Contacts of the strand formed by residues 231 - 239 (chain F) in PDB entry 3J8B
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 MET 231 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184F VAL* 6.3 2.0 - - - -
218F SER* 3.3 4.9 - - - +
219F THR 2.5 46.7 + - - +
220F LEU* 5.3 0.7 - - - -
221F MET 5.9 0.9 - - - +
229F GLY 4.5 3.4 - - - +
230F VAL* 1.3 78.4 - - - +
232F PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F TYR* 3.9 22.7 - - + -
217F VAL 3.5 5.2 - - - +
218F SER* 4.3 3.6 - - - +
231F MET* 1.3 78.1 - - - +
233F THR* 1.3 60.7 + - - +
234F PRO 3.9 1.4 - - - -
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Residues in contact with THR 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216F TYR* 3.1 8.1 - - - -
217F VAL* 2.7 39.3 + - - -
219F THR* 4.9 12.6 - - - -
231F MET 3.7 1.4 + - - -
232F PHE* 1.3 72.3 - - - +
234F PRO* 1.3 62.0 - - - +
235F LEU* 3.6 2.1 + - - +
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Residues in contact with PRO 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F ALA 3.5 6.7 - - - +
216F TYR* 4.7 2.2 - - + -
232F PHE 3.9 2.8 - - - -
233F THR* 1.3 71.5 - - - +
235F LEU* 1.3 60.5 + - - +
236F THR 4.3 0.3 + - - -
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Residues in contact with LEU 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F GLY 5.5 4.3 - - - +
90F ARG 4.8 5.2 - - - +
91F VAL* 4.7 13.9 - - - +
92F VAL* 5.1 1.6 - - + -
215F ALA* 2.8 38.2 + - + +
216F TYR* 5.1 1.1 - - - +
217F VAL 5.7 0.9 - - - +
233F THR 3.6 3.1 + - - +
234F PRO* 1.3 74.1 - - - +
236F THR* 1.3 69.1 + - - +
237F VAL* 3.6 1.6 + - - +
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Residues in contact with THR 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F ARG 4.3 12.8 + - - -
91F VAL* 3.4 9.3 - - - +
92F VAL* 2.9 26.6 + - - +
234F PRO 4.3 0.6 + - - -
235F LEU* 1.3 74.2 - - - +
237F VAL* 1.3 59.3 + - - +
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Residues in contact with VAL 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F VAL* 6.2 0.2 - - - -
92F VAL* 3.2 13.2 - - + +
94F LEU* 6.1 2.9 - - + -
213F ILE* 4.2 28.9 - - + +
215F ALA* 5.1 6.5 - - + +
235F LEU 3.6 3.5 + - - +
236F THR* 1.3 76.8 - - - +
238F LYS* 1.3 65.2 + - - +
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Residues in contact with LYS 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F VAL 2.9 8.6 + - - +
93F ARG* 3.2 8.3 - - + -
94F LEU* 3.0 26.3 + - - +
237F VAL* 1.3 78.2 - - - +
239F TYR* 1.3 64.5 + - - +
240F ALA* 5.7 2.2 - - + -
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Residues in contact with TYR 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU* 3.4 12.6 - - + +
96F PRO* 5.7 5.8 - - + -
238F LYS* 1.3 75.3 - - - +
240F ALA* 1.3 60.8 + - - +
217H GLU* 3.8 41.9 - - + +
218H LEU* 4.8 4.4 - - - +
219H GLU 5.7 0.3 + - - -
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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