Contacts of the helix formed by residues 218 - 229 (chain C) in PDB entry 4CFE
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 HIS 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216C ASP* 3.2 10.4 + - - +
217C GLU* 1.3 76.5 - - - +
219C VAL* 1.3 59.8 + - - +
220C PRO* 3.4 36.6 - - + +
221C THR* 2.5 28.6 + - - +
222C LEU* 2.9 26.5 + - - +
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Residues in contact with VAL 219 (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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177C PRO* 5.2 9.4 - - + -
216C ASP 5.0 1.1 - - - +
217C GLU 3.4 8.7 + - - +
218C HIS* 1.3 71.7 - - - +
220C PRO* 1.4 72.6 - - + +
222C LEU* 3.0 16.9 + - + +
223C PHE* 3.0 49.8 + - + -
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Residues in contact with PRO 220 (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 HIS* 3.4 33.4 - - + +
219C VAL* 1.4 94.7 - - + +
221C THR* 1.3 58.9 + - - +
223C PHE* 3.5 10.9 + - + +
224C LYS* 3.2 19.8 + - - +
227C ARG* 5.3 0.7 + - - -
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Residues in contact with THR 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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216C ASP* 3.2 23.1 - - - +
218C HIS* 2.5 41.9 + - - +
220C PRO* 1.3 75.5 - - - +
222C LEU* 1.3 65.6 + - - +
224C LYS* 3.3 20.9 + - + +
225C LYS* 3.1 30.1 + - + +
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Residues in contact with LEU 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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177C PRO* 4.0 33.2 - - + -
178C ASN* 4.5 5.2 - - + +
214C PHE* 3.4 39.3 - - + +
215C ASP* 3.7 12.1 - - - +
216C ASP* 3.9 20.4 - - - +
218C HIS 2.9 12.7 + - - +
219C VAL* 3.0 16.6 + - + +
221C THR* 1.3 77.8 - - - +
223C PHE* 1.3 65.0 + - + +
225C LYS* 3.2 5.9 + - + +
226C ILE* 3.1 35.5 + - + +
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Residues in contact with PHE 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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177C PRO* 4.2 25.4 - - + -
185C ILE* 3.8 46.4 - - + -
219C VAL* 3.0 37.2 + - + -
220C PRO* 3.8 11.0 - - + +
221C THR 3.3 0.2 - - - -
222C LEU* 1.3 76.8 - - + +
224C LYS* 1.3 65.6 + - - +
226C ILE* 3.3 4.8 + - + +
227C ARG* 3.0 57.0 + - - +
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Residues in contact with LYS 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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220C PRO 3.2 13.2 + - - +
221C THR* 3.3 24.4 - - + +
222C LEU 3.2 0.2 - - - -
223C PHE* 1.3 77.3 - - - +
225C LYS* 1.3 64.4 + - - +
227C ARG* 3.6 9.6 + - - +
228C GLY* 3.0 24.9 + - - -
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Residues in contact with LYS 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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213C PRO 5.9 0.4 - - - +
214C PHE* 3.2 25.4 - - + -
215C ASP 3.1 30.9 + - - +
216C ASP* 3.1 29.6 + - + +
221C THR* 3.1 18.7 + - + +
222C LEU* 3.2 7.4 + - - +
224C LYS* 1.3 81.5 - - + +
226C ILE* 1.3 59.8 + - - +
228C GLY* 3.4 2.3 + - - -
229C GLY 3.0 22.0 + - - -
230C VAL* 3.8 7.2 + - - +
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Residues in contact with ILE 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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177C PRO 3.5 24.9 - - - +
178C ASN* 4.8 4.5 - - - +
180C ALA 3.8 20.9 - - - +
182C PRO* 3.8 21.6 - - + +
185C ILE* 3.7 29.6 - - + -
198C TRP* 3.8 16.1 - - + -
214C PHE* 3.8 27.5 - - + -
222C LEU* 3.1 24.9 + - + +
223C PHE* 3.7 3.4 - - + +
224C LYS 3.3 0.2 - - - -
225C LYS* 1.3 74.1 - - - +
227C ARG* 1.3 65.7 + - - +
229C GLY* 3.0 15.2 + - - -
251C VAL* 4.5 0.5 - - - +
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Residues in contact with ARG 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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182C PRO* 4.4 13.2 - - + +
185C ILE* 3.6 32.1 + - + +
186C SER* 2.9 26.1 + - - +
220C PRO 5.3 0.8 + - - -
223C PHE* 3.0 53.2 + - - +
224C LYS* 4.1 7.6 - - - +
226C ILE* 1.3 75.0 - - - +
228C GLY* 1.3 60.0 + - - +
251C VAL* 3.6 18.0 - - - +
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Residues in contact with GLY 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 LYS 3.0 17.5 + - - -
225C LYS* 3.4 3.1 + - - -
226C ILE 3.1 0.4 - - - -
227C ARG* 1.3 80.0 - - - +
229C GLY* 1.3 63.5 + - - +
230C VAL* 3.2 16.4 + - - +
251C VAL* 4.1 5.2 - - - +
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Residues in contact with GLY 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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198C TRP* 6.1 0.2 - - - -
214C PHE* 3.7 15.7 - - - -
225C LYS 3.0 7.1 + - - -
226C ILE 3.0 12.8 + - - -
228C GLY* 1.3 78.5 - - - +
230C VAL* 1.3 61.3 + - - +
231C PHE* 4.0 12.2 - - - -
249C LEU 5.1 4.8 - - - +
251C VAL* 3.6 17.8 - - - +
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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