Contacts of the helix formed by residues 221 - 232 (chain F) in PDB entry 1ZWS
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 THR 221 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E SER* 4.3 6.1 - - - +
59E GLU* 4.6 15.9 + - + +
60E GLU* 3.0 35.0 - - + +
63E ARG* 4.4 6.7 - - - +
219F GLY 4.5 0.4 - - - -
220F ASP* 1.3 87.9 - - + +
222F LYS* 1.3 58.1 + - - +
223F GLN* 3.4 18.7 + - - +
224F GLU* 2.5 43.5 + - - +
225F THR* 2.7 16.3 + - - -
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Residues in contact with LYS 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLU* 5.1 0.2 + - - -
176E ASN* 3.7 16.8 - - - +
177E ILE* 2.5 33.9 + - + +
178E PHE* 3.6 14.0 - - - +
181F PRO* 4.0 27.1 - - + -
221F THR* 1.3 69.9 - - - +
223F GLN* 1.3 67.7 + - - +
225F THR* 2.7 21.6 + - - -
226F LEU* 2.8 32.8 + - + +
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Residues in contact with GLN 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLU* 4.4 4.8 + - - +
63E ARG* 2.8 34.6 + - - +
166E HIS* 4.1 3.3 + - - -
174E PHE* 3.0 37.6 - - + -
175E LYS 4.2 10.2 - - - +
176E ASN* 3.0 27.7 + - - +
191E TYR* 4.2 3.3 + - - -
221F THR* 3.4 14.1 + - - +
222F LYS* 1.3 79.6 - - - +
224F GLU* 1.3 62.3 + - - +
226F LEU* 3.8 3.8 + - - +
227F ALA* 3.6 15.8 + - - +
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Residues in contact with GLU 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLU* 5.6 1.2 - - - +
219F GLY* 3.9 9.0 - - - -
220F ASP* 3.1 45.9 + - - +
221F THR* 2.5 27.6 + - - +
223F GLN* 1.3 76.9 - - - +
225F THR* 1.3 63.8 + - - +
227F ALA* 3.2 15.9 + - - +
228F ASN* 2.9 21.2 + - - +
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Residues in contact with THR 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F PRO* 4.4 7.8 - - + +
182F GLU* 4.3 18.4 - - + +
217F PHE* 3.2 21.1 - - + +
218F LEU* 4.3 5.5 - - + +
219F GLY* 3.0 20.5 + - - +
221F THR 2.7 18.5 + - - -
222F LYS* 2.7 12.3 + - - -
224F GLU* 1.3 71.4 - - - +
226F LEU* 1.3 55.9 + - + +
228F ASN* 2.6 35.9 + - - +
229F ILE* 3.0 27.7 + - + +
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Residues in contact with LEU 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ASN* 3.0 24.9 - - - +
177E ILE* 3.4 35.9 - - + +
191E TYR* 3.5 18.6 - - + +
181F PRO* 4.4 20.6 - - + +
184F VAL* 5.6 0.9 - - + -
189F VAL* 4.2 22.9 - - + -
222F LYS* 2.8 38.0 + - + +
223F GLN 4.0 1.8 - - - +
225F THR* 1.3 71.3 - - - +
227F ALA* 1.3 51.3 + - - +
229F ILE* 3.5 5.3 + - + +
230F THR* 2.8 40.7 + - - +
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Residues in contact with ALA 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E TYR* 3.2 15.8 + - - +
223F GLN 3.6 7.7 + - - +
224F GLU* 3.2 12.1 + - - +
225F THR 3.0 0.6 - - - -
226F LEU* 1.3 75.5 - - - +
228F ASN* 1.3 54.8 + - - +
230F THR* 2.9 4.2 + - - -
231F SER* 2.4 43.7 + - - -
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Residues in contact with ASN 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F PHE* 3.3 39.5 + - + +
218F LEU 5.2 0.2 + - - -
219F GLY* 4.2 3.6 - - - -
224F GLU* 2.9 33.8 + - - +
225F THR* 2.6 15.0 + - - +
227F ALA* 1.3 72.0 - - - +
229F ILE* 1.3 52.5 + - - +
231F SER* 3.3 5.4 - - - -
232F VAL 2.5 31.2 + - - -
233F SER* 2.7 30.2 + - - +
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Residues in contact with ILE 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181F PRO 3.1 28.9 - - - +
182F GLU 4.0 8.1 - - - +
184F VAL* 3.5 21.8 - - + +
185F ALA 3.9 2.2 - - - -
186F PRO* 3.6 36.8 - - + +
189F VAL* 3.9 13.9 - - + -
201F TRP* 3.9 5.0 - - + -
217F PHE* 3.8 30.1 - - + -
225F THR* 3.0 15.1 + - + +
226F LEU* 3.8 8.3 - - + +
228F ASN* 1.3 76.5 - - - +
230F THR* 1.3 59.7 + - - +
232F VAL* 3.0 23.2 + - - +
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Residues in contact with THR 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E TYR* 3.6 15.1 - - + -
186F PRO* 4.8 6.1 - - - -
189F VAL* 3.4 24.5 - - + -
190F ASN* 3.1 35.4 - - - +
226F LEU 2.8 24.7 + - - +
227F ALA* 2.9 17.2 + - - -
229F ILE* 1.3 74.9 - - - +
231F SER* 1.3 60.3 + - - +
232F VAL* 3.1 8.0 + - - +
258F LYS* 4.3 17.0 + - - +
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Residues in contact with SER 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F ALA* 2.4 29.3 + - - -
228F ASN* 3.0 8.8 + - - -
230F THR* 1.3 73.3 + - - +
232F VAL* 1.3 72.0 + - - +
233F SER* 2.8 21.1 + - - -
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Residues in contact with VAL 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F PRO* 4.9 0.7 - - + -
201F TRP* 4.3 15.0 - - + -
217F PHE* 4.1 4.3 - - - -
228F ASN 2.5 14.0 + - - -
229F ILE 3.0 15.1 + - - +
230F THR 3.7 7.4 - - - +
231F SER* 1.3 80.4 - - - +
233F SER* 1.3 58.8 + - - +
234F TYR* 3.9 17.9 + - + -
256F LEU 4.3 18.4 - - - +
258F LYS* 4.1 29.6 - - + +
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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