Contacts of the helix formed by residues 206 - 215 (chain I) in PDB entry 1FQV
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 GLU 206 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182I MET 2.8 9.1 + - - -
183I ASP* 4.1 22.1 - - + +
184I GLN 4.7 4.9 - - - +
204I VAL* 4.3 0.6 - - - +
205I ILE* 1.3 69.9 - - - +
207I VAL* 1.3 68.8 + - - +
208I SER* 2.8 42.1 + - - +
209I THR* 2.7 38.4 + - - +
210I LEU 2.8 10.2 + - - -
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Residues in contact with VAL 207 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205I ILE 3.0 6.9 + - - +
206I GLU* 1.3 82.4 + - - +
208I SER* 1.3 65.1 + - - +
210I LEU* 3.3 4.4 + - - -
211I HIS* 3.0 20.4 + - + +
229I ARG* 3.3 40.6 - - + +
230I LEU* 3.7 17.5 - - - +
231I SER* 4.3 19.5 - - - +
234I ILE* 3.4 8.1 - - + +
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Residues in contact with SER 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I GLN 5.0 1.7 + - - -
185I PRO* 5.5 4.2 - - - +
187I ALA* 3.0 22.2 + - - +
206I GLU* 2.8 32.4 + - - +
207I VAL* 1.3 79.3 - - - +
209I THR* 1.3 58.3 + - - +
211I HIS* 3.3 6.8 + - - +
212I GLY 2.9 23.7 + - - -
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Residues in contact with THR 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I PRO* 3.4 28.4 - - + +
182I MET* 4.3 13.0 - - + -
184I GLN 2.7 27.4 + - - -
185I PRO 5.0 0.9 - - - -
186I LEU 5.3 0.7 - - - +
187I ALA* 4.3 8.1 - - - +
188I GLU 4.7 0.7 + - - +
205I ILE* 3.9 13.2 - - + -
206I GLU* 2.7 26.6 + - - +
208I SER* 1.3 73.2 + - - +
210I LEU* 1.3 65.5 + - - +
212I GLY* 3.5 0.5 + - - -
213I ILE* 3.2 33.4 + - + +
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Residues in contact with LEU 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200I LEU* 3.8 28.9 - - + -
205I ILE* 3.5 30.2 - - + +
206I GLU 2.8 7.0 + - - +
207I VAL* 3.5 10.3 - - - +
209I THR* 1.3 79.8 - - - +
211I HIS* 1.3 62.2 + - - +
213I ILE* 3.3 4.7 + - + +
214I LEU* 3.1 35.8 + - + +
225I LEU* 4.3 4.9 - - + -
228I LEU* 3.9 18.8 - - + -
229I ARG 3.9 8.5 - - - +
230I LEU* 3.4 33.0 - - + -
234I ILE* 3.6 11.9 - - + -
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Residues in contact with HIS 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I ALA* 5.4 3.6 - - + -
207I VAL* 3.0 10.7 + - + +
208I SER* 3.6 9.9 - - - +
209I THR 3.2 0.2 - - - -
210I LEU* 1.3 74.4 - - - +
212I GLY* 1.3 70.4 + - - +
214I LEU* 3.8 2.8 - - - -
215I SER* 2.9 36.7 + - - -
231I SER* 5.5 0.2 - - - +
233I PRO* 3.0 37.6 + - + +
234I ILE* 3.6 19.5 + - + +
237I THR* 2.9 27.3 + - + -
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Residues in contact with GLY 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187I ALA* 3.3 23.1 - - - -
188I GLU* 2.5 35.1 - - - +
208I SER 2.9 11.5 + - - -
209I THR 3.5 0.2 + - - -
210I LEU 3.4 0.2 - - - -
211I HIS* 1.3 78.6 - - - +
213I ILE* 1.3 60.1 + - - +
215I SER* 2.5 16.8 + - - -
216I GLN* 3.5 2.9 - - - +
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Residues in contact with ILE 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I PRO 5.3 0.4 - - - +
164I THR* 3.4 27.4 - - - +
165I GLY 5.6 0.4 - - - +
168I LEU* 3.7 28.0 - - + -
175I PHE* 6.0 1.8 - - + -
182I MET* 4.0 20.2 - - + -
188I GLU* 3.6 19.3 - - + -
193I PHE* 4.0 2.6 - - + -
198I MET* 4.6 14.6 - - + -
200I LEU* 5.5 7.9 - - + -
205I ILE* 5.6 1.3 - - + -
209I THR* 3.2 25.4 + - + +
210I LEU* 3.7 6.3 - - + +
211I HIS 3.1 0.6 - - - -
212I GLY* 1.3 71.9 - - - +
214I LEU* 1.3 61.5 + - + +
215I SER 3.0 4.7 - - - -
216I GLN* 3.0 24.9 + - - +
217I CYS* 3.4 9.3 - - - -
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Residues in contact with LEU 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I MET* 4.3 19.1 - - - -
200I LEU* 5.0 1.8 - - + -
210I LEU* 3.1 25.7 + - + +
211I HIS* 4.3 2.7 - - - +
213I ILE* 1.3 76.3 - - + +
215I SER* 1.3 57.5 + - - +
216I GLN 3.1 2.8 + - - -
217I CYS* 3.5 23.2 + - + +
220I LEU* 4.2 14.6 - - + -
223I LEU* 4.2 20.6 - - + -
225I LEU* 3.6 31.9 - - + -
234I ILE* 3.8 20.2 - - + -
237I THR* 3.4 20.8 - - - +
238I LEU* 4.2 12.7 - - + +
241I ASN* 4.7 0.9 - - - +
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Residues in contact with SER 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I GLU 3.6 1.7 + - - -
211I HIS* 2.9 25.7 + - - -
212I GLY* 2.5 27.5 + - - -
214I LEU* 1.3 75.7 - - - +
216I GLN* 1.3 73.3 + - - +
237I THR* 3.0 21.8 - - - -
240I LYS* 2.4 22.8 + - - -
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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