 - - - +
908I TRP* 3.5 2.1 - - - -
909I VAL* 2.6 46.6 + - + +
911I PHE* 3.5 34.5 - - + -
916I GLN* 1.3 74.1 - - - +
918I VAL* 1.3 62.7 + - - +
919I VAL* 4.1 10.3 - - + +
926J ILE* 3.8 23.3 - - + -
927J SER 3.5 14.1 - - - +
928J TYR* 4.2 17.5 - - + -
948J ILE* 4.9 9.6 - - + +
951J LYS* 4.0 23.1 - - + +
952J LEU* 4.4 13.5 - - + +
955J LEU* 5.0 4.7 - - + -
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Residues in contact with VAL 918 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906I ALA* 5.3 4.3 - - + -
907I VAL 3.3 9.9 - - - +
908I TRP* 3.9 23.1 - - + -
916I GLN* 5.4 5.4 - - + +
917I LEU* 1.3 77.9 - - - +
919I VAL* 1.3 65.5 + - - +
920I GLN* 4.0 19.9 + - + +
925J SER 4.1 0.3 - - - +
926J ILE* 3.6 2.1 - - - +
927J SER* 2.8 57.7 + - - +
929J THR* 6.1 3.8 - - + -
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Residues in contact with VAL 919 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906I ALA* 3.3 4.2 - - - -
907I VAL* 2.7 53.9 + - + +
909I VAL* 6.1 1.3 - - + -
917I LEU* 4.9 10.5 - - + -
918I VAL* 1.3 78.3 - - - +
920I GLN* 1.3 66.2 + - - +
921I ALA* 4.0 4.7 + - + +
923J VAL* 3.9 33.7 - - + -
925J SER 3.8 2.7 - - - +
926J ILE* 4.6 13.2 - - + +
952J LEU* 4.5 22.7 - - + -
955J LEU* 5.5 7.9 - - + -
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Residues in contact with GLN 920 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901I GLN* 5.6 1.9 + - - -
905I GLY 3.7 5.5 - - - +
906I ALA* 3.8 23.0 - - - +
918I VAL* 4.7 14.7 - - + +
919I VAL* 1.3 74.5 - - - +
921I ALA* 1.3 54.2 + - - +
923J VAL* 3.4 5.7 - - - +
924J SER* 2.7 38.2 + - - +
925J SER* 2.8 36.6 + - - +
937J ARG* 4.7 7.2 - - - +
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Residues in contact with ALA 921 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904I SER* 3.3 5.5 - - - -
905I GLY* 2.8 40.8 + - - +
907I VAL* 6.3 2.5 - - + -
919I VAL* 4.0 5.1 + - + +
920I GLN* 1.3 75.5 - - - +
922I GLY* 1.3 58.9 + - - +
921J ALA* 4.7 13.0 - - + -
922J GLY 3.3 15.3 - - - +
923J VAL* 4.4 6.7 - - + -
924J SER* 4.0 3.6 - - - +
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Residues in contact with GLY 922 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903I THR 4.1 6.5 - - - -
904I SER* 4.1 4.7 - - - -
921I ALA* 1.3 75.8 - - - +
923I VAL* 1.3 63.3 + - - -
924I SER* 3.4 0.5 + - - -
940I GLU* 6.1 0.2 - - - -
921J ALA* 4.2 3.1 - - - -
922J GLY 2.7 43.4 + - - +
924J SER* 4.6 6.8 - - - +
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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