Contacts of the helix formed by residues 220 - 230 (chain C) in PDB entry 5FL6
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 SER 220 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149C GLU* 4.2 0.7 - - - -
150C GLY 3.5 10.3 - - - -
151C PRO 5.0 3.1 - - - -
152C GLU 3.4 21.2 + - - -
153C GLU* 4.1 8.1 + - - +
219C LEU* 1.3 76.9 - - - +
221C ALA* 1.3 64.7 + - - +
222C LYS* 3.5 9.7 + - - +
223C GLN* 3.0 37.4 + - - +
224C LEU* 3.1 22.5 + - - +
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Residues in contact with ALA 221 (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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149C GLU* 3.7 35.0 - - - +
150C GLY 4.3 1.4 + - - -
220C SER* 1.3 74.6 - - - +
222C LYS* 1.3 62.1 + - - +
224C LEU* 3.4 5.7 + - - +
225C HIS* 3.0 24.0 + - - +
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Residues in contact with LYS 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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153C GLU* 5.9 2.0 - - - +
220C SER* 3.2 9.5 + - - +
221C ALA* 1.3 78.0 - - - +
223C GLN* 1.3 58.9 + - + +
225C HIS* 3.3 7.1 + - - +
226C THR* 2.8 35.0 + - - +
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Residues in contact with GLN 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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153C GLU* 3.4 12.3 - - + +
154C ASN* 2.8 54.6 + - - +
158C GLU* 3.2 32.3 + - - +
161C LEU* 3.5 25.2 - - + +
219C LEU* 3.6 8.5 - - + -
220C SER* 3.0 34.6 + - - +
222C LYS* 1.3 78.0 - - + +
224C LEU* 1.3 57.0 + - - +
226C THR* 3.2 8.2 + - - -
227C LEU* 3.0 28.1 + - - +
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Residues in contact with LEU 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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115C PRO* 3.8 31.9 - - + +
116C ALA* 4.4 17.3 - - + -
147C LEU* 4.7 4.7 - - + -
148C GLU 4.2 1.6 - - - +
149C GLU* 3.9 37.2 - - + +
219C LEU* 3.9 25.4 - - + -
220C SER 3.1 15.9 + - - +
221C ALA* 3.8 4.9 - - - +
223C GLN* 1.3 72.3 - - - +
225C HIS* 1.3 65.3 + - - +
227C LEU* 3.3 9.9 + - + +
228C SER* 3.1 25.1 + - - -
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Residues in contact with HIS 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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100C ALA* 5.2 17.1 - - + +
221C ALA 3.0 14.5 + - - +
222C LYS* 3.5 11.4 - - - +
224C LEU* 1.3 76.1 - - - +
226C THR* 1.3 58.6 + - - +
228C SER* 3.2 8.1 + - - -
229C ASP* 2.9 70.6 + - + +
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Residues in contact with THR 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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161C LEU* 3.5 34.5 - - + +
162C SER* 5.7 0.2 - - - -
164C LEU* 3.9 4.9 - - + +
222C LYS* 2.8 20.5 + - - +
223C GLN* 3.2 11.9 + - - -
225C HIS* 1.3 75.3 + - - +
227C LEU* 1.3 62.6 + - - +
229C ASP* 5.0 0.9 - - - -
230C THR* 2.6 41.1 + - + +
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Residues in contact with LEU 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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70C VAL* 4.6 1.6 - - + -
95C LEU* 3.6 32.3 - - + -
97C TRP* 3.6 46.3 - - + -
116C ALA* 4.0 27.6 - - + -
147C LEU* 4.6 9.0 - - + -
161C LEU* 3.8 16.6 - - + -
164C LEU* 4.0 17.7 - - + +
219C LEU* 5.1 2.0 - - + -
223C GLN 3.0 12.8 + - - +
224C LEU* 3.5 16.6 - - + +
225C HIS 3.2 0.4 - - - -
226C THR* 1.3 78.7 - - - +
228C SER* 1.3 60.1 + - - +
229C ASP 3.7 0.2 + - - -
230C THR 4.4 2.3 + - - -
231C LEU* 4.8 4.0 + - - +
239C LEU 5.0 0.2 - - - +
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Residues in contact with SER 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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97C TRP* 3.6 24.2 - - - -
98C GLY 3.9 13.5 - - - -
99C ALA* 4.1 16.8 - - - -
100C ALA* 4.6 2.4 + - - -
224C LEU 3.1 15.8 + - - -
225C HIS* 3.3 12.5 + - - -
227C LEU* 1.3 76.5 - - - +
229C ASP* 1.3 59.4 + - - +
230C THR 3.7 0.7 - - - -
231C LEU 5.2 1.2 - - - +
238C ARG* 5.1 0.3 - - - -
239C LEU 3.9 4.2 - - - +
240C GLN* 3.0 31.7 + - - +
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Residues in contact with ASP 229 (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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225C HIS* 2.9 51.3 + - + +
226C THR* 5.0 1.1 - - - -
227C LEU 3.4 0.2 - - - -
228C SER* 1.3 80.2 - - - +
230C THR* 1.3 59.0 + - - +
231C LEU 3.8 0.7 - - - -
232C TRP* 5.1 0.5 + - - -
238C ARG* 2.7 51.1 + - - +
240C GLN* 4.5 3.4 - - - +
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Residues in contact with THR 230 (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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164C LEU* 3.5 20.2 - - + +
165C GLU* 3.5 36.8 - - + +
168C ALA* 3.4 17.6 - - + +
226C THR* 2.6 36.8 + - + +
227C LEU 4.4 0.6 + - - -
228C SER 3.7 0.2 - - - -
229C ASP* 1.3 80.9 - - - +
231C LEU* 1.3 62.6 + - + +
232C TRP* 3.6 9.1 + - - -
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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