Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 1FBQ
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 PRO 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ALA* 1.3 76.6 + - + +
197A PHE* 3.1 4.7 - - - -
198A VAL* 3.2 15.1 + - + +
199A ASN* 3.2 27.1 + - - +
255A TYR* 3.2 29.8 - - + +
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Residues in contact with ALA 196 (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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195A PRO* 1.3 85.4 - - + +
197A PHE* 1.3 62.5 + - - +
199A ASN* 3.5 5.2 + - - +
200A LYS* 3.3 27.8 + - + +
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Residues in contact with PHE 197 (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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195A PRO 3.1 2.1 - - - -
196A ALA* 1.3 79.5 - - - +
198A VAL* 1.3 54.6 + - + +
200A LYS* 3.0 7.9 + - - +
201A LEU* 2.7 46.3 + - + +
240A PHE* 3.6 32.1 - + - -
248A PHE* 3.9 26.5 - + - -
251A GLN* 3.4 65.1 - - + +
252A LEU* 3.8 23.8 - - + -
255A TYR* 3.8 30.3 - + + -
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Residues in contact with VAL 198 (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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195A PRO* 3.2 14.0 + - + +
197A PHE* 1.3 78.3 - - + +
199A ASN* 1.3 66.0 + - - +
201A LEU* 3.1 9.2 + - + +
202A TRP* 3.0 54.8 + - + +
255A TYR* 3.5 44.9 - - + -
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Residues in contact with ASN 199 (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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195A PRO* 3.2 13.3 + - - +
196A ALA* 4.0 8.1 - - - +
198A VAL* 1.3 80.6 - - - +
200A LYS* 1.3 58.3 + - + +
202A TRP* 4.3 3.7 - - - +
203A SER* 2.8 33.2 + - - -
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Residues in contact with LYS 200 (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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196A ALA* 3.3 15.6 + - - +
197A PHE* 3.0 6.1 + - - +
199A ASN* 1.3 76.2 - - + +
201A LEU* 1.3 67.1 + - - +
203A SER* 3.0 9.4 + - - +
204A MET* 3.0 25.3 + - - +
239A TYR* 2.7 35.3 + - + +
240A PHE* 3.4 45.3 - - + +
241A LYS* 4.6 3.6 - - - +
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Residues in contact with LEU 201 (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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197A PHE* 2.7 30.9 + - + +
198A VAL* 3.1 13.0 + - + +
200A LYS* 1.3 74.2 - - - +
202A TRP* 1.3 91.2 + - + +
204A MET* 3.3 20.7 - - + +
205A VAL* 2.8 42.9 + - + +
214A ILE* 5.3 0.4 - - + -
223A ILE* 5.0 5.4 - - + -
240A PHE* 4.2 2.6 - - - -
248A PHE* 4.0 17.3 - - + -
252A LEU* 3.7 25.6 - - + -
255A TYR* 6.0 1.3 - - + -
257A TRP* 4.9 7.2 - - + +
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Residues in contact with TRP 202 (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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198A VAL* 3.0 44.5 + - + +
199A ASN* 4.3 3.1 - - - +
201A LEU* 1.3 88.0 - - + +
203A SER* 1.3 68.6 + - - +
204A MET 2.9 2.2 - - - -
205A VAL* 4.2 12.6 - - + +
206A ASN* 2.9 50.7 + - - +
216A TRP* 3.6 31.0 - + - -
223A ILE* 4.0 16.8 - - + -
257A TRP* 3.9 28.5 - + - -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A ASN* 2.8 22.7 + - - -
200A LYS* 3.0 20.1 + - - +
201A LEU 3.4 0.2 - - - -
202A TRP* 1.3 73.4 - - - +
204A MET* 1.3 54.9 + - - +
206A ASN 4.6 0.3 - - - -
207A ASP* 3.2 26.7 + - - +
239A TYR* 3.8 19.9 - - - -
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Residues in contact with MET 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A LYS 3.0 13.1 + - - +
201A LEU* 3.3 16.6 - - + +
202A TRP 2.9 1.2 - - - -
203A SER* 1.3 77.6 + - - +
205A VAL* 1.3 65.9 + - + +
207A ASP 3.5 3.3 + - - -
210A ASN* 2.9 32.1 + - - +
214A ILE* 4.1 17.0 - - + +
231A PHE* 3.9 10.3 - - + -
235A VAL* 3.5 36.1 - - + +
236A LEU* 4.9 0.2 - - - -
239A TYR* 3.9 19.3 - - + -
240A PHE* 4.0 20.0 - - + -
248A PHE* 3.6 37.0 - - + -
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Residues in contact with VAL 205 (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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201A LEU* 2.8 38.5 + - + +
202A TRP* 4.2 10.8 - - + -
204A MET* 1.3 75.5 - - + +
206A ASN* 1.3 59.0 + - - +
207A ASP 3.3 7.0 + - - +
214A ILE* 3.7 39.7 - - + +
215A HIS* 4.7 8.0 - - - -
216A TRP* 3.8 42.9 - - + +
223A ILE* 4.3 16.6 - - + -
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Residues in contact with ASN 206 (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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202A TRP* 2.9 47.8 + - - +
203A SER* 4.6 0.4 - - - -
205A VAL* 1.3 70.6 - - - +
207A ASP* 1.3 59.0 + - - +
208A LYS* 3.7 12.3 + - - +
216A TRP* 2.8 34.6 + - - +
246B ALA* 4.3 6.0 - - - +
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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