Contacts of the helix formed by residues 208 - 213 (chain C) in PDB entry 1FZB
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 TRP 208 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C ASN* 1.3 74.8 - - - +
209C ILE* 1.3 79.1 + - + +
211C TYR* 3.0 4.7 + - - +
212C LYS* 2.9 24.8 + - + +
230C ASN* 5.2 1.5 - - - +
270C GLU* 2.9 33.4 + - + -
273C LYS* 4.1 23.3 - - + -
274C TYR* 3.7 35.2 - + - -
312C PHE* 3.7 39.7 - + + -
313C SER 4.5 0.7 - - - -
314C THR* 3.5 17.7 + - + +
316C ASP* 2.9 20.7 + - - +
317C ASN* 3.1 42.5 - - + +
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Residues in contact with ILE 209 (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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216B ARG 3.9 21.5 - - - +
217B LYS* 4.1 15.9 - - + -
218B GLY* 4.4 1.3 - - - +
207C ASN* 2.8 24.2 + - - +
208C TRP* 1.3 83.2 - - + +
210C GLN* 1.3 59.5 + - + +
212C LYS* 2.9 11.6 + - + +
213C GLU* 2.8 36.2 + - + +
316C ASP* 3.8 13.0 - - - +
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B VAL* 6.4 0.2 - - - -
217B LYS 4.6 6.3 - - - -
218B GLY* 2.9 40.4 + - - -
220B GLU* 3.5 22.9 + - - +
206C LYS* 3.1 35.6 - - + +
207C ASN* 2.8 44.2 + - - +
209C ILE* 1.3 77.5 - - + +
211C TYR* 1.3 57.1 + - - +
214C GLY* 2.9 26.1 + - - +
215C PHE* 3.3 21.9 - - + +
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Residues in contact with TYR 211 (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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204C PHE* 2.5 49.2 + - - +
206C LYS* 3.2 39.7 - - + -
207C ASN 3.0 13.9 + - - +
208C TRP* 3.0 4.9 + - + +
210C GLN* 1.3 75.9 - - - +
212C LYS* 1.3 52.3 + - - +
214C GLY 4.2 0.4 - - - -
215C PHE* 3.5 16.8 - + - -
227C TRP* 3.2 28.8 + + - -
229C GLY* 3.4 0.7 - - - -
230C ASN* 2.8 33.5 + - - +
312C PHE* 3.6 27.8 - + + -
314C THR* 4.1 7.2 - - + -
333C GLY* 3.3 22.9 + - - -
345C ASN* 3.3 24.1 + - - +
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Residues in contact with LYS 212 (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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208C TRP* 2.9 16.8 + - + +
209C ILE* 2.9 14.1 + - + +
211C TYR* 1.3 81.1 - - - +
213C GLU* 1.3 78.3 + - + +
229C GLY 3.4 2.9 - - - -
230C ASN* 3.4 10.8 + - - +
231C GLU* 3.1 41.9 + - + +
232C LYS* 4.5 1.0 + - - +
270C GLU* 3.1 30.9 + - - +
274C TYR* 3.0 33.7 - - + +
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Residues in contact with GLU 213 (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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205B VAL* 4.2 2.4 - - - +
206B VAL* 4.7 6.1 - - + -
207B SER 5.6 0.2 + - - -
217B LYS* 3.0 67.5 + - + +
209C ILE* 2.8 21.5 + - + +
210C GLN 4.7 0.2 - - - +
212C LYS* 1.3 102.7 + - + +
214C GLY* 1.3 62.4 + - - +
229C GLY* 4.0 2.5 - - - -
231C GLU* 5.4 4.9 - - - +
232C LYS* 3.3 33.3 + - - +
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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