Contacts of the strand formed by residues 1154 - 1159 (chain N) in PDB entry 3O3U
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 THR1154 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1153N GLY* 1.3 80.3 - - - +
1155N LEU* 1.3 68.7 + - - +
1156N SER* 4.7 6.6 + - - -
1175N GLU* 6.1 0.4 - - - -
1188N LEU* 3.8 6.4 - - - +
1210N PHE* 3.5 5.1 - - - -
1211N SER* 3.0 42.8 + - - -
1213N GLY* 6.6 0.2 - - - -
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Residues in contact with LEU1155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124N PRO* 4.8 1.3 - - + -
1144N CYS* 3.6 33.2 - - - +
1146N SER* 3.8 22.9 - - - +
1154N THR* 1.3 76.0 - - - +
1156N SER* 1.3 65.2 + - - +
1157N TRP* 5.6 0.5 - - - -
1175N GLU* 4.1 16.2 + - - +
1188N LEU* 3.8 30.4 - - + +
1189N GLN 3.9 0.7 - - - -
1190N SER* 3.8 28.6 + - - +
1208N CYS* 4.0 14.1 - - - -
1209N SER 3.3 11.7 - - - +
1210N PHE* 3.9 16.4 - - + -
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Residues in contact with SER1156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154N THR* 4.7 7.4 + - - -
1155N LEU* 1.3 77.1 + - - +
1157N TRP* 1.3 67.2 + - - +
1158N HIS* 3.6 12.4 - - - -
1163N PRO* 6.4 1.1 - - - -
1208N CYS* 3.2 4.6 - - - -
1209N SER* 2.8 42.9 + - - -
1211N SER* 5.9 2.3 - - - -
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Residues in contact with TRP1157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126N ILE* 3.8 42.4 - - + -
1141N VAL* 4.3 10.5 - - + -
1142N GLY 3.7 16.4 - - - -
1144N CYS* 3.7 17.4 - - + +
1156N SER* 1.3 77.4 - - - +
1158N HIS* 1.3 69.3 + - - +
1163N PRO* 3.8 1.0 - - - +
1164N LEU* 2.9 44.8 + - + +
1173N VAL* 4.3 13.2 - - + -
1190N SER* 3.0 48.5 + - - -
1192N LEU* 3.5 38.3 - - + +
1206N PHE* 4.3 9.2 - - + -
1207N SER 3.4 22.2 - - - -
1208N CYS* 4.2 2.9 - - + -
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Residues in contact with HIS1158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1156N SER* 3.6 18.6 + - - -
1157N TRP* 1.3 81.5 - - - +
1159N LEU* 1.3 60.6 + - - +
1160N ASP 4.2 0.2 - - - -
1161N GLY* 4.9 7.5 - - - +
1162N LYS* 3.2 15.4 - - - +
1163N PRO* 3.6 26.3 - - + +
1164N LEU* 4.0 4.3 - - - +
1205N THR 4.4 0.2 - - - -
1206N PHE* 3.3 10.7 - - - -
1207N SER* 2.8 50.4 + - - +
1208N CYS 4.3 0.2 - - - -
1209N SER* 2.8 33.1 + - - -
1221N ARG* 6.3 0.4 - - + -
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Residues in contact with LEU1159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158N HIS* 1.3 73.7 - - - +
1160N ASP* 1.3 91.0 + - + +
1161N GLY 3.2 1.6 - - - -
1162N LYS* 2.8 24.9 + - - +
1163N PRO 5.6 0.7 - - - +
1164N LEU* 3.8 29.7 - - + +
1169N LYS* 4.3 15.0 - - - +
1204N PRO* 3.6 31.2 - - + -
1205N THR 3.4 6.3 - - - +
1206N PHE* 3.7 16.8 - - + -
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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