Contacts of the strand formed by residues 918 - 923 (chain B) in PDB entry 3HS0
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 THR 918 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914B GLY* 3.9 0.9 - - - -
915B VAL* 2.8 31.9 + - - +
916B GLY* 3.4 6.1 + - - +
917B GLY* 1.3 81.5 - - - +
919B GLN* 1.3 66.3 + - - +
920B LEU* 4.1 3.4 - - + +
1292C THR* 3.8 27.6 - - + -
1293C ALA 3.6 6.5 - - - +
1294C SER* 3.6 16.0 - - - -
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Residues in contact with GLN 919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907B LYS 3.3 21.6 + - - -
908B LEU* 3.5 12.8 - - - +
909B ASP 2.9 30.9 + - - -
910B PRO* 3.7 5.0 - - + +
913B LYS* 3.9 27.4 - - - +
914B GLY* 4.1 11.7 - - - -
915B VAL* 5.2 1.1 - - - -
918B THR* 1.3 77.5 - - - +
920B LEU* 1.3 61.7 + - - +
921B GLU* 3.6 32.8 + - + +
1291C VAL 3.5 4.7 - - - +
1292C THR* 3.6 1.0 - - - -
1293C ALA* 2.8 37.6 + - + +
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Residues in contact with LEU 920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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915B VAL* 5.6 3.4 - - + +
918B THR* 4.1 3.6 + - + +
919B GLN* 1.3 73.7 - - - +
921B GLU* 1.3 68.2 + - - +
922B VAL* 4.2 14.4 - - + -
1258C GLU* 5.5 0.7 - - - +
1290C THR* 3.8 22.0 - - + -
1291C VAL 3.7 0.9 - - - +
1292C THR* 3.6 30.1 - - + +
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Residues in contact with GLU 921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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906B VAL* 3.8 23.9 - - + +
908B LEU* 4.6 3.8 - - + -
913B LYS* 4.4 9.2 + - - -
919B GLN* 3.6 30.6 + - + +
920B LEU* 1.3 79.5 - - - +
922B VAL* 1.3 63.1 + - - +
923B ILE* 3.7 22.1 + - + +
1289C ILE 3.6 3.1 - - - +
1290C THR* 3.6 0.4 - - - -
1291C VAL* 2.9 51.1 + - + +
1301C MET* 6.2 0.2 - - - -
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Residues in contact with VAL 922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920B LEU* 4.2 14.8 - - + -
921B GLU* 1.3 75.5 + - - +
923B ILE* 1.3 75.7 + - - +
924B LYS* 3.7 8.1 + - + +
1288C ASP* 4.7 19.1 - - + +
1289C ILE 3.7 6.1 - - - +
1290C THR* 4.2 23.8 - - + +
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Residues in contact with ILE 923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904B THR* 4.9 13.9 - - + -
906B VAL* 4.0 23.8 - - + -
921B GLU* 3.7 26.9 - - + +
922B VAL* 1.3 82.8 - - - +
924B LYS* 1.3 72.5 + - - +
926B ARG* 4.3 18.2 - - + +
1287C GLN 4.1 1.0 - - - +
1288C ASP* 3.5 1.1 - - - -
1289C ILE* 3.0 43.3 + - + +
1291C VAL* 5.6 6.3 - - + -
1301C MET* 6.1 0.2 - - - -
1303C ILE* 4.8 20.6 - - + -
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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