Contacts of the helix formed by residues 222 - 231 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D TYR* 4.6 22.6 + + - -
221D GLY* 1.3 73.4 - - - -
223D ILE* 1.3 68.2 + - - +
224D VAL* 3.2 5.6 - - + +
225D ASP* 3.1 31.7 + - - +
226D GLN* 3.1 9.7 + - - +
251D GLN* 5.8 6.7 - - - -
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Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ILE* 5.6 2.5 - - + -
197D VAL* 4.0 28.7 - - + -
216D LEU* 3.4 42.4 - - + -
217D ASN 5.1 2.7 - - - +
218D TYR* 5.1 11.0 - - + +
221D GLY 3.4 3.3 + - - -
222D HIS* 1.3 73.0 - - - +
224D VAL* 1.3 61.3 + - + +
226D GLN* 3.1 15.4 + - + +
227D VAL* 2.8 33.7 + - + +
251D GLN* 3.9 32.3 - - + +
255D MET* 3.8 18.4 - - + -
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D HIS* 3.2 4.2 - - + +
223D ILE* 1.3 75.8 - - + +
225D ASP* 1.3 63.4 + - - +
227D VAL* 3.3 3.0 + - - +
228D MET* 2.9 45.3 + - + +
251D GLN* 3.6 44.2 - - + +
254D LYS* 3.9 35.9 - - + +
255D MET* 4.1 10.3 - - + +
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Residues in contact with ASP 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D GLY* 5.5 1.3 - - - -
222D HIS* 3.1 28.8 + - - +
224D VAL* 1.3 80.9 - - - +
226D GLN* 1.3 66.3 + - + +
228D MET* 3.8 7.6 - - - +
229D LYS* 3.0 25.1 + - - +
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Residues in contact with GLN 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D LEU* 3.7 23.6 - - + +
217D ASN 2.8 31.4 + - - +
220D ASN* 3.3 35.5 + - - +
221D GLY* 2.9 20.2 + - - -
222D HIS 3.1 9.3 + - - +
223D ILE* 3.1 23.4 + - + +
225D ASP* 1.3 75.2 - - + +
227D VAL* 1.3 65.2 + - - +
229D LYS* 3.3 5.8 + - - +
230D LEU* 3.0 28.1 + - - +
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D VAL* 4.1 11.7 - - + -
195D ILE* 4.9 2.2 - - + -
216D LEU* 3.5 23.1 - - + -
223D ILE* 2.8 24.3 + - + +
224D VAL 3.8 3.6 - - - +
226D GLN* 1.3 72.0 - - - +
228D MET* 1.3 63.3 + - - +
230D LEU* 3.3 5.3 + - - +
231D THR* 3.0 32.6 + - + +
235D GLY* 5.0 1.3 - - - -
236D VAL* 3.9 26.7 - - + -
255D MET* 4.0 43.3 - - + +
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Residues in contact with MET 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D VAL* 2.9 31.0 + - + +
225D ASP* 3.8 8.7 - - - +
226D GLN 3.3 0.2 - - - -
227D VAL* 1.3 77.7 - - - +
229D LYS* 1.3 56.9 + - - +
231D THR* 3.1 2.0 + - - -
232D ASN 2.7 11.6 + - - -
233D GLY* 2.7 63.2 + - - +
234D LYS 4.9 0.4 - - - -
235D GLY* 4.2 20.4 - - - +
254D LYS 4.8 13.7 - - - +
255D MET* 4.9 5.4 - - - +
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Residues in contact with LYS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ASP 3.0 17.4 + - - +
226D GLN* 3.9 5.4 - - - +
228D MET* 1.3 77.0 - - - +
230D LEU* 1.3 63.4 + - + +
231D THR 3.5 0.3 + - - -
232D ASN* 3.6 8.5 + - - +
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D ARG* 3.2 36.9 + - - +
195D ILE* 4.1 18.8 - - + -
214D ASP* 4.2 15.7 - - + +
216D LEU* 3.5 41.3 - - + -
226D GLN 3.0 15.8 + - - +
227D VAL* 3.5 9.0 - - - +
228D MET 3.2 0.2 - - - -
229D LYS* 1.3 77.9 - - + +
231D THR* 1.3 64.0 + - + +
232D ASN 3.4 1.6 + - - -
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Residues in contact with THR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D SER* 5.7 2.0 - - - +
193D ARG* 4.9 7.9 - - - +
195D ILE* 4.5 7.6 - - + -
227D VAL* 3.0 19.2 + - + +
228D MET* 3.1 6.4 + - - -
230D LEU* 1.3 83.4 - - + +
232D ASN* 1.3 63.4 + - - +
234D LYS* 2.8 33.6 + - - +
235D GLY* 2.9 40.1 + - - +
236D VAL* 3.9 18.6 - - + -
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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