Contacts of the helix formed by residues 221 - 232 (chain D) in PDB entry 3ZXT
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D GLY 3.8 2.9 - - - +
220D ASP* 1.3 79.4 - - - +
222D LYS* 1.3 57.8 - - - +
223D GLN* 4.2 7.6 - - - -
224D GLU* 2.8 39.2 + - - +
225D THR* 2.8 15.1 + - - -
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Residues in contact with LYS 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO* 6.1 5.4 - - + -
220D ASP 4.2 0.8 + - - -
221D THR* 1.3 70.6 - - - +
223D GLN* 1.3 56.2 + - - +
225D THR* 3.1 12.1 + - - -
226D LEU* 3.0 39.6 + - + +
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Residues in contact with GLN 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D THR* 3.2 7.3 - - - -
222D LYS* 1.3 77.9 - - - +
224D GLU* 1.3 58.4 + - - +
226D LEU* 3.7 12.7 + - - +
227D ALA* 3.3 20.8 + - - +
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Residues in contact with GLU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D GLY* 4.7 1.8 - - - -
220D ASP* 3.8 29.4 + - - +
221D THR* 2.8 38.2 + - - +
223D GLN* 1.3 73.1 - - - +
225D THR* 1.3 61.6 + - - +
226D LEU 3.3 0.2 - - - -
227D ALA* 3.4 7.7 + - + +
228D ASN* 3.0 35.6 + - - +
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Residues in contact with THR 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO* 4.5 8.3 - - + -
182C GLU* 4.0 30.1 - - + +
217D PHE 3.5 21.1 - - - +
218D LEU* 3.8 13.5 - - + +
219D GLY 2.8 23.4 + - - +
221D THR 2.8 12.5 + - - -
222D LYS* 3.3 13.1 - - - -
224D GLU* 1.3 75.0 - - - +
226D LEU* 1.3 59.6 + - - +
228D ASN* 2.9 20.8 + - - +
229D VAL* 3.0 15.1 + - + +
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO* 3.6 32.8 - - + -
189C VAL* 3.8 31.7 - - + +
222D LYS* 3.0 24.3 + - + +
223D GLN* 3.8 12.1 - - - +
224D GLU 3.3 0.2 - - - -
225D THR* 1.3 78.5 - - - +
227D ALA* 1.3 56.7 + - - +
229D VAL* 3.4 5.8 + - + +
230D SER* 2.9 29.9 + - - -
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D GLN 3.3 12.1 + - - +
224D GLU* 3.7 10.5 - - + +
225D THR 3.3 0.4 - - - -
226D LEU* 1.3 76.4 - - - +
228D ASN* 1.3 61.2 + - - +
230D SER* 3.7 6.3 - - - -
231D ALA* 2.8 33.4 + - - +
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Residues in contact with ASN 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D PHE* 2.8 35.6 + - + +
218D LEU 4.0 8.9 + - - -
219D GLY* 4.0 5.7 - - - -
224D GLU* 3.0 25.9 + - - +
225D THR* 2.9 10.1 + - - +
227D ALA* 1.3 75.5 - - - +
229D VAL* 1.3 52.4 + - - +
231D ALA* 3.0 1.6 + - - -
232D VAL* 2.7 31.9 + - - -
233D ASN* 2.9 45.7 + - - +
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C PRO 3.7 19.7 - - - +
182C GLU 4.3 2.0 - - - +
184C VAL 3.0 26.0 - - - +
186C PRO* 3.7 24.9 - - + +
189C VAL* 3.8 17.0 - - + -
201D TRP* 4.0 7.1 - - + -
217D PHE* 3.5 30.1 - - + -
225D THR* 3.0 17.6 + - + +
226D LEU* 3.7 7.4 - - - +
227D ALA 3.2 0.2 - - - -
228D ASN* 1.3 73.8 - - - +
230D SER* 1.3 66.7 + - - +
232D VAL* 3.0 12.6 + - - +
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Residues in contact with SER 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PRO* 4.6 5.6 - - - -
189C VAL* 4.3 7.8 - - - +
190C ASN* 2.8 31.0 + - - -
226D LEU 2.9 18.0 + - - -
227D ALA* 3.8 7.0 - - - -
229D VAL* 1.3 81.1 - - - +
231D ALA* 1.3 58.8 + - - +
232D VAL 3.4 0.2 + - - -
258D LYS* 2.9 36.1 + - - +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A THR* 3.9 15.4 - - - +
37A LEU* 5.8 1.2 - - - +
227D ALA 2.8 21.5 + - - +
228D ASN 3.8 2.7 - - - +
230D SER* 1.3 74.6 - - - +
232D VAL* 1.3 71.4 + - - +
233D ASN* 4.1 14.1 - - + +
258D LYS* 5.3 1.6 - - - +
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A SER* 3.7 27.3 + - - +
35A THR* 4.4 8.7 - - + +
186C PRO* 4.2 1.8 - - + -
201D TRP* 3.9 17.0 - - + -
217D PHE* 3.8 6.5 - - - -
228D ASN 2.7 7.0 + - - -
229D VAL 3.0 13.6 + - - +
230D SER 4.1 3.6 - - - +
231D ALA* 1.3 81.8 - - - +
233D ASN* 1.3 57.3 + - - +
234D TYR* 3.4 24.3 + - + +
256D LEU 3.5 24.7 - - - +
258D LYS* 3.8 24.9 - - + -
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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