Contacts of the strand formed by residues 231 - 236 (chain J) in PDB entry 3FKS
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 SER 231 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J GLY* 2.9 24.7 + - - -
108J ARG 4.1 1.6 + - - +
185J ILE* 4.7 8.1 - - - -
203J CYS* 3.2 19.3 - - - -
205J TYR* 5.9 1.3 - - - -
222J LEU* 4.2 12.2 - - - +
227J ALA 3.2 14.5 + - - -
228J MET* 3.1 27.7 + - - +
229J LYS 3.3 1.2 + - - -
230J TYR* 1.3 81.2 - - - +
232J ILE* 1.3 67.0 + - - +
233J ILE* 4.3 4.5 + - - +
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Residues in contact with ILE 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102J GLY 4.6 1.1 - - - +
105J LEU* 3.1 48.7 - - + +
106J LEU* 3.6 18.4 - - + +
108J ARG 4.1 1.8 - - - +
110J VAL* 5.0 3.8 - - + -
203J CYS 2.8 13.9 + - - +
204J VAL* 3.3 13.2 - - + +
205J TYR 2.8 28.6 + - - +
231J SER* 1.3 76.9 - - - +
233J ILE* 1.3 71.0 + - - +
234J VAL* 4.0 9.9 - - + -
255J ILE* 3.5 31.6 - - + -
259J PHE* 4.0 17.9 - - + -
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Residues in contact with ILE 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ARG 3.3 8.5 + - - +
109J VAL* 3.5 36.2 - - + +
110J VAL* 2.9 31.7 + - - +
205J TYR* 3.6 37.5 - - + +
207J ALA* 5.3 1.6 - - + -
215J VAL* 4.3 18.8 - - + -
218J LEU* 5.2 2.5 - - + -
219J VAL* 4.1 11.0 - - + -
222J LEU* 4.1 21.5 - - + -
228J MET* 4.7 9.9 - - - -
231J SER* 4.9 4.5 - - - +
232J ILE* 1.3 78.9 - - - +
234J VAL* 1.3 65.7 + - - +
235J ALA* 4.8 1.3 - - + -
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Residues in contact with VAL 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J VAL* 3.3 5.8 - - + -
111J ASP 3.9 18.4 - - - +
112J ALA* 4.4 2.9 - - - -
204J VAL* 4.5 9.2 - - + -
205J TYR 3.1 9.8 + - - +
206J VAL* 3.6 4.9 - - + +
207J ALA 3.0 27.2 + - - +
232J ILE* 4.6 4.5 - - + -
233J ILE* 1.3 73.7 - - - +
235J ALA* 1.3 61.1 + - - +
236J ALA 4.0 0.2 + - - -
248J ALA* 3.9 31.1 - - + +
251J THR* 4.8 3.4 - - + -
252J ALA* 3.6 27.4 - - + +
255J ILE* 3.7 23.6 - - + -
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Residues in contact with ALA 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J VAL* 4.7 4.0 - - + -
110J VAL 2.8 10.3 + - - +
111J ASP* 3.2 25.9 - - - +
112J ALA 3.6 2.2 + - - -
117J ILE* 3.6 26.7 - - + -
207J ALA* 3.8 8.3 - - + -
215J VAL* 4.6 20.2 - - + -
233J ILE* 3.8 0.9 + - + -
234J VAL* 1.3 73.4 - - - +
236J ALA* 1.3 60.2 + - - +
237J THR* 3.8 11.4 - - + -
240J GLU* 3.8 5.9 - - - +
124M PHE* 6.1 0.2 - - + -
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Residues in contact with ALA 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ALA* 4.4 2.2 - - + -
207J ALA 3.0 13.7 + - - +
208J VAL* 3.7 1.6 - - + -
209J GLY 3.5 13.2 + - - -
234J VAL 4.0 0.6 + - - -
235J ALA* 1.3 72.8 - - - +
237J THR* 1.3 67.6 + - - +
240J GLU* 3.7 11.2 - - - +
244J LEU 3.6 15.5 - - - +
245J GLN* 3.4 23.1 - - + +
248J ALA* 3.6 27.8 - - + +
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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