Contacts of the helix formed by residues 216 - 222 (chain A) in PDB entry 4ZPF
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 ASP 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A LYS 4.3 0.2 + - - -
215A MET* 1.3 72.4 - - - +
217A CYS* 1.3 61.4 + - - +
218A LYS* 3.1 32.2 + - - +
219A GLU* 3.0 39.6 + - + +
220A TYR* 4.1 1.6 + - - -
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Residues in contact with CYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 3.6 20.0 - - - +
215A MET 3.2 3.8 + - - +
216A ASP* 1.3 75.9 + - - +
218A LYS* 1.4 62.2 + - - +
219A GLU 3.1 0.2 - - - -
220A TYR* 3.1 30.5 + - + +
221A ASN* 3.2 15.4 + - - -
378A ASP 5.1 1.8 - - - -
381A ASP* 4.4 4.0 - - - -
382A CYS* 2.1 56.1 - - + -
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ASP* 3.1 19.7 + - + +
217A CYS* 1.4 77.6 - - - +
219A GLU* 1.3 63.4 + - + +
221A ASN* 3.3 5.0 + - - -
222A TYR* 3.3 22.7 + - - +
381A ASP* 3.0 51.5 + - - +
382A CYS 3.5 12.4 - - - +
383A GLY 4.5 10.8 - - - +
384A TYR* 5.4 4.8 - - - +
385A ASN* 6.0 1.8 - - - +
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A MET* 4.1 15.3 - - + -
216A ASP* 3.0 28.2 + - + +
218A LYS* 1.3 80.5 - - + +
220A TYR* 1.4 59.1 + - - +
221A ASN 3.3 0.9 + - - -
222A TYR* 3.4 25.0 + - - +
237A PRO* 3.5 11.4 - - - +
239A LYS* 3.1 43.6 + - + +
240A VAL* 3.5 24.5 - - + +
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 4.0 29.0 - - + +
204A VAL 4.4 0.2 - - - -
205A ARG* 3.8 21.3 - - - -
206A VAL* 3.7 31.1 + - + -
212A ASP* 4.4 2.1 + - - -
213A LEU* 3.6 16.2 - - + +
214A LYS 4.0 1.7 + - - -
215A MET* 3.4 46.0 + - + +
217A CYS* 3.1 33.9 + - + +
219A GLU* 1.4 76.7 - - - +
221A ASN* 1.3 57.9 + - - +
222A TYR 3.5 0.4 + - - -
225A SER* 3.0 7.1 + - - -
237A PRO* 4.3 0.2 - - - +
240A VAL* 3.8 28.7 - - + -
331A THR* 2.7 28.0 + - - -
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Residues in contact with ASN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ARG* 6.2 0.4 - - - +
200A GLU* 6.0 1.3 - - - +
201A VAL 4.6 2.0 - - - +
202A ILE* 3.7 9.1 - - + +
203A ILE* 2.7 47.7 + - - +
217A CYS 3.2 11.1 + - - -
218A LYS 3.3 5.0 + - - -
219A GLU 3.2 0.6 - - - -
220A TYR* 1.3 77.2 - - - +
222A TYR* 1.3 57.3 + - - +
223A ASP 3.0 4.5 - - - -
224A LYS* 2.9 20.4 + - - -
225A SER* 2.7 32.3 + - - +
382A CYS* 3.1 32.0 + - - +
383A GLY* 4.9 1.1 - - - -
384A TYR* 3.5 14.9 - - - +
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LYS 3.3 13.4 + - - +
219A GLU* 3.4 23.3 + - - +
220A TYR 3.5 1.0 + - - -
221A ASN* 1.3 76.6 - - - +
223A ASP* 1.3 59.0 + - + +
224A LYS 3.4 1.3 - - - -
237A PRO* 3.3 21.3 - - + +
239A LYS* 6.0 3.1 - - - -
328A SER 6.0 2.0 - - - -
330A GLY* 3.3 17.2 + - - -
384A TYR* 3.6 42.5 + + + -
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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