Contacts of the helix formed by residues 230 - 241 (chain A) in PDB entry 1FIB
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 ASN 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TRP* 5.2 2.8 + - - -
211A TYR* 2.8 24.6 + - - +
212A LYS* 3.3 3.4 + - - +
227A TRP* 3.1 30.4 + - - -
229A GLY* 1.3 70.6 - - - -
231A GLU* 1.3 57.0 + - - +
233A ILE* 3.3 9.4 + - - +
234A HIS* 2.9 29.6 + - - +
267A VAL* 4.3 3.0 - - + +
274A TYR* 3.7 40.3 - - + -
312A PHE* 3.4 40.1 - - - -
335A TRP* 4.9 3.1 - - - -
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Residues in contact with GLU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LYS* 3.2 29.2 + - + +
213A GLU* 5.8 0.2 - - - -
230A ASN* 1.3 78.0 - - - +
232A LYS* 1.3 59.2 + - + +
234A HIS* 3.3 18.4 + - - +
235A LEU* 3.0 50.0 + - + +
270A GLU* 4.6 5.4 + - - +
274A TYR* 2.7 39.9 + - - +
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Residues in contact with LYS 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A PHE* 3.9 52.4 - - + +
179A LEU 5.5 1.4 + - - -
212A LYS 5.7 0.7 - - - +
213A GLU* 3.3 23.3 + - - +
214A GLY* 5.0 0.6 - - - -
228A LEU* 3.2 37.0 + - + +
229A GLY* 3.2 7.7 + - - +
231A GLU* 1.3 76.0 - - + +
233A ILE* 1.3 66.6 + - - +
235A LEU* 3.3 8.5 + - + +
236A ILE* 3.1 31.2 + - - +
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A PHE* 3.3 49.6 - - + -
227A TRP* 3.7 26.9 - - + -
228A LEU* 4.5 4.7 - - + -
229A GLY 3.0 19.9 + - - +
230A ASN* 3.3 9.6 + - - +
232A LYS* 1.3 75.4 - - - +
234A HIS* 1.3 60.1 + - - +
236A ILE* 4.1 6.7 - - - +
237A SER* 2.9 29.0 + - - -
265A PHE* 4.4 14.8 - - + -
267A VAL* 3.8 26.0 - - + -
335A TRP* 5.4 2.7 - - + -
386A ILE* 5.3 3.9 - - + +
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASN 2.9 17.9 + - - +
231A GLU* 3.4 24.9 - - - +
232A LYS 3.2 0.2 - - - -
233A ILE* 1.3 77.4 - - - +
235A LEU* 1.3 67.4 + - + +
237A SER* 3.6 0.7 + - - -
238A THR* 2.7 56.2 + - + -
267A VAL* 2.8 29.8 + - + +
268A GLY 3.4 16.7 + - - +
269A PRO* 3.6 37.8 - - + +
274A TYR* 4.2 3.8 - - + -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A PRO* 3.8 18.8 - - + +
173A LYS* 3.8 33.6 + - + +
174A ALA* 3.9 23.1 - - + -
178A PHE* 4.8 5.6 - - + -
231A GLU* 3.0 44.3 + - + +
232A LYS* 3.3 9.8 + - + +
234A HIS* 1.3 84.7 - - + +
236A ILE* 1.3 63.5 + - - +
238A THR* 4.1 3.0 + - - -
239A GLN* 3.5 23.4 + - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP* 4.3 12.1 - - + -
169A ILE* 3.8 20.4 - - + -
171A PRO* 3.7 19.1 - - + -
178A PHE* 4.0 12.3 - - + -
192A THR* 4.2 11.2 - - + -
194A PHE* 6.4 0.2 - - + -
228A LEU* 4.1 17.5 - - + -
232A LYS 3.1 17.3 + - - +
233A ILE* 4.1 4.7 - - - +
235A LEU* 1.3 77.8 - - - +
237A SER* 1.3 60.9 + - - +
238A THR 3.3 1.4 + - - -
239A GLN* 3.4 20.4 - - - +
244A TYR* 3.1 34.3 - - + +
386A ILE* 3.6 25.4 - - + -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE 2.9 21.9 + - - -
234A HIS 3.6 4.0 + - - -
236A ILE* 1.3 76.8 - - - +
238A THR* 1.3 59.2 + - - +
239A GLN 3.7 0.2 - - - -
242A ILE 4.1 5.2 - - - +
244A TYR* 3.5 23.2 - - - -
265A PHE* 3.9 31.8 - - - +
266A LYS* 3.9 17.5 - - - +
267A VAL* 3.1 24.0 + - - +
386A ILE* 4.7 5.2 - - - -
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A HIS* 2.7 34.7 + - + +
235A LEU* 4.1 3.1 + - - -
237A SER* 1.3 81.9 - - - +
239A GLN* 1.3 65.5 + - - +
240A SER 3.3 2.9 + - - -
241A ALA* 3.5 12.1 + - - +
242A ILE 5.2 0.2 - - - -
266A LYS* 4.4 20.2 - - + -
267A VAL 3.5 25.6 - - - +
268A GLY* 5.3 1.3 - - - -
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LYS* 3.1 41.8 + - - +
152A ASP* 3.9 3.0 + - - +
171A PRO* 3.1 10.1 - - - +
172A LEU* 3.0 41.1 + - + +
173A LYS* 5.4 3.4 - - + +
235A LEU 3.5 12.5 + - - +
236A ILE* 3.4 17.8 + - - +
238A THR* 1.3 74.9 - - - +
240A SER* 1.3 63.6 + - - +
241A ALA 3.0 5.9 + - - -
242A ILE* 3.1 22.5 + - + +
244A TYR* 2.8 25.9 + - + +
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.1 30.4 - - - +
238A THR 3.3 2.2 + - - -
239A GLN* 1.3 69.8 - - - +
241A ALA* 1.3 72.4 + - - +
242A ILE* 3.0 18.7 + - - +
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A THR* 3.5 10.4 + - - +
239A GLN 3.0 3.0 + - - -
240A SER* 1.3 77.7 - - - +
242A ILE* 1.3 64.9 + - - +
243A PRO* 3.3 9.2 - - - +
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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