Contacts of the helix formed by residues 221 - 229 (chain A) in PDB entry 1FPQ
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A ASP* 5.7 0.7 - - - -
218A GLY 2.9 11.5 + - - -
219A GLY 3.2 0.8 - - - -
220A SER* 1.3 78.1 - - - +
222A ARG* 1.3 59.5 + - - +
223A ASN 3.4 2.5 - - - -
224A LEU* 3.3 10.5 + - - +
225A GLU 3.0 22.5 + - - -
238A ASN* 3.3 25.7 - - - +
251A LEU* 3.5 17.4 - - - +
254A ILE* 3.9 0.4 - - - +
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Residues in contact with ARG 222 (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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218A GLY 4.6 0.6 + - - -
220A SER* 3.3 22.1 + - - +
221A GLY* 1.3 75.8 - - - +
223A ASN* 1.3 69.1 + - - +
225A GLU* 3.0 30.2 + - - +
226A LEU* 3.2 26.1 + - - +
249A PRO* 3.4 28.1 - - - +
251A LEU* 3.3 23.7 - - - +
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Residues in contact with ASN 223 (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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193A CYS* 3.7 16.4 - - - +
197A MSE 3.5 31.4 - - + +
215A ASP* 4.2 10.9 + - - +
218A GLY* 5.4 5.6 + - - +
221A GLY 3.4 0.6 - - - -
222A ARG* 1.3 78.1 - - - +
224A LEU* 1.3 64.2 + - - +
226A LEU* 3.1 21.7 + - - +
227A ILE* 3.3 18.3 + - + +
274A LYS* 3.6 20.7 - - + +
1699A SAM 3.3 27.9 + - - -
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Residues in contact with LEU 224 (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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213A LEU* 3.6 38.1 - - + +
215A ASP* 3.7 25.4 + - + +
221A GLY* 3.3 12.6 + - - +
222A ARG 3.3 0.2 - - - -
223A ASN* 1.3 78.7 - - - +
225A GLU* 1.3 63.6 + - - +
227A ILE* 3.0 10.4 + - + +
228A ILE* 2.9 38.0 + - + +
236A GLY* 3.9 5.6 - - - -
237A ILE 3.6 42.2 - - - +
238A ASN* 3.8 7.0 - - - +
254A ILE* 3.8 15.7 - - + -
272A ILE* 5.4 0.2 - - + -
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Residues in contact with GLU 225 (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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221A GLY 3.0 14.0 + - - +
222A ARG* 3.0 41.1 + - - +
224A LEU* 1.3 76.5 - - - +
226A LEU* 1.3 62.5 + - + +
228A ILE* 3.5 3.3 + - - +
229A SER* 2.9 35.0 + - - -
251A LEU* 3.6 19.3 - - + +
252A SER 5.7 1.2 + - - +
254A ILE* 3.5 16.1 - - + +
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Residues in contact with LEU 226 (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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194A ALA* 5.0 13.2 - - + +
197A MSE 3.9 31.0 - - + -
198A LYS 5.6 0.4 - - - +
201A LEU* 3.7 20.7 - - + +
222A ARG* 3.2 13.4 + - + +
223A ASN* 3.1 13.1 + - - +
225A GLU* 1.3 82.1 - - + +
227A ILE* 1.3 56.5 + - - +
229A SER* 2.6 34.3 - - - +
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Residues in contact with ILE 227 (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 MSE 3.9 20.0 - - + -
201A LEU* 4.1 8.5 - - + -
207A PHE* 3.4 49.8 - - + -
213A LEU* 4.0 25.6 - - + -
215A ASP* 5.6 1.1 - - - +
223A ASN* 3.6 14.8 - - + +
224A LEU* 3.0 13.8 + - + +
226A LEU* 1.3 73.9 - - - +
228A ILE* 1.3 62.4 + - + +
229A SER 3.0 5.1 + - - -
230A LYS* 3.6 0.9 + - - +
231A TYR* 3.1 27.5 + - + +
234A ILE* 4.6 7.4 - - + -
272A ILE* 3.9 19.1 - - + -
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Residues in contact with ILE 228 (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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224A LEU* 2.9 23.6 + - + +
225A GLU* 4.0 5.2 - - - +
227A ILE* 1.3 77.7 - - + +
229A SER* 1.3 57.3 + - - +
230A LYS 3.2 0.2 + - - -
231A TYR* 3.7 8.3 - - - +
232A PRO* 3.0 33.3 - - + +
234A ILE* 3.9 22.9 - - + +
236A GLY* 3.7 19.5 - - - +
252A SER 4.5 12.3 - - - +
253A GLY* 3.4 17.0 - - - +
254A ILE* 3.2 35.0 - - + -
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Residues in contact with SER 229 (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* 4.9 1.0 - - - +
225A GLU* 2.9 22.9 + - - -
226A LEU* 2.6 25.2 - - - +
228A ILE* 1.3 74.6 - - - +
230A LYS* 1.3 63.0 + - - +
232A PRO* 5.3 0.7 - - - -
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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