Contacts of the strand formed by residues 226 - 233 (chain D) in PDB entry 1ZQ1
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 ILE 226 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.8 5.6 - - + -
22D HIS 3.7 3.6 - - - +
23D ARG* 3.0 50.7 - - - +
213D LEU* 5.9 0.7 - - + -
220D LYS 4.9 0.4 - - - +
221D ARG* 5.5 0.7 - - - -
222D GLY 4.3 13.9 - - - +
223D LEU 4.3 3.3 + - - +
225D THR* 1.3 83.4 - - - +
227D ARG* 1.3 64.5 + - - +
228D GLN* 3.9 26.0 + - + +
245D VAL 5.6 1.6 - - - +
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Residues in contact with ARG 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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20D GLU 3.8 0.8 - - - +
21D ILE* 3.1 6.4 - - - +
22D HIS* 2.6 68.3 + - + +
24D GLN* 3.8 11.3 - - - +
164D ASP* 2.6 30.9 + - - -
182D ARG* 3.4 33.1 - - - +
187D LEU* 3.4 18.4 - - - +
224D GLY 4.1 17.8 + - - -
225D THR* 4.2 7.0 + - - +
226D ILE* 1.3 75.7 - - - +
228D GLN* 1.3 60.4 + - - +
229D ASP* 4.3 6.5 - - - +
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Residues in contact with GLN 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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19D LEU* 5.2 5.5 - - + +
20D GLU 3.4 4.0 - - - -
21D ILE* 3.8 31.8 - - + +
206D ALA* 4.0 19.5 - - - +
226D ILE* 3.9 20.2 + - + +
227D ARG* 1.3 78.4 - - - +
229D ASP* 1.3 70.5 + - - +
244D GLY* 4.1 1.5 + - - -
245D VAL* 3.4 36.7 + - + +
246D GLN 4.5 13.7 + - - -
247D GLU 5.4 0.4 - - - -
248D LEU* 4.5 17.3 - - - +
251D ILE* 4.1 9.9 - - + +
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Residues in contact with ASP 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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19D LEU* 3.2 11.2 - - - +
20D GLU* 2.8 50.4 + - + +
22D HIS* 4.8 12.8 - - - -
227D ARG* 5.1 4.2 - - - +
228D GLN* 1.3 79.3 + - - +
230D LEU* 1.3 65.3 - - - +
241D GLU* 6.5 0.4 - - + -
242D ILE 3.7 6.3 - - - +
243D LYS* 3.2 37.2 + - + +
244D GLY* 3.0 28.2 + - - -
245D VAL* 4.8 0.2 - - - -
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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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17D VAL* 3.9 16.2 - - + -
18D GLY 3.6 9.9 - - - +
19D LEU* 3.2 30.1 - - + -
202D ALA* 4.8 1.8 - - + -
228D GLN 6.0 0.2 - - - -
229D ASP* 1.3 76.3 - - - +
231D ASN* 1.3 56.1 + - - +
232D VAL* 4.2 4.0 - - + -
241D GLU* 3.5 3.0 - - - +
242D ILE* 2.5 53.2 + - + +
245D VAL* 4.1 18.6 - - + -
251D ILE* 4.3 20.4 - - + -
254D ILE* 4.2 15.5 - - + -
255D ILE* 3.6 29.8 - - + -
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Residues in contact with ASN 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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16D LYS 3.6 5.0 - - - +
17D VAL* 3.6 1.2 - - - -
18D GLY* 2.8 43.5 + - - -
20D GLU* 5.6 7.2 - - - +
194D PRO* 4.2 8.7 - - - +
230D LEU* 1.3 75.3 - - - +
232D VAL* 1.3 61.1 + - - +
239D ARG* 2.7 44.8 - - + +
240D ILE 2.9 11.7 - - - +
241D GLU* 4.2 16.6 - - + -
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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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15D LEU* 3.9 26.2 - - + -
16D LYS 3.6 4.3 - - - +
17D VAL* 4.1 8.7 - - + -
230D LEU* 4.6 5.6 - - + -
231D ASN* 1.3 78.9 - - - +
233D SER* 1.3 64.6 + - - +
234D ILE* 5.6 0.9 - - + -
238D ALA 2.9 4.3 - - - +
239D ARG* 4.4 0.9 - - - -
240D ILE* 2.8 36.2 + - - +
242D ILE* 3.5 31.6 - - + -
255D ILE* 4.2 23.3 - - + +
258D GLU* 3.9 17.7 - - + -
259D VAL* 4.5 4.5 - - + -
262D GLN* 3.5 6.1 + - - +
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Residues in contact with SER 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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14D GLY 2.8 11.4 + - - +
15D LEU* 3.4 7.3 - - - +
16D LYS* 3.1 41.4 + - - +
232D VAL* 1.3 76.6 - - - +
234D ILE* 1.3 69.5 + - - +
238D ALA 3.5 23.3 - - - -
239D ARG* 3.9 14.7 + - - -
262D GLN* 3.9 3.6 - - - +
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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