Contacts of the helix formed by residues 221 - 231 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57G SER* 4.4 9.2 - - - +
59G GLU* 5.1 11.9 - - + +
60G GLU* 3.5 26.2 - - + +
63G ARG* 5.6 1.1 - - - +
219H GLY 3.1 1.1 - - - -
220H ASP* 1.3 91.4 - - + +
222H LYS* 1.3 66.6 + - - +
223H GLN* 3.6 21.8 + - - +
224H GLU* 2.6 33.3 + - - +
225H THR* 2.7 15.7 + - - -
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Residues in contact with LYS 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G GLU* 5.4 0.6 + - - -
176G ASN* 4.0 14.1 - - - +
177G ILE* 2.9 28.9 + - + +
178G PHE* 4.3 9.1 - - - +
181H PRO* 4.0 28.0 - - + -
221H THR* 1.3 71.0 - - - +
223H GLN* 1.3 66.2 + - - +
225H THR* 2.8 21.2 + - - -
226H LEU* 2.9 39.6 + - + +
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Residues in contact with GLN 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G GLU* 4.4 7.2 + - - +
63G ARG* 3.3 28.1 - - - +
166G HIS* 4.7 3.1 + - - -
174G PHE* 4.0 30.0 - - + -
175G LYS 4.9 6.7 - - - +
176G ASN* 3.6 25.8 + - - +
191G TYR* 4.6 2.8 + - - -
221H THR* 3.6 18.7 + - - +
222H LYS* 1.3 81.3 - - - +
224H GLU* 1.3 60.8 + - - +
226H LEU* 3.9 3.3 + - - +
227H ALA* 3.7 16.3 + - - +
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Residues in contact with GLU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H GLY* 3.9 9.3 - - - -
220H ASP* 3.1 45.1 + - - +
221H THR* 2.6 27.7 + - - +
223H GLN* 1.3 75.1 - - + +
225H THR* 1.3 63.6 + - - +
227H ALA* 3.2 18.0 + - - +
228H ASN* 2.8 19.2 + - - +
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Residues in contact with THR 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H PRO* 4.3 23.1 - - + +
182H GLU* 4.4 9.2 - - + +
217H PHE* 3.3 26.9 - - + +
218H LEU* 4.3 7.0 - - + +
219H GLY* 2.9 20.5 + - - +
221H THR 2.7 17.7 + - - -
222H LYS* 2.8 12.4 + - - -
224H GLU* 1.3 71.1 - - - +
226H LEU* 1.3 56.5 + - - +
228H ASN* 2.6 36.0 + - - +
229H ILE* 2.9 13.2 + - + -
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Residues in contact with LEU 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G ASN* 3.1 27.4 - - - +
177G ILE* 4.0 24.2 - - + +
191G TYR* 3.6 23.6 - - + +
181H PRO* 4.3 22.0 - - + +
184H VAL* 5.5 0.9 - - + -
189H VAL* 4.1 21.8 - - + -
222H LYS* 2.9 38.9 + - + +
223H GLN* 4.1 2.5 - - - +
225H THR* 1.3 71.7 - - - +
227H ALA* 1.3 49.6 + - - +
229H ILE* 3.8 5.9 - - + +
230H THR* 2.6 43.0 + - - +
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Residues in contact with ALA 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G TYR* 3.5 9.3 + - - +
223H GLN 3.7 9.0 + - - +
224H GLU* 3.2 13.2 + - - +
225H THR 3.0 0.8 - - - -
226H LEU* 1.3 76.0 - - - +
228H ASN* 1.3 54.8 + - - +
230H THR* 2.9 7.0 + - - -
231H SER* 2.4 45.7 + - - +
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Residues in contact with ASN 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H PHE* 3.1 39.9 + - + +
218H LEU 4.8 0.2 - - - -
219H GLY* 4.1 4.0 - - - -
224H GLU* 2.8 33.5 + - - +
225H THR* 2.6 15.4 + - - +
227H ALA* 1.3 73.2 - - - +
229H ILE* 1.3 51.9 + - - +
231H SER* 3.4 5.8 - - - -
232H VAL* 2.6 29.8 + - - -
233H SER* 2.7 30.9 + - - +
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Residues in contact with ILE 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181H PRO 3.2 28.0 - - - +
182H GLU 3.8 10.8 - - - +
184H VAL* 3.2 21.5 - - + +
186H PRO* 3.7 35.5 - - + +
189H VAL* 3.8 16.8 - - + -
201H TRP* 4.0 4.9 - - + -
217H PHE* 3.8 29.6 - - + -
225H THR* 2.9 17.9 + - + +
226H LEU* 3.9 7.4 - - - +
228H ASN* 1.3 75.5 - - - +
230H THR* 1.3 65.0 + - - +
232H VAL* 2.9 19.2 + - - +
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Residues in contact with THR 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G TYR* 3.5 14.2 + - + -
186H PRO* 4.9 5.6 - - - -
189H VAL* 3.2 27.4 - - + -
190H ASN* 3.1 31.9 - - - +
226H LEU 2.6 26.0 + - - +
227H ALA* 2.9 16.6 + - - -
229H ILE* 1.3 76.9 - - + +
231H SER* 1.3 57.4 + - - +
232H VAL* 3.4 8.5 + - - +
258H LYS* 4.3 17.2 + - - +
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Residues in contact with SER 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H ALA* 2.4 31.4 + - - +
228H ASN* 3.3 4.7 + - - -
230H THR* 1.3 72.4 + - - +
232H VAL* 1.3 71.7 + - - +
233H SER* 2.9 20.9 + - - -
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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