Contacts of the helix formed by residues 222 - 231 (chain B) in PDB entry 3FTN
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 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLY* 1.3 71.2 - - - -
223B ILE* 1.3 81.5 + - - +
224B VAL* 3.2 34.2 + - + +
225B ASP* 3.0 30.6 + - - +
226B GLN* 3.0 19.4 + - - +
251B GLN* 4.0 22.8 + - + +
254B LYS* 5.9 4.6 + - + -
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Residues in contact with ILE 223 (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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173B ILE* 5.5 1.3 - - + -
197B VAL* 3.8 41.5 - - + -
216B LEU* 4.7 7.4 - - + -
217B ASN 4.3 1.3 - - - -
218B TYR* 3.8 36.8 - - + +
221B GLY 3.3 1.8 + - - -
222B HIS* 1.3 74.2 + - - +
224B VAL* 1.3 57.4 + - - +
226B GLN* 3.1 12.9 + - - +
227B VAL* 2.8 33.2 + - + +
251B GLN* 4.2 23.3 - - - +
255B MET* 3.7 21.5 - - + -
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Residues in contact with VAL 224 (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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222B HIS* 3.2 24.6 + - + +
223B ILE* 1.3 75.0 - - - +
225B ASP* 1.3 62.6 + - - +
227B VAL* 3.1 5.5 + - - +
228B MET* 2.8 44.1 + - + +
251B GLN* 3.7 35.4 - - + +
254B LYS* 3.9 36.8 - - + +
255B MET* 4.2 8.3 - - + +
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Residues in contact with ASP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLY* 5.3 0.4 - - - -
222B HIS* 3.0 32.7 + - + +
224B VAL* 1.3 80.1 - - - +
226B GLN* 1.3 58.7 + - + +
228B MET* 3.3 8.2 + - - +
229B LYS* 2.8 28.8 + - - +
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Residues in contact with GLN 226 (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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216B LEU* 3.7 33.6 - - + +
217B ASN 2.9 25.0 + - - +
218B TYR* 4.2 1.0 - - - +
220B ASN* 3.3 34.3 + - - +
221B GLY* 2.7 27.3 + - - +
222B HIS 3.0 12.5 + - - +
223B ILE* 3.1 12.2 + - - +
225B ASP* 1.3 76.4 - - + +
227B VAL* 1.3 59.4 + - - +
229B LYS* 3.2 8.6 + - + +
230B LEU* 2.8 33.3 + - + +
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Residues in contact with VAL 227 (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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171B VAL* 4.3 9.9 - - + -
195B ILE* 5.0 4.7 - - + -
216B LEU* 3.8 17.5 - - + -
223B ILE* 2.8 23.6 + - + +
224B VAL 3.7 5.2 - - - +
226B GLN* 1.3 68.6 - - - +
228B MET* 1.3 65.9 + - + +
230B LEU* 3.2 6.4 + - - +
231B THR* 2.8 34.0 + - + +
235B GLY* 4.6 5.2 - - - -
236B VAL* 3.8 29.8 - - + -
255B MET* 3.9 40.6 - - + -
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Residues in contact with MET 228 (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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224B VAL* 2.8 33.8 + - + +
225B ASP* 3.6 8.3 - - - +
227B VAL* 1.3 72.9 - - - +
229B LYS* 1.3 58.3 + - - +
231B THR* 3.8 1.3 - - - -
232B ASN* 3.0 8.3 + - - -
233B GLY* 2.6 60.4 + - - +
234B LYS 4.8 0.4 - - - -
235B GLY* 3.9 23.1 - - - +
254B LYS 4.8 12.6 - - - +
255B MET* 5.0 3.8 - - - +
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Residues in contact with LYS 229 (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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225B ASP 2.8 16.7 + - - +
226B GLN* 3.5 9.9 - - + +
227B VAL 3.1 0.2 - - - -
228B MET* 1.3 77.2 - - - +
230B LEU* 1.3 66.9 + - + +
231B THR 3.2 0.7 + - - -
232B ASN* 3.3 11.8 + - - +
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Residues in contact with LEU 230 (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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193B ARG* 3.0 45.3 + - - +
195B ILE* 4.1 16.6 - - + -
214B ASP* 4.2 12.6 - - + +
216B LEU* 3.7 36.1 - - + -
226B GLN 2.8 21.2 + - - +
227B VAL* 3.2 6.0 + - - +
229B LYS* 1.3 77.8 - - + +
231B THR* 1.3 62.6 + - + +
232B ASN 3.3 1.0 + - - -
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Residues in contact with THR 231 (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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169B SER* 5.6 2.7 - - - +
193B ARG* 4.7 8.7 - - - +
195B ILE* 4.9 3.8 - - + -
227B VAL* 2.8 23.6 + - + +
228B MET* 3.6 2.4 + - - -
230B LEU* 1.3 83.9 - - + +
232B ASN* 1.3 66.4 + - - +
234B LYS* 3.0 29.1 + - - +
235B GLY* 2.9 42.1 + - - +
236B VAL* 4.0 19.5 - - + -
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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