Contacts of the helix formed by residues 196 - 209 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192C SER* 2.9 25.9 + - - +
193C ASP 3.5 10.5 - - - +
194C ARG 3.1 1.4 - - - -
195C ALA* 1.3 75.6 - - - +
197C ASN* 1.3 65.0 + - - +
198C ALA 3.0 2.0 - - - -
199C ARG* 2.9 48.6 + - - +
200C SER* 3.2 11.8 + - - -
230C SER* 3.0 29.7 + - - -
231C ILE* 5.2 0.2 - - - -
134D ASP* 4.1 9.2 + - - +
137D ILE* 5.9 4.2 - - + +
196D GLN* 4.2 4.2 - - - +
197D ASN* 3.7 20.4 - - + +
200D SER* 3.6 26.0 + - - +
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Residues in contact with ASN 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C LYS* 2.8 25.1 + - - -
194C ARG 3.0 11.6 + - - +
196C GLN* 1.3 77.7 - - - +
198C ALA* 1.3 61.3 + - - +
200C SER* 3.2 9.5 + - - +
201C GLU* 3.0 42.2 + - - +
4003C ACY 3.3 9.2 - - - +
193D ASP* 3.5 33.1 + - - +
196D GLN* 3.8 14.5 - - + +
5K C 2.9 31.3 + - - -
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C SER* 4.2 2.0 - - - +
187C LYS* 4.0 5.6 - - - -
195C ALA 3.2 12.3 + - - +
196C GLN 3.0 0.8 - - - -
197C ASN* 1.3 83.7 + - - +
199C ARG* 1.3 59.5 + - - +
201C GLU* 4.0 2.2 - - - +
202C GLY* 3.0 24.1 + - - -
216C ILE* 5.2 2.1 - - - +
218C VAL* 4.0 22.0 - - + -
231C ILE* 3.6 14.6 - - + -
238C ILE* 4.2 7.7 - - + +
4003C ACY 3.4 20.6 - - + -
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C GLN* 2.9 32.8 + - - +
198C ALA* 1.3 76.7 - - - +
200C SER* 1.3 60.0 + - - +
202C GLY 3.3 0.5 + - - -
203C LEU* 2.9 29.7 + - - +
229C SER 4.3 1.4 + - - -
230C SER 2.9 23.4 + - - -
231C ILE* 3.5 31.2 + - + +
233C LEU* 3.1 28.3 + - - +
234C GLY* 4.8 6.5 + - - -
237C GLU* 3.0 46.2 + - + +
238C ILE* 4.1 6.8 - - + +
134D ASP* 3.2 15.2 + - - -
200D SER* 4.4 15.3 - - - -
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Residues in contact with SER 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP* 4.8 6.9 + - - -
196C GLN 3.2 5.0 + - - -
197C ASN* 3.2 19.4 + - - +
199C ARG* 1.3 77.5 - - - +
201C GLU* 1.3 68.7 + - - +
203C LEU* 3.3 9.1 + - - +
204C ASN* 3.0 28.9 + - - +
196D GLN* 3.5 29.4 + - - +
199D ARG* 4.4 17.3 - - - -
200D SER* 6.1 0.4 - - - -
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Residues in contact with GLU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ASP* 5.7 2.0 - - - +
137C ILE* 4.6 15.8 - - + +
138C THR 3.8 23.4 - - - +
139C PRO* 4.3 5.5 - - - +
185C SER* 5.9 0.3 - - - -
197C ASN* 3.0 35.5 + - + +
198C ALA* 4.1 4.0 - - - +
200C SER* 1.3 78.8 + - - +
202C GLY* 1.3 63.5 + - - +
204C ASN* 3.2 11.7 + - - +
205C LEU* 3.1 30.4 + - + +
4003C ACY 3.6 24.7 - - + +
5K C 4.9 3.3 - - - -
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Residues in contact with GLY 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ALA 3.0 17.9 + - - -
199C ARG 3.7 1.6 - - - -
200C SER 3.3 0.2 - - - -
201C GLU* 1.3 77.8 - - - +
203C LEU* 1.3 61.4 + - - +
205C LEU* 3.2 6.2 + - - +
206C VAL* 3.0 28.1 + - - +
216C ILE* 3.9 17.0 - - - +
237C GLU* 4.0 19.1 - - - -
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Residues in contact with LEU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 6.3 0.9 - - + -
199C ARG 2.9 17.6 + - - +
200C SER* 3.3 8.7 + - - +
202C GLY* 1.3 75.3 - - - +
204C ASN* 1.3 60.6 + - - +
206C VAL* 3.2 14.7 + - + +
207C ARG* 2.8 90.8 + - + +
236C GLY 5.2 3.6 - - - +
237C GLU* 4.7 11.5 - - + +
203D LEU* 3.8 18.4 - - + -
207D ARG* 3.7 20.2 - - - +
237D GLU* 4.2 7.2 - - + +
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Residues in contact with ASN 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ASP* 2.1 57.5 + - - +
135C TYR* 4.6 3.1 - - - +
137C ILE* 3.6 21.2 - - + +
200C SER 3.0 18.7 + - - +
201C GLU* 3.6 8.9 - - - +
202C GLY 3.2 0.2 - - - -
203C LEU* 1.3 77.9 - - - +
205C LEU* 1.3 63.6 + - - +
207C ARG* 4.7 7.7 + - - -
208C ASN* 3.1 41.2 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ILE* 4.0 14.4 - - + -
111C TYR* 2.7 51.6 + - + +
137C ILE* 3.5 26.9 - - + -
139C PRO* 5.1 1.3 - - + -
180C LEU* 4.6 3.4 - - + -
183C SER* 3.6 31.9 - - - +
201C GLU* 3.1 17.6 + - + +
202C GLY* 3.2 10.3 + - - +
204C ASN* 1.3 76.2 - - - +
206C VAL* 1.3 62.4 + - - +
209C ARG* 3.5 4.7 + - - +
213C LEU* 3.4 6.0 - - + +
214C PRO* 5.0 4.0 - - + -
216C ILE* 4.0 24.5 - - + -
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Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 6.5 0.2 - - + -
206B VAL* 3.8 23.6 - - + -
209B ARG* 4.6 1.8 - - - +
236B GLY* 3.5 10.7 - - - +
202C GLY 3.0 19.9 + - - +
203C LEU* 3.5 15.9 - - + +
205C LEU* 1.3 79.8 - - - +
207C ARG* 1.3 69.8 + - + +
208C ASN 3.4 0.5 + - - -
209C ARG* 2.9 37.0 + - - +
213C LEU* 3.6 30.5 - - + -
216C ILE* 4.4 3.8 - - + -
236C GLY 4.3 17.3 - - - +
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Residues in contact with ARG 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ARG* 4.8 31.4 - - - +
235B THR* 2.7 37.5 + - - +
236B GLY* 3.9 9.2 - - - -
203C LEU* 2.8 63.9 + - + +
204C ASN* 4.3 8.4 + - - +
206C VAL* 1.3 76.7 - - + +
208C ASN* 1.3 61.0 + - - +
209C ARG 3.6 0.2 - - - -
203D LEU* 3.8 20.8 - - - +
207D ARG* 4.5 2.0 - - - +
235D THR 4.8 6.3 + - - -
236D GLY* 5.5 4.2 + - - -
237D GLU* 2.7 27.9 + - - -
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Residues in contact with ASN 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B THR* 3.8 8.2 + - - -
110C GLN 3.7 0.5 - - - +
111C TYR* 3.8 13.4 - - + -
113C HIS* 2.9 34.5 + - - +
114C LEU* 4.4 21.3 - - + +
117C LEU* 5.4 4.5 - - - +
135C TYR* 4.1 21.1 - - - +
137C ILE* 5.3 0.6 - - + +
204C ASN* 3.1 36.5 + - - +
207C ARG* 1.3 85.7 - - - +
209C ARG* 1.3 60.8 + - - +
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Residues in contact with ARG 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B VAL* 4.6 1.4 - - - +
213B LEU* 4.0 21.0 - - - +
216B ILE* 4.1 3.4 - - - +
235B THR* 3.4 21.8 - - - +
236B GLY 2.9 27.5 + - - +
237B GLU 3.1 28.7 + - - -
238B ILE 4.9 2.6 - - - +
239B ASP* 2.8 32.6 + - - +
273B ARG* 4.6 2.8 + - - -
110C GLN* 3.7 8.5 - - + +
111C TYR* 3.5 14.1 - - + +
205C LEU 3.5 12.9 + - - +
206C VAL* 2.9 25.5 + - - +
207C ARG 3.6 1.4 - - - -
208C ASN* 1.3 79.2 - - - +
210C LYS* 1.3 60.6 + - - +
211C GLY 3.4 14.3 + - - +
213C LEU* 3.8 31.3 - - - +
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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