Contacts of the strand formed by residues 225 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C GLY* 3.9 13.7 + - - -
197C SER 2.7 9.7 + - - +
198C ASN* 3.2 25.9 + - - +
199C VAL* 2.8 31.7 + - - +
219C LEU* 4.4 2.2 - - - -
223C ASN* 4.6 5.0 + - - +
224C ALA* 1.3 80.0 - - - +
226C VAL* 1.3 63.8 + - - +
227C ALA* 5.7 0.2 - - - -
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Residues in contact with VAL 226 (chain C).
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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199C VAL 3.7 2.9 - - - -
201C ILE* 4.2 5.2 - - + -
216C ILE* 4.2 29.2 - - + -
219C LEU* 3.9 21.8 - - + -
224C ALA 5.7 0.4 - - - +
225C ASN* 1.3 72.8 - - - +
227C ALA* 1.3 62.6 + - - +
228C GLY* 3.8 8.5 - - - +
229C ILE* 3.7 35.7 - - + -
244C ASP* 4.4 8.7 - - - +
245C GLU 5.8 0.2 - - - +
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Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 5.3 0.2 - - - -
129C ARG* 2.8 40.4 + - + +
131C ILE* 4.2 19.3 - - + -
198C ASN* 4.1 18.8 - - + +
199C VAL 2.7 30.0 + - - +
200C LEU* 4.7 0.7 - - - -
225C ASN* 3.4 2.9 + - - -
226C VAL* 1.3 73.3 - - - +
228C GLY* 1.3 57.4 + - - +
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Residues in contact with GLY 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 3.8 16.6 - - - -
129C ARG* 4.0 3.8 - - - -
199C VAL 3.6 2.9 + - - +
200C LEU* 3.5 11.7 - - - +
201C ILE 2.9 23.0 + - - -
226C VAL* 3.3 5.6 + - - +
227C ALA* 1.3 81.6 - - - +
229C ILE* 1.3 69.1 + - - +
245C GLU* 5.5 3.4 - - - -
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Residues in contact with ILE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 3.5 13.4 - - - -
201C ILE* 3.3 26.2 - - + +
212C ILE* 4.2 26.2 - - + -
216C ILE* 4.0 23.6 - - + -
226C VAL* 3.7 21.5 - - + -
228C GLY* 1.3 80.2 - - - +
230C GLY* 1.3 60.9 + - - +
231C VAL* 4.5 3.6 - - + -
243C VAL* 4.8 1.3 - - + -
244C ASP* 4.0 10.3 - - - +
245C GLU* 3.4 21.8 + - - +
246C TYR* 3.4 18.9 - - + +
247C MET 2.8 25.1 + - - -
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Residues in contact with GLY 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PHE* 3.7 20.2 - - - -
126C PHE* 4.3 6.2 - - - -
200C LEU* 4.4 0.2 - - - +
201C ILE 2.8 9.5 + - - +
202C ILE* 3.3 13.9 - - - +
203C ASP 3.0 23.9 + - - +
229C ILE* 1.3 75.7 - - - +
231C VAL* 1.3 65.1 + - - +
247C MET 3.3 6.5 - - - -
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PHE* 3.7 8.0 - - - -
203C ASP* 3.1 13.9 - - + +
206C MET* 4.4 16.4 - - + +
212C ILE* 3.6 31.0 - - + -
229C ILE* 4.5 7.4 - - + -
230C GLY* 1.3 81.7 - - - +
232C LEU* 1.3 61.7 + - - +
233C VAL 4.1 19.3 - - - +
234C GLU* 4.2 6.7 - - + -
246C TYR* 4.4 2.9 - - + -
247C MET 2.8 8.9 + - - +
248C SER* 3.3 25.6 - - - -
249C LEU 3.1 17.2 + - - -
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Residues in contact with LEU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 3.7 26.9 - - + -
91C LEU* 5.5 0.9 - - + -
105C LEU* 4.5 11.0 - - + -
108C ILE* 4.5 15.5 - - + -
109C LEU* 4.2 24.5 - - + -
118C VAL* 4.1 15.0 - - + -
122C PHE* 4.1 3.6 - - - -
144C LEU* 3.9 15.3 - - + -
203C ASP 3.1 7.9 + - - -
204C ASP* 3.2 10.8 - - - +
231C VAL* 1.3 73.0 - - - +
233C VAL* 1.3 72.1 + - + +
249C LEU* 3.4 27.3 - - + +
250C LEU* 2.9 30.9 + - + +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 4.2 19.3 - - + -
103C VAL* 5.2 5.2 - - + -
105C LEU* 4.2 18.2 - - + -
204C ASP 2.9 11.7 + - - +
205C PHE* 3.2 21.8 - - + -
206C MET 2.9 24.6 + - - -
231C VAL* 4.1 5.1 - - - +
232C LEU* 1.3 92.6 - - + +
234C GLU* 1.3 62.3 + - - +
250C LEU* 3.3 15.9 - - + +
251C THR 4.7 0.2 - - - -
252C LEU* 3.8 30.7 - - + +
264C ILE* 6.1 3.1 - - + -
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C MET* 3.6 24.1 - - + +
231C VAL* 4.2 1.7 - - + +
233C VAL* 1.3 76.4 - - - +
235C ALA* 1.3 67.7 + - - +
236C GLU* 5.6 0.9 - - - -
238C VAL* 4.6 3.5 - - - +
246C TYR* 2.6 31.7 + - - -
248C SER* 2.6 28.6 + - - +
250C LEU 2.9 13.9 + - - +
251C THR* 3.3 24.7 + - + +
252C LEU 2.8 26.1 + - - -
267C GLY 4.9 0.2 - - - -
268C ASN* 4.5 7.4 + - - +
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Residues in contact with ALA 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLY 5.7 0.2 - - - +
205C PHE* 4.1 15.4 - - + -
206C MET 2.9 17.6 + - - +
207C LYS* 3.7 26.2 - - + +
233C VAL 4.2 0.4 + - - -
234C GLU* 1.3 76.4 - - - +
236C GLU* 1.3 71.4 + - - +
238C VAL* 3.2 21.8 + - - +
252C LEU* 3.6 13.5 - - + +
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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