Contacts of the strand formed by residues 230 - 235 (chain G) in PDB entry 1F9E
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 PHE 230 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G TYR* 3.8 13.9 - - + -
166G LEU* 4.1 23.1 - - + -
218G TYR* 4.1 22.7 - + + -
224G HIS* 4.0 15.3 - + - +
229G CYS* 1.3 77.0 - - - +
231G ILE* 1.3 75.9 + - - +
232G CYS* 4.1 18.8 - - + -
265G PHE* 3.5 47.1 - + - -
273G LEU* 3.7 24.2 - - + -
277G PRO 3.1 7.9 + - - +
278G LYS* 3.5 10.7 - - + -
279G VAL 2.9 24.3 + - - -
280G PHE* 4.3 6.7 - + - -
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Residues in contact with ILE 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G TYR 3.1 10.4 + - - +
165G CYS* 3.1 18.8 - - - -
166G LEU 2.9 24.1 + - - -
193G PHE* 3.4 33.2 - - + -
198G PHE* 3.6 30.7 - - + -
229G CYS* 3.9 5.6 - - - -
230G PHE* 1.3 86.6 - - - +
232G CYS* 1.3 64.8 + - - +
233G CYS* 4.1 14.1 - - - -
279G VAL* 3.3 15.7 - - + +
281G PHE* 4.2 15.0 - - + -
400H PHE* 4.2 10.8 - - + -
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Residues in contact with CYS 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166G LEU* 4.0 12.8 - - + -
168G ILE* 5.0 2.7 - - - -
215G LEU* 4.1 19.7 - - - -
230G PHE* 4.1 14.1 - - + -
231G ILE* 1.3 76.9 - - - +
233G CYS* 1.3 65.6 + - - +
234G ILE* 3.9 24.0 + - - +
279G VAL 2.9 9.1 + - - +
280G PHE* 3.2 35.8 - - + +
281G PHE 3.0 22.8 + - - +
282G ILE* 5.7 0.2 - - - +
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Residues in contact with CYS 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165G CYS* 4.2 8.7 - - - -
166G LEU 3.1 16.8 + - - +
167G ILE* 3.3 6.1 - - + -
168G ILE* 2.8 26.9 + - - +
189G LEU* 4.0 37.2 - - + -
193G PHE* 4.6 1.1 - - - -
231G ILE* 4.1 10.1 - - - -
232G CYS* 1.3 75.6 - - - +
234G ILE* 1.3 66.3 + - - +
235G LEU* 4.2 4.5 - - + -
281G PHE* 3.3 31.6 - - + +
350H ILE* 5.9 0.2 - - + -
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Residues in contact with ILE 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G ILE* 3.6 24.9 - - + +
211G ILE* 5.2 7.0 - - + -
215G LEU* 5.6 1.6 - - + -
232G CYS* 3.9 20.9 - - - +
233G CYS* 1.3 81.0 - - - +
235G LEU* 1.3 61.3 + - - +
236G SER* 4.4 11.7 - - - -
243G ILE* 3.8 26.5 - - + -
261G LEU* 3.6 33.2 - - + -
280G PHE* 5.4 2.9 - - + -
281G PHE 2.9 11.9 + - - +
282G ILE* 4.4 15.8 - - + +
283G GLN 2.8 32.7 + - - +
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Residues in contact with LEU 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167G ILE* 4.3 8.7 - - + -
168G ILE 2.9 13.9 + - - +
169G ASN* 4.0 7.6 - - - +
170G ASN* 2.8 29.5 + - - +
179G ARG* 3.7 8.1 - - - +
182G THR* 3.4 31.4 - - + -
185G ASP* 3.6 20.0 - - + +
186G ALA* 3.9 11.2 - - - +
189G LEU* 4.0 23.3 - - + -
233G CYS* 4.7 1.3 - - + -
234G ILE* 1.3 82.4 - - - +
236G SER* 1.3 63.2 + - - +
281G PHE 5.5 0.2 - - - +
283G GLN* 3.6 21.1 - - + +
350H ILE* 4.1 11.7 - - + -
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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