Contacts of the helix formed by residues 196 - 209 (chain B) in PDB entry 1FIU
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 GLN 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ASP* 3.5 13.5 + - - +
196A GLN* 4.3 3.6 - - - +
197A ASN* 3.7 19.3 - - + +
200A SER* 3.5 24.3 + - - +
192B SER* 2.9 26.8 + - - +
193B ASP 3.5 9.4 - - - +
194B ARG 3.1 1.8 - - - -
195B ALA* 1.3 77.5 - - - +
197B ASN* 1.3 64.5 + - - +
198B ALA 3.0 2.5 - - - -
199B ARG* 2.8 49.0 + - - +
200B SER* 3.3 11.1 + - - -
230B SER* 3.1 27.8 + - - -
231B ILE* 5.5 0.2 - - - -
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Residues in contact with ASN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ASP* 3.6 33.1 + - - +
196A GLN* 3.8 13.4 - - + +
187B LYS* 2.7 25.6 + - - -
194B ARG 3.0 10.4 + - - +
196B GLN* 1.3 77.7 - - - +
198B ALA* 1.3 61.5 + - - +
200B SER* 3.1 10.6 + - - +
201B GLU* 3.0 41.2 + - - +
3002B ACY 3.4 10.0 - - - +
5I C 2.8 31.5 + - - -
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Residues in contact with ALA 198 (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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185B SER* 4.1 2.0 - - - +
187B LYS* 4.0 6.1 - - - -
195B ALA 3.3 13.0 + - - +
196B GLN 3.0 0.6 - - - -
197B ASN* 1.3 82.6 + - - +
199B ARG* 1.3 57.4 + - - +
201B GLU* 4.0 2.2 - - - +
202B GLY* 3.0 21.5 + - - -
216B ILE* 5.3 0.5 - - - +
218B VAL* 4.0 22.0 - - + -
231B ILE* 3.7 14.8 - - + -
238B ILE* 3.5 12.7 - - + +
3002B ACY 3.4 20.0 - - + -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASP* 3.8 18.8 + - - -
200A SER* 4.3 16.6 - - - -
196B GLN* 2.8 33.6 + - - +
198B ALA* 1.3 76.7 - - - +
200B SER* 1.3 60.1 + - - +
202B GLY* 3.3 1.2 + - - -
203B LEU* 2.9 30.2 + - - +
229B SER 4.5 0.6 + - - -
230B SER 2.9 24.8 + - - -
231B ILE* 3.6 29.7 + - + +
233B LEU* 3.0 29.1 + - - +
234B GLY* 4.7 6.9 + - - -
237B GLU* 2.9 47.3 + - + +
238B ILE* 4.5 3.9 - - + +
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Residues in contact with SER 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLN* 3.5 28.3 + - - +
199A ARG* 4.4 18.2 - - - -
200A SER* 6.1 0.2 - - - -
203A LEU* 6.4 0.7 - - - -
196B GLN 3.3 5.3 + - - -
197B ASN* 3.1 23.0 + - - +
199B ARG* 1.3 79.5 - - - +
201B GLU* 1.3 64.4 + - - +
203B LEU* 3.4 8.9 + - - +
204B ASN* 3.1 32.1 + - - -
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 3.2 47.0 - - + +
138B THR 4.2 6.9 - - - +
139B PRO* 4.4 8.7 - - + +
183B SER* 6.2 0.2 - - - +
197B ASN* 3.0 34.2 + - + +
198B ALA* 4.1 4.5 - - - +
200B SER* 1.3 79.0 + - - +
202B GLY* 1.3 64.4 + - - +
204B ASN* 3.2 11.0 + - - +
205B LEU* 3.1 28.8 + - + +
3002B ACY 3.8 28.2 - - + +
5I C 5.0 2.6 - - - -
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Residues in contact with GLY 202 (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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198B ALA 3.0 16.3 + - - -
199B ARG 3.3 3.3 + - - -
201B GLU* 1.3 77.4 - - - +
203B LEU* 1.3 55.8 + - - +
205B LEU* 3.1 7.4 + - - +
206B VAL* 3.0 32.5 + - - +
216B ILE* 3.7 17.9 - - - +
237B GLU* 4.1 18.2 - - - -
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Residues in contact with LEU 203 (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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203A LEU* 3.3 24.9 - - + -
207A ARG* 3.9 16.4 - - - +
237A GLU* 4.0 4.5 - - - +
199B ARG 2.9 16.8 + - - +
200B SER* 3.7 8.5 - - - +
201B GLU 3.3 0.2 - - - -
202B GLY* 1.3 72.7 - - - +
204B ASN* 1.3 62.3 + - - +
206B VAL* 3.2 14.7 + - + +
207B ARG* 2.8 92.5 + - + +
236B GLY 5.6 3.1 - - - +
237B GLU* 4.7 10.6 - - + +
206C VAL* 6.5 0.2 - - + -
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Residues in contact with ASN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B TYR* 4.4 0.9 - - - -
134B ASP* 3.9 31.5 + - - +
135B TYR* 4.1 16.6 - - - +
137B ILE* 5.7 0.2 - - - +
200B SER* 3.1 23.6 + - - -
201B GLU* 3.2 13.3 + - - +
203B LEU* 1.3 78.1 - - - +
205B LEU* 1.3 63.2 + - + +
207B ARG* 4.7 6.0 + - - -
208B ASN* 3.0 43.1 + - - +
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Residues in contact with LEU 205 (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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105B ILE* 3.4 32.5 - - + -
111B TYR* 2.7 46.0 + - + +
137B ILE 5.7 1.6 - - - +
139B PRO* 4.8 4.9 - - + -
180B LEU* 4.6 3.6 - - + -
183B SER* 3.6 34.3 - - - +
201B GLU* 3.1 16.7 + - + +
202B GLY* 3.1 11.0 + - - +
204B ASN* 1.3 76.8 - - + +
206B VAL* 1.3 63.2 + - - +
209B ARG* 3.5 4.3 + - - +
213B LEU* 3.4 6.7 - - + +
214B PRO* 5.1 3.6 - - + -
216B ILE* 4.0 22.0 - - + -
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLY 3.0 21.0 + - - +
203B LEU* 3.2 15.9 + - + +
205B LEU* 1.3 79.4 - - - +
207B ARG* 1.3 67.8 + - + +
208B ASN 3.4 0.3 + - - -
209B ARG* 3.0 35.6 + - - +
213B LEU* 3.6 27.8 - - + -
216B ILE* 4.3 3.6 - - + -
236B GLY 4.2 17.9 - - - +
237B GLU 5.1 0.2 - - - +
203C LEU* 6.3 1.1 - - + -
206C VAL* 3.8 25.4 - - + -
209C ARG* 4.6 1.6 - - - +
236C GLY* 3.6 11.6 - - - +
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.6 21.0 - - - +
207A ARG* 4.4 3.8 - - - +
235A THR 4.8 7.1 + - - -
236A GLY* 5.3 4.8 + - - -
237A GLU* 3.0 25.9 + - - -
203B LEU* 2.8 61.8 + - + +
204B ASN* 4.7 5.5 + - - +
206B VAL* 1.3 78.8 - - + +
208B ASN* 1.3 68.7 + - - +
209B ARG 3.6 0.2 - - - -
235C THR* 2.8 30.0 + - - +
236C GLY* 4.0 6.7 - - - -
207D ARG* 4.6 40.7 - - - +
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Residues in contact with ASN 208 (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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110B GLN 3.6 0.7 - - - +
111B TYR* 3.8 13.3 - - + -
113B HIS* 2.9 34.7 + - - +
114B LEU* 4.3 22.4 - - + +
117B LEU* 5.0 6.2 - - - +
135B TYR* 4.2 15.5 - - - +
204B ASN* 3.0 39.6 + - - +
207B ARG* 1.3 84.9 - - - +
209B ARG* 1.3 62.5 + - - +
235C THR* 3.8 7.6 + - - -
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Residues in contact with ARG 209 (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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110B GLN* 3.7 9.4 - - + +
111B TYR* 3.5 23.3 - - + +
205B LEU 3.5 3.6 + - - +
206B VAL* 3.0 24.4 + - - +
207B ARG 3.6 1.6 - - - -
208B ASN* 1.3 78.1 - - - +
210B LYS* 1.3 60.3 + - - +
211B GLY 3.4 15.2 + - - +
212B ARG 5.3 0.2 - - - +
213B LEU* 3.7 30.6 - - - +
206C VAL* 4.6 1.0 - - - +
213C LEU* 3.9 20.6 - - - +
216C ILE* 4.0 4.0 - - - +
235C THR* 3.3 22.7 - - - +
236C GLY 3.0 27.6 + - - +
237C GLU* 3.1 28.3 + - - +
238C ILE 4.1 3.1 - - - +
239C ASP* 2.9 32.4 + - - +
273C ARG* 4.6 2.6 + - - -
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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