Contacts of the helix formed by residues 221 - 228 (chain C) in PDB entry 1FSJ
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 LYS 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C GLY 3.2 1.6 + - - -
220C ASP* 1.3 88.1 + - - +
222C TRP* 1.3 64.2 + - - +
223C LEU 3.2 3.4 - - - -
224C ASP* 3.0 45.8 + - + +
225C ASP* 4.3 2.1 + - - +
270C ASN* 3.1 40.7 + - + +
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Residues in contact with TRP 222 (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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218C VAL* 3.6 22.0 - - + -
219C GLY 3.0 20.9 + - - +
220C ASP 3.3 8.6 - - - -
221C LYS* 1.3 77.2 - - - +
223C LEU* 1.3 101.1 + - + +
225C ASP* 3.1 26.2 + - - +
232C ALA* 3.7 13.8 - - + +
233C PRO* 3.7 15.0 - - + -
235C PRO* 3.7 35.2 - - + -
257C VAL* 5.9 2.5 - - + -
258C TRP* 4.5 6.7 - + - -
261C VAL* 4.0 28.9 - - + -
267C LEU* 3.0 43.7 + - + +
321C VAL* 4.0 19.1 - - + -
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Residues in contact with LEU 223 (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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221C LYS 3.1 1.8 + - - -
222C TRP* 1.3 121.1 - - + +
224C ASP* 1.3 65.4 + - - +
225C ASP 3.1 2.2 - - - -
226C ALA* 3.0 21.3 + - + +
227C GLY 4.6 0.5 + - - -
232C ALA* 5.0 0.9 - - + -
258C TRP* 4.4 9.0 - - + -
261C VAL* 6.1 0.4 - - + -
267C LEU 5.1 2.0 - - - +
271C LEU* 4.1 28.5 - - + -
299C TYR* 4.0 36.0 + - + +
321C VAL* 4.0 21.8 - - + -
323C THR* 5.3 0.9 - - - +
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Residues in contact with ASP 224 (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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221C LYS* 3.0 46.6 + - + +
223C LEU* 1.3 79.0 - - - +
225C ASP* 1.3 64.9 + - - +
226C ALA 3.4 0.7 + - - -
227C GLY* 4.0 6.2 + - - -
228C LYS* 3.8 20.3 - - - +
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Residues in contact with ASP 225 (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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221C LYS 5.2 1.3 - - - +
222C TRP* 3.1 18.5 + - - +
223C LEU 3.1 0.8 - - - -
224C ASP* 1.3 79.1 - - - +
226C ALA* 1.3 63.1 + - - +
227C GLY 3.2 1.3 - - - -
228C LYS* 3.1 44.5 + - + +
231C GLY* 3.3 16.8 - - - +
232C ALA* 3.9 13.2 - - + -
233C PRO* 5.1 6.4 - - - +
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Residues in contact with ALA 226 (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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223C LEU* 3.0 20.3 + - - +
225C ASP* 1.3 78.3 - - - +
227C GLY* 1.3 59.3 + - - +
228C LYS 3.3 0.4 + - - -
231C GLY* 3.9 2.6 - - - -
232C ALA* 4.0 3.9 - - + +
299C TYR* 3.8 26.5 - - + -
321C VAL* 3.5 26.2 - - + +
322C THR* 3.3 6.8 - - - -
323C THR* 3.1 25.7 + - + +
326C ARG* 3.6 8.8 - - - +
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Residues in contact with GLY 227 (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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223C LEU 4.6 0.6 + - - -
224C ASP 4.0 5.5 + - - -
225C ASP 3.2 1.0 - - - -
226C ALA* 1.3 77.5 - - - +
228C LYS* 1.3 63.0 + - - +
291C GLN* 3.7 27.4 + - - +
323C THR* 3.7 9.8 - - - +
326C ARG* 3.5 17.0 - - - +
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Residues in contact with LYS 228 (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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224C ASP* 3.8 23.1 - - - +
225C ASP* 3.1 33.7 + - + +
227C GLY* 1.3 85.1 - - - +
229C ASP* 1.3 73.7 + - - +
230C SER 3.2 1.6 - - - -
231C GLY* 2.7 19.0 + - - +
326C ARG* 3.6 5.4 + - - +
628E LYS* 3.2 29.9 - - - +
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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