Contacts of the strand formed by residues 190 - 197 (chain B) in PDB entry 1FIC
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 GLY 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B CYS* 3.3 24.7 - - - +
154B GLN* 2.8 40.5 + - - +
157B ALA* 4.0 6.7 - - - -
183B GLU 3.4 5.2 - - - -
184B ILE* 4.3 3.1 - - - -
188B GLY 3.6 1.0 + - - -
189B ASN* 1.3 73.4 - - - +
191B TRP* 1.3 59.3 + - - -
192B THR* 3.9 1.4 + - - -
386B ILE 4.5 1.2 - - - +
387B ILE* 3.9 6.8 - - - +
388B PRO* 4.9 0.3 - - - +
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Residues in contact with TRP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B CYS* 3.5 2.0 - - - -
182B CYS* 3.3 6.4 - - - -
183B GLU* 2.8 61.8 + - + +
185B ASP* 4.0 8.7 + - - -
189B ASN* 4.0 24.4 - - + +
190B GLY* 1.3 72.8 - - - -
192B THR* 1.3 61.6 + - - +
193B VAL* 3.7 0.9 + - + -
245B ALA* 4.6 2.0 - - + -
246B LEU 5.1 0.2 - - - -
247B ARG* 3.6 60.1 - - + -
261B ASP* 5.4 0.2 - - - -
385B LYS* 3.7 42.6 - - + +
386B ILE 3.7 10.1 - - - -
387B ILE* 3.5 46.7 - - + -
392B LEU* 4.2 11.7 - - + -
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B ASP* 3.8 9.3 - - - +
153B CYS* 3.3 37.1 + - - +
169B ILE* 4.5 4.3 - - + -
180B VAL* 4.3 18.4 - - + -
190B GLY 4.5 0.9 + - - -
191B TRP* 1.3 70.3 - - - +
193B VAL* 1.3 66.3 + - - +
194B PHE* 3.8 2.5 + - + -
228B LEU* 4.9 1.1 - - + -
236B ILE* 4.0 26.7 - - + -
244B TYR* 5.6 0.3 - - - -
385B LYS* 3.3 2.2 - - - -
386B ILE* 3.0 46.5 + - + +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL* 5.2 0.2 - - - +
181B TYR* 3.2 43.4 + - + +
183B GLU* 3.9 24.9 - - + +
191B TRP 4.3 2.9 - - - +
192B THR* 1.3 75.8 - - - +
194B PHE* 1.3 62.3 + - - +
195B GLN 3.6 15.7 - - - +
196B LYS* 4.8 5.6 - - + -
226B PHE* 3.5 28.0 - - + -
228B LEU* 4.2 10.0 - - - +
383B THR* 4.1 9.4 - - + -
384B MET 3.6 11.9 - - - +
385B LYS* 3.9 12.3 - - + -
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B THR* 3.8 2.4 + - + +
193B VAL* 1.3 75.2 - - - +
195B GLN* 1.3 61.8 + - + +
226B PHE* 3.7 6.1 - - - -
227B TRP* 3.6 11.9 - + - -
228B LEU* 2.9 40.7 + - + -
233B ILE* 3.3 41.9 - - + +
236B ILE* 6.0 1.1 - - + -
246B LEU* 3.9 8.1 - - + -
265B PHE* 3.8 23.8 - + - -
335B TRP* 4.8 2.2 - + - -
384B MET* 3.0 55.8 + - + -
385B LYS* 4.5 2.2 - - - -
386B ILE* 3.7 38.1 - - + -
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Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B VAL* 3.6 6.5 - - - +
194B PHE* 1.3 77.3 - - - +
196B LYS* 1.3 69.2 + - - +
197B ARG* 3.6 8.9 - - - +
204B PHE* 4.4 2.2 - - + -
226B PHE* 3.4 11.0 - - - +
227B TRP* 3.4 31.9 - - + -
344B LEU* 2.8 36.6 + - - +
345B ASN* 2.9 11.7 + - - +
382B THR* 2.8 27.8 + - - +
383B THR* 3.5 4.2 + - - -
384B MET* 3.1 46.3 + - + +
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Residues in contact with LYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B TYR* 6.5 0.9 - - - -
183B GLU* 5.3 3.6 + - - -
193B VAL* 4.8 5.2 - - + -
195B GLN* 1.3 79.6 + - - +
197B ARG* 1.3 69.8 + - - +
198B LEU* 4.1 15.9 - - + -
222B GLY* 4.0 21.8 - - - +
224B THR 3.5 22.7 - - - +
225B GLU* 3.1 20.9 - - - +
226B PHE* 3.2 27.7 + - + +
249B GLU* 5.8 0.6 + - - -
381B LYS* 5.5 9.1 - - - +
382B THR 3.5 6.6 + - - +
383B THR* 2.7 36.6 + - + +
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Residues in contact with ARG 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLN* 3.6 7.2 - - - +
196B LYS* 1.3 76.8 - - - +
198B LEU* 1.3 66.6 + - - +
200B GLY* 5.4 0.6 - - - -
202B VAL 4.6 4.8 + - - -
204B PHE* 3.1 54.2 - - - +
225B GLU* 3.4 12.9 + - - +
344B LEU 2.8 30.2 + - - +
345B ASN* 3.5 5.5 - - - +
346B GLY 2.8 29.3 + - - -
347B VAL* 4.7 0.2 - - - +
348B TYR* 4.1 18.4 - - + +
367B ILE* 3.4 27.7 - - + +
380B LYS 4.5 0.4 - - - -
381B LYS* 3.3 5.3 - - - +
382B THR* 3.1 47.9 + - - +
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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