Contacts of the helix formed by residues 223 - 230 (chain F) in PDB entry 6C3P
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 ASN 223 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71F HIS* 4.4 15.5 - - + -
75F TRP* 4.8 15.1 - - + -
121F VAL* 6.1 1.0 - - - +
125F HIS* 3.9 39.0 + - + +
221F PHE 3.8 1.4 + - - -
222F VAL* 1.3 73.6 - - - +
224F LEU* 1.3 53.2 + - - +
225F LEU* 3.6 24.2 - - - +
226F SER* 2.5 46.5 + - - +
227F LYS* 2.7 36.6 + - - +
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Residues in contact with LEU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F HIS* 3.4 32.6 + - + +
72F ASN* 4.7 13.7 - - + +
75F TRP* 4.5 18.6 - - + -
76F ILE 5.9 0.2 - - - +
79F PHE* 4.5 19.5 - - + -
223F ASN* 1.3 74.8 - - - +
225F LEU* 1.3 64.9 + - - +
227F LYS* 3.2 18.4 + - + +
228F GLY* 2.9 19.4 + - - -
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F TRP* 5.2 7.0 - - + -
79F PHE* 3.8 33.1 - - + -
121F VAL* 5.6 10.1 - - + -
223F ASN* 3.1 22.2 - - - +
224F LEU* 1.3 80.9 - - - +
226F SER* 1.3 58.6 + - - +
228F GLY* 2.9 17.7 + - - -
229F THR* 2.9 26.0 + - + +
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Residues in contact with SER 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F VAL* 3.1 19.5 - - - +
223F ASN* 2.5 37.3 + - - -
225F LEU* 1.3 68.7 - - - +
227F LYS* 1.3 53.8 + - - +
228F GLY 2.8 4.9 - - - -
229F THR* 2.7 17.5 + - - -
230F TYR* 2.5 28.6 + - - -
231F TRP* 3.9 26.5 - - - -
232F TRP* 3.9 14.0 + - - -
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Residues in contact with LYS 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F HIS* 5.7 1.8 - - + +
218F LEU* 5.2 2.2 - - - +
219F GLN* 3.3 69.5 + - + +
220F PRO* 4.2 8.6 - - + +
222F VAL* 3.6 20.2 - - + +
223F ASN 2.7 27.6 + - - +
224F LEU* 3.3 18.4 - - + +
226F SER* 1.3 71.4 + - - +
228F GLY* 1.3 55.8 + - - +
230F TYR* 4.8 5.4 + - - -
232F TRP* 4.8 0.2 - - - +
375F ALA* 5.9 3.1 - - - +
378F TYR* 5.9 0.3 - - - -
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Residues in contact with GLY 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F LEU* 2.9 7.0 + - - -
225F LEU 2.9 8.4 + - - -
226F SER 2.8 1.4 - - - -
227F LYS* 1.3 79.5 - - - +
229F THR* 1.3 56.9 + - - +
230F TYR* 3.8 15.4 - - - -
371F THR* 3.8 23.5 + - - +
374F GLN* 4.3 11.3 - - - +
375F ALA* 5.9 6.1 - - - -
1249F VAL* 4.4 3.3 - - - +
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Residues in contact with THR 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225F LEU* 2.9 28.8 + - + +
226F SER* 2.7 19.8 + - - +
228F GLY* 1.3 74.3 - - - +
230F TYR* 1.3 71.5 + - - +
231F TRP* 3.4 11.8 + - + +
371F THR* 5.2 1.6 - - - -
1246F TRP* 4.1 0.7 - - - -
1249F VAL* 3.8 21.6 - - - +
1250F ARG* 3.8 21.0 + - - +
1253F TYR* 4.3 12.3 - - - -
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Residues in contact with TYR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLN* 3.8 19.9 + - - -
226F SER 2.5 19.5 + - - -
227F LYS 4.8 5.0 + - - -
228F GLY 3.9 16.8 - - - -
229F THR* 1.3 77.0 - - - +
231F TRP* 1.3 60.3 + - - +
232F TRP* 3.3 29.2 - + - +
233F MET* 3.6 13.9 - - + -
234F ASN 2.9 20.6 + - - -
374F GLN* 4.4 9.6 + - + -
375F ALA* 5.7 0.2 - - - -
378F TYR* 3.1 43.8 - + - +
1242F ALA* 4.3 10.1 - - - -
1245F ARG* 3.6 27.1 - - + +
1246F TRP* 3.1 21.8 - - + -
1249F VAL* 4.1 13.7 - - + -
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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