Contacts of the strand formed by residues 231 - 236 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107L GLY* 2.7 34.0 + - - -
108L ARG 4.3 0.2 + - - -
185L ILE* 3.8 15.6 - - - +
203L CYS* 3.3 9.0 - - - +
205L TYR* 6.0 1.6 - - - -
222L LEU* 4.4 4.9 - - - +
227L ALA 2.7 24.1 + - - -
228L MET* 3.0 12.1 + - - +
230L TYR* 1.3 89.0 - - - +
232L ILE* 1.3 63.3 + - - +
233L ILE* 4.0 18.1 + - - -
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Residues in contact with ILE 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L GLY 5.1 0.7 - - - +
105L LEU* 3.8 27.8 - - + +
106L LEU* 3.5 31.0 - - + +
108L ARG 4.1 7.6 - - - +
110L VAL* 4.9 3.4 - - + -
202L TYR* 6.0 0.2 - - + -
203L CYS 2.8 12.6 + - - +
204L VAL* 3.3 13.8 - - + +
205L TYR 2.9 24.8 + - - +
231L SER* 1.3 80.3 - - - +
233L ILE* 1.3 62.7 + - - +
234L VAL* 3.6 13.2 + - + -
255L ILE* 3.8 33.0 - - + -
259L PHE* 3.9 20.6 - - + -
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Residues in contact with ILE 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ARG 3.7 7.0 + - - +
109L VAL* 3.3 23.6 - - + +
110L VAL 3.1 23.0 + - - -
205L TYR* 3.2 30.5 - - + +
207L ALA* 5.1 0.7 - - + -
215L VAL* 3.9 27.8 - - + -
218L LEU* 4.6 2.2 - - + -
219L VAL* 4.3 9.2 - - + -
222L LEU* 3.8 19.7 - - + -
228L MET* 3.6 32.1 - - + -
231L SER* 4.0 9.2 - - - -
232L ILE* 1.3 76.0 - - - +
234L VAL* 1.3 66.8 + - - +
235L ALA* 4.5 0.7 - - + +
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Residues in contact with VAL 234 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L VAL* 3.2 28.7 - - + +
111L ASP 3.8 16.4 - - - +
112L ALA* 4.3 8.7 - - - -
204L VAL* 4.7 2.7 - - + -
205L TYR 3.0 8.1 + - - +
206L VAL* 3.5 6.6 - - - +
207L ALA 3.0 21.8 + - - -
232L ILE* 3.6 15.9 + - + +
233L ILE* 1.3 72.3 - - - +
235L ALA* 1.3 59.7 + - - +
236L ALA 4.1 0.2 + - - -
248L ALA* 4.4 8.9 - - - +
251L THR* 4.5 4.5 - - - +
252L ALA* 4.0 34.5 - - + -
255L ILE* 4.4 10.1 - - + -
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Residues in contact with ALA 235 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L VAL* 4.6 1.6 - - + -
110L VAL 2.9 10.5 + - - +
111L ASP* 3.3 23.7 - - - -
112L ALA 3.7 2.1 + - - -
117L ILE* 4.6 16.6 - - + +
207L ALA* 3.8 17.9 - - + -
215L VAL* 4.1 17.9 - - + -
233L ILE* 3.7 5.3 + - + -
234L VAL* 1.3 74.5 - - - +
236L ALA* 1.3 61.5 + - - +
237L THR* 3.8 12.3 - - + -
240L GLU* 3.8 7.1 - - - +
124O PHE* 5.7 1.3 - - + -
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Residues in contact with ALA 236 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ALA* 4.3 3.4 - - + -
207L ALA 2.8 12.9 + - - +
208L VAL* 3.8 1.1 - - - -
209L GLY 3.3 16.8 + - - -
234L VAL 4.1 1.0 + - - -
235L ALA* 1.3 72.8 - - - +
237L THR* 1.3 67.6 + - - +
240L GLU* 3.8 13.5 - - - +
244L LEU* 3.7 15.7 - - + +
245L GLN* 3.7 14.0 - - + +
248L ALA* 3.4 29.6 - - + -
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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