Contacts of the helix formed by residues 210 - 219 (chain B) in PDB entry 4F4W
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 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B LYS* 1.3 74.7 - - - +
211B TYR* 1.3 65.0 + - - +
212B ASN* 2.7 37.8 + - - +
213B GLU* 2.7 45.5 + - - +
214B LEU* 2.8 23.5 + - - +
227B LEU* 4.5 2.9 - - - -
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Residues in contact with TYR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ASN* 1.3 72.9 - - - +
212B ASN* 1.3 77.1 + - + +
214B LEU* 2.8 3.8 + - - +
215B GLU* 2.6 53.0 + - + +
220B LYS* 3.4 36.9 - - + +
223B ALA* 3.7 27.8 - - + -
224B LEU* 3.9 27.4 - - + -
227B LEU* 3.7 23.0 - - + +
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Residues in contact with ASN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 5.9 0.6 + - - -
210B ASN* 2.7 15.2 + - - +
211B TYR* 1.3 87.5 - - + +
213B GLU* 1.3 62.5 + - + +
215B GLU* 3.7 4.8 + - - +
216B LYS* 2.6 55.2 + - - +
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Residues in contact with GLU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B SER 4.4 2.1 - - - +
209B LYS* 3.2 37.3 - - + +
210B ASN* 2.7 53.1 + - - +
212B ASN* 1.3 72.9 - - + +
214B LEU* 1.3 56.9 + - - +
216B LYS* 3.2 15.2 + - - +
217B ILE* 2.6 29.6 - - - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LEU* 4.2 16.6 - - + -
200B ILE* 4.7 8.3 - - + -
206B ILE* 4.1 24.5 - - + +
209B LYS* 4.7 11.4 - - + -
210B ASN 2.8 16.1 + - - +
211B TYR* 2.8 10.0 + - - +
213B GLU* 1.3 71.2 - - - +
215B GLU* 1.3 55.8 + - - +
217B ILE* 2.7 32.0 + - + +
218B THR* 2.8 34.1 + - + +
223B ALA* 3.7 31.9 - - + +
226B LEU* 4.3 7.9 - - + -
227B LEU* 3.9 17.3 - - + -
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TYR* 2.6 54.0 + - + +
212B ASN* 3.9 5.7 - - - +
214B LEU* 1.3 71.7 - - - +
216B LYS* 1.3 78.3 + - - +
218B THR* 4.1 1.3 - - - -
219B GLY* 2.8 33.9 + - - -
220B LYS* 3.9 14.3 + - + +
223B ALA* 4.0 9.3 - - - +
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ASP* 5.4 3.2 + - - -
279A LYS* 3.8 24.3 - - - +
194B ARG* 3.8 11.6 + - - -
212B ASN* 2.6 42.2 + - - +
213B GLU* 3.2 12.8 + - - +
214B LEU 3.1 1.0 - - - -
215B GLU* 1.3 88.1 + - - +
217B ILE* 1.3 62.2 + - + +
219B GLY 4.9 0.2 - - - -
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 3.6 12.4 - - + +
194B ARG* 3.7 35.2 + - + +
195B LEU* 3.9 24.0 - - + -
198B LEU* 3.4 35.4 - - + -
200B ILE* 6.2 0.4 - - + -
209B LYS* 4.5 15.0 - - - +
213B GLU 2.6 36.6 - - - +
214B LEU* 2.7 19.8 + - + +
216B LYS* 1.3 79.6 - - + +
218B THR* 1.3 58.9 + - + +
219B GLY 3.8 0.4 - - - -
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Residues in contact with THR 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B LEU* 4.0 17.6 - - + +
195B LEU* 3.9 26.7 - - + -
214B LEU* 2.8 26.6 + - + +
217B ILE* 1.3 81.1 - - - +
219B GLY* 1.3 72.6 + - - +
222B LYS* 3.5 27.8 - - - +
223B ALA* 3.2 15.6 + - - +
226B LEU* 4.2 14.1 - - + -
12F C 4.2 3.1 + - - -
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Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B GLU* 2.8 25.5 + - - -
217B ILE 3.8 0.6 - - - -
218B THR* 1.3 95.5 + - - +
220B LYS* 1.3 65.5 + - - -
221B ALA 3.6 1.6 - - - -
222B LYS 3.6 1.0 + - - -
223B ALA* 3.1 7.4 + - - +
12F C 3.3 14.4 - - - -
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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