Contacts of the strand formed by residues 225 - 235 (chain D) in PDB entry 1P4A
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 ASN 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D GLY* 3.6 17.6 + - - -
197D SER 2.9 5.9 + - - -
198D ASN* 3.1 26.6 + - - +
199D VAL* 2.7 34.1 + - - +
219D LEU* 4.6 2.2 - - - -
223D ASN* 4.5 8.0 + - - +
224D ALA* 1.3 78.1 - - - +
226D VAL* 1.3 61.7 + - - +
227D ALA* 3.1 2.2 + - - +
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Residues in contact with VAL 226 (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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199D VAL 3.6 4.3 - - - +
201D ILE* 4.5 4.7 - - + -
216D ILE* 4.0 27.1 - - + -
219D LEU* 3.8 22.7 - - + -
224D ALA 4.2 1.1 + - - +
225D ASN* 1.3 70.3 - - - +
227D ALA* 1.3 61.5 + - - +
228D GLY* 3.7 10.5 - - - +
229D ILE* 3.7 33.9 - - + -
244D ASP* 4.1 17.5 - - + +
245D GLU 5.7 0.2 - - - +
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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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126D PHE* 5.4 0.4 - - - -
129D ARG* 2.9 34.1 + - + -
130D GLU 3.4 25.6 - - - +
131D ILE* 4.0 13.0 - - + -
198D ASN* 4.2 5.2 - - + +
199D VAL 2.8 25.5 + - - +
200D LEU* 4.8 0.7 - - - -
225D ASN* 3.1 3.5 + - - -
226D VAL* 1.3 74.2 - - - +
228D GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 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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126D PHE* 4.0 16.8 - - - -
129D ARG* 4.0 3.4 - - - -
199D VAL 3.6 1.2 + - - -
200D LEU* 3.4 11.8 - - - +
201D ILE 2.9 24.1 + - - -
226D VAL* 3.3 7.0 - - - +
227D ALA* 1.3 81.1 - - - +
229D ILE* 1.3 66.7 + - - +
245D GLU* 5.4 3.1 - - - -
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Residues in contact with ILE 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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126D PHE* 3.6 11.7 - - - -
201D ILE* 3.3 23.6 - - + +
212D ILE* 4.0 24.2 - - + -
216D ILE* 4.1 4.3 - - + -
226D VAL* 3.7 16.6 - - + -
228D GLY* 1.3 78.4 - - - +
230D GLY* 1.3 60.8 + - - +
231D VAL* 4.3 15.0 - - + -
243D VAL* 3.6 20.9 - - + +
244D ASP* 3.7 11.4 - - + -
245D GLU* 3.6 24.4 + - - +
246D TYR* 3.4 13.5 - - + +
247D MET 2.8 27.0 + - - -
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Residues in contact with GLY 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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122D PHE* 3.8 21.1 - - - -
126D PHE* 4.2 6.7 - - - -
200D LEU* 4.2 1.4 - - - +
201D ILE 2.7 13.9 + - - +
202D ILE* 3.2 12.6 - - - +
203D ASP 2.8 31.4 + - - +
229D ILE* 1.3 72.7 - - - +
231D VAL* 1.3 58.5 - - - +
247D MET* 3.7 4.3 - - - -
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Residues in contact with VAL 231 (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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122D PHE* 3.7 8.4 - - - -
203D ASP* 3.3 11.0 - - + +
204D ASP 4.4 0.2 - - - +
206D MET* 4.0 22.2 - - + +
212D ILE* 3.8 28.9 - - + -
229D ILE* 4.3 9.0 - - + -
230D GLY* 1.3 79.5 - - - +
232D LEU* 1.3 59.5 + - - +
233D VAL 3.2 32.8 - - - +
234D GLU* 4.1 7.2 - - + +
246D TYR* 4.8 3.1 - - + -
247D MET 2.9 12.5 + - - +
248D SER* 3.2 7.7 - - - -
249D LEU* 3.1 22.7 + - - +
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Residues in contact with LEU 232 (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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87D LEU* 3.8 27.6 - - + -
91D LEU* 5.6 1.6 - - + -
105D LEU* 5.1 5.8 - - + -
108D ILE* 4.6 15.5 - - + -
109D LEU* 3.9 28.0 - - + -
114D VAL* 6.2 0.2 - - + -
118D VAL* 4.1 14.6 - - + -
122D PHE* 4.0 3.8 - - + -
144D LEU* 4.1 13.9 - - + -
203D ASP 3.1 8.1 + - - -
204D ASP* 3.1 13.0 - - + +
231D VAL* 1.3 72.5 - - - +
233D VAL* 1.3 74.7 + - + +
249D LEU* 3.5 24.6 + - + +
250D LEU* 2.9 29.6 + - + +
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Residues in contact with VAL 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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91D LEU* 4.1 24.5 - - + -
103D VAL* 4.8 7.0 - - + -
105D LEU* 4.3 13.5 - - + -
204D ASP 2.9 11.0 + - - +
205D PHE* 3.2 29.9 - - + -
206D MET 2.9 25.1 + - - -
231D VAL* 3.2 5.5 - - - +
232D LEU* 1.3 92.6 - - + +
234D GLU* 1.3 63.4 + - - +
250D LEU* 3.5 13.9 - - + +
251D THR 5.1 0.2 - - - -
252D LEU* 3.9 21.3 - - + +
264D ILE* 6.1 1.8 - - + -
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Residues in contact with GLU 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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206D MET* 3.4 23.3 - - + +
231D VAL* 4.4 1.1 - - + -
233D VAL* 1.3 77.2 - - - +
235D ALA* 1.3 66.6 + - - +
236D GLU* 3.6 2.3 + - - -
238D VAL* 4.7 2.8 - - - +
240D GLU* 5.5 1.0 - - - +
246D TYR* 2.7 30.3 + - - -
248D SER* 2.6 29.6 + - - +
250D LEU 3.0 18.8 + - - +
251D THR* 3.3 19.4 + - + +
252D LEU 2.8 25.9 + - - -
267D GLY* 4.5 1.0 - - - -
268D ASN* 4.6 4.7 + - - +
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Residues in contact with ALA 235 (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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101D GLY 5.2 0.4 - - - +
205D PHE* 3.9 21.0 - - + -
206D MET 2.9 10.7 + - - +
207D LYS* 3.8 29.6 - - + +
234D GLU* 1.3 74.8 - - - +
236D GLU* 1.3 67.4 + - - +
238D VAL* 3.1 23.0 + - - +
252D LEU* 3.7 15.9 - - + +
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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