Contacts of the helix formed by residues 211 - 216 (chain B) 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 CYS 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B GLU* 1.3 73.3 + - - +
212B GLU* 1.3 64.7 + - - +
214B ILE* 3.0 7.1 + - - +
215B ILE* 2.8 20.4 + - - +
227B ILE* 4.3 0.8 - - - +
238B VAL* 4.1 2.5 - - - -
239B TYR 4.0 1.8 - - - -
240B CYS* 2.0 56.4 - - + -
242B MET* 3.5 4.7 - - + +
248B GLY* 3.4 21.8 - - - +
249B TRP 3.8 0.4 - - - -
250B THR* 3.1 42.4 - - - +
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Residues in contact with GLU 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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210B GLU* 2.7 25.9 + - - +
211B CYS* 1.3 71.8 - - - +
213B GLU* 1.3 66.1 + - - +
215B ILE* 2.8 30.0 + - - +
216B ARG* 3.0 33.8 + - - +
247B GLY 5.0 1.0 - - - +
248B GLY* 3.4 17.0 + - - +
455B ARG* 4.4 14.8 - - + +
456B PRO* 3.8 17.3 - - + -
458B PHE* 3.5 33.1 - - + -
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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 GLY* 3.3 5.8 - - - -
209B LYS* 2.6 64.2 + - - +
210B GLU* 2.7 27.7 + - - +
212B GLU* 1.3 72.4 - - - +
214B ILE* 1.3 58.7 + - - +
216B ARG* 3.0 32.4 + - + +
217B LYS* 2.8 50.2 + - + +
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Residues in contact with ILE 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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206B VAL* 4.1 9.4 - - + -
207B SER* 4.0 6.5 - - - -
208B GLY 3.8 21.5 - - - +
210B GLU 3.0 13.0 + - - +
211B CYS* 3.0 12.1 + - - +
213B GLU* 1.3 75.4 - - - +
215B ILE* 1.3 65.1 + - - +
217B LYS* 2.8 20.9 + - - +
219B GLY* 3.1 22.8 + - - -
225B TYR* 3.7 41.3 - - + -
226B LEU 4.4 0.4 - - - +
227B ILE* 3.6 29.8 - - + -
240B CYS* 4.2 0.4 - - - -
242B MET* 3.7 14.6 - - + -
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Residues in contact with ILE 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 CYS 2.8 13.3 + - - +
212B GLU* 2.8 36.5 + - - +
214B ILE* 1.3 74.4 - - - +
216B ARG* 1.3 65.9 + - + +
218B GLY* 3.2 13.7 + - - -
219B GLY 3.1 20.0 + - - +
220B GLU* 4.8 8.4 - - + +
242B MET* 3.9 27.1 - - + +
246B ASN 3.6 23.8 - - - +
247B GLY* 4.1 8.7 - - - +
248B GLY* 4.1 5.6 - - - +
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Residues in contact with ARG 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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209B LYS* 5.0 5.9 - - - +
210B GLU* 4.7 1.0 + - - -
212B GLU* 3.1 30.0 + - - +
213B GLU* 3.0 45.8 + - - +
215B ILE* 1.3 83.3 - - + +
217B LYS* 1.3 57.1 + - + +
218B GLY* 3.0 9.7 + - - -
458B PHE* 4.1 23.4 - - - -
209C ILE* 3.9 11.6 - - - +
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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