Contacts of the helix formed by residues 222 - 234 (chain D) in PDB entry 5ZRV
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 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D VAL 3.7 17.5 - - - -
215D SER* 4.1 1.8 - - - +
221D GLU* 1.3 76.2 - - - +
223D MET* 1.3 66.8 + - - +
224D GLY 3.2 3.5 + - - +
225D HIS* 3.8 8.4 + - - +
226D SER* 4.0 6.4 + - - -
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Residues in contact with MET 223 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D VAL 4.2 5.9 + - - -
222D THR* 1.3 71.7 - - - +
224D GLY* 1.3 57.3 + - - +
226D SER* 3.5 2.6 + - - -
227D ALA* 3.0 23.6 + - - -
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Residues in contact with GLY 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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222D THR 3.2 1.4 - - - -
223D MET* 1.3 76.7 - - - +
225D HIS* 1.3 60.5 + - - +
227D ALA* 4.2 2.0 - - - -
228D ASP* 2.9 26.0 + - - -
296D PHE* 5.5 13.2 - - - -
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Residues in contact with HIS 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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222D THR* 3.8 8.3 + - - +
223D MET 3.4 0.6 - - - -
224D GLY* 1.3 75.8 - - - +
226D SER* 1.3 56.7 + - - +
228D ASP* 4.0 0.3 - - - -
229D ARG* 3.0 25.8 + - - -
296D PHE 5.4 5.5 + - - -
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Residues in contact with SER 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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222D THR 4.0 6.8 + - - -
223D MET 3.5 5.4 + - - -
224D GLY 3.3 0.4 - - - -
225D HIS* 1.3 73.9 - - - +
227D ALA* 1.3 62.5 + - - +
229D ARG* 4.5 1.3 - - - +
230D LEU* 3.0 21.0 + - - -
351D LEU* 6.5 1.1 - - - +
352D LEU 5.7 4.6 + - - -
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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 MET 3.0 16.6 + - - -
224D GLY* 3.2 5.6 + - - -
225D HIS 3.2 0.6 - - - -
226D SER* 1.3 78.5 - - - +
228D ASP* 1.3 56.5 + - - +
230D LEU* 3.4 0.9 + - - -
231D ALA* 2.9 23.7 + - - -
385D GLN* 5.9 2.4 + - - -
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Residues in contact with ASP 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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224D GLY 2.9 17.5 + - - -
225D HIS 4.2 0.4 - - - -
227D ALA* 1.3 70.6 - - - +
229D ARG* 1.3 60.3 + - - +
231D ALA* 3.6 3.8 - - - +
232D ALA* 2.8 25.8 + - - -
302D THR 5.9 5.2 - - - +
303D VAL* 5.8 7.6 - - - +
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Residues in contact with ARG 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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225C LEU* 6.0 4.3 - - - +
225D HIS 3.0 17.6 + - - -
226D SER* 3.8 2.0 - - - +
227D ALA 3.2 0.2 - - - -
228D ASP* 1.3 77.3 - - - +
230D LEU* 1.3 57.6 + - - +
232D ALA 3.8 0.3 - - - -
233D ALA* 2.9 27.5 + - - -
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Residues in contact with LEU 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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226D SER 3.0 15.4 + - - -
227D ALA 3.8 1.1 - - - -
229D ARG* 1.3 73.6 - - - +
231D ALA* 1.3 61.7 + - - +
233D ALA* 3.6 6.1 + - - +
234D PHE* 3.7 8.5 + - - -
385D GLN* 6.3 1.3 - - - -
388D ALA* 5.5 6.1 - - - -
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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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227D ALA 2.9 16.4 + - - -
228D ASP* 3.8 3.1 - - - +
229D ARG 3.1 0.2 - - - -
230D LEU* 1.3 80.3 - - - +
232D ALA* 1.3 61.5 + - - +
233D ALA 3.4 0.3 + - - -
234D PHE* 3.6 7.6 + - - -
236D VAL* 3.8 19.0 + - - -
384D GLY* 5.3 14.1 - - - -
385D GLN* 5.5 2.9 - - - +
388D ALA* 6.2 1.8 - - - +
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Residues in contact with ALA 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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228D ASP* 2.8 21.1 + - - +
229D ARG 3.9 0.4 - - - -
231D ALA* 1.3 72.0 - - - +
233D ALA* 1.3 62.6 + - - +
234D PHE 3.2 0.7 + - - -
235D ALA* 3.4 11.9 + - - +
236D VAL 4.7 6.7 + - - +
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Residues in contact with ALA 233 (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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227C PRO 4.6 12.8 - - - -
228C GLY* 4.1 16.9 - - - -
229C LEU 4.5 2.6 + - - -
229D ARG 2.9 16.7 + - - -
230D LEU* 3.6 3.8 + - - +
231D ALA 3.2 0.8 - - - -
232D ALA* 1.3 78.8 - - - +
234D PHE* 1.3 56.1 + - - +
235D ALA 3.5 0.9 + - - -
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Residues in contact with PHE 234 (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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228C GLY* 5.9 0.2 - - - -
229C LEU 5.6 3.4 - - - +
230D LEU 3.7 8.0 + - - -
231D ALA 3.6 6.3 + - - -
232D ALA 3.2 0.8 - - - -
233D ALA* 1.3 77.9 - - - +
235D ALA* 1.3 62.1 + - - +
236D VAL* 3.5 2.3 - - - -
388D ALA* 5.7 8.6 - - - +
391D LYS* 5.7 5.7 - - - -
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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