Contacts of the helix formed by residues 221 - 231 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219G GLY 3.1 1.1 - - - -
220G ASP* 1.3 89.8 - - + +
222G LYS* 1.3 56.9 + - - +
223G GLN* 3.3 19.9 + - - +
224G GLU* 2.5 43.4 + - - +
225G THR* 2.7 15.6 + - - -
57H SER* 4.0 10.5 - - - +
59H GLU* 4.3 20.8 + - + +
60H GLU* 3.4 27.8 - - + +
63H ARG* 4.6 2.5 - - - +
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Residues in contact with LYS 222 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PRO* 4.1 26.9 - - + -
221G THR* 1.3 69.5 - - - +
223G GLN* 1.3 67.1 + - - +
225G THR* 2.7 21.8 + - - -
226G LEU* 2.8 34.0 + - + +
60H GLU* 4.8 2.6 + - - -
164H LEU* 5.9 1.0 - - - +
176H ASN* 3.6 20.9 - - - +
177H ILE* 2.8 29.3 + - + +
178H PHE* 3.9 12.9 - - - +
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Residues in contact with GLN 223 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G THR* 3.3 14.1 + - - +
222G LYS* 1.3 79.9 - - - +
224G GLU* 1.3 63.4 + - - +
226G LEU* 3.9 4.0 + - - +
227G ALA* 3.6 15.4 + - - +
59H GLU* 3.9 7.6 + - - +
63H ARG* 2.6 34.7 - - - +
166H HIS* 3.8 6.4 + - - -
174H PHE* 3.3 37.5 - - + -
175H LYS 4.6 6.4 - - - +
176H ASN* 3.3 25.6 + - - +
191H TYR* 4.6 1.7 + - - -
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Residues in contact with GLU 224 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G GLY* 3.7 10.7 - - - -
220G ASP* 3.1 43.4 + - - +
221G THR* 2.5 27.9 + - - +
223G GLN* 1.3 75.3 - - + +
225G THR* 1.3 64.7 + - - +
227G ALA* 3.0 17.1 + - - +
228G ASN* 2.9 19.4 + - - +
59H GLU* 5.7 0.7 - - - +
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Residues in contact with THR 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PRO* 4.2 25.7 - - + +
182G GLU* 4.3 11.4 - - + +
217G PHE* 3.3 20.2 - - + +
218G LEU* 4.3 5.3 - - + +
219G GLY 3.0 20.9 + - - +
221G THR 2.7 17.9 + - - -
222G LYS* 2.7 11.9 + - - -
224G GLU* 1.3 71.3 - - - +
226G LEU* 1.3 55.1 + - - +
228G ASN* 2.5 37.4 + - - +
229G ILE* 3.0 17.8 + - + -
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Residues in contact with LEU 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PRO* 4.5 21.8 - - + +
184G VAL* 5.5 1.6 - - + -
189G VAL* 4.2 20.2 - - + -
222G LYS* 2.8 36.9 + - + +
223G GLN 3.9 3.1 - - - +
225G THR* 1.3 72.4 - - - +
227G ALA* 1.3 50.0 + - - +
229G ILE* 3.6 7.0 + - + +
230G THR* 2.6 40.5 + - - +
176H ASN* 2.8 27.1 - - - +
177H ILE* 3.6 27.4 - - + +
191H TYR* 3.1 26.6 + - + +
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Residues in contact with ALA 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G GLN 3.6 8.8 + - - +
224G GLU* 3.0 12.9 + - - +
225G THR 2.8 2.2 + - - -
226G LEU* 1.3 71.9 - - - +
228G ASN* 1.3 55.4 + - - +
230G THR* 3.0 7.2 + - - -
231G SER* 2.4 45.1 + - - +
191H TYR* 3.2 8.7 + - - +
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Residues in contact with ASN 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217G PHE* 3.3 32.7 + - + +
218G LEU 4.8 0.2 - - - -
219G GLY* 4.2 3.4 - - - -
224G GLU* 2.9 35.1 + - - +
225G THR* 2.5 22.4 + - - +
227G ALA* 1.3 72.4 - - - +
229G ILE* 1.3 52.7 + - - +
231G SER* 3.3 5.6 - - - -
232G VAL* 2.5 29.6 + - - -
233G SER* 2.6 31.4 + - - +
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Residues in contact with ILE 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181G PRO 3.1 28.3 - - - +
182G GLU 4.1 8.7 - - - +
184G VAL* 3.3 28.0 - - + +
186G PRO* 3.5 29.8 - - + +
189G VAL* 3.9 15.7 - - + -
201G TRP* 3.9 4.8 - - + -
217G PHE* 3.8 31.0 - - + -
225G THR* 3.0 17.1 + - + +
226G LEU* 3.9 8.1 - - + +
228G ASN* 1.3 77.2 - - - +
230G THR* 1.3 60.1 + - - +
232G VAL* 3.0 24.1 + - - +
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Residues in contact with THR 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G PRO* 4.8 5.4 - - - -
189G VAL* 3.3 18.4 - - + -
190G ASN* 3.1 32.8 - - - +
226G LEU 2.6 22.2 + - - +
227G ALA* 3.0 17.2 + - - -
229G ILE* 1.3 76.7 - - - +
231G SER* 1.3 57.8 + - - +
232G VAL* 3.3 8.8 + - - +
258G LYS* 4.4 17.1 + - - +
191H TYR* 3.2 25.9 + - + -
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Residues in contact with SER 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G ALA* 2.4 32.1 + - - -
228G ASN* 3.2 4.7 + - - -
230G THR* 1.3 72.4 + - - +
232G VAL* 1.3 72.3 + - - +
233G SER* 2.7 24.7 + - - -
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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