Contacts of the strand formed by residues 225 - 235 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A GLY* 4.0 14.5 + - - -
197A SER 2.9 6.3 + - - -
198A ASN* 3.3 26.6 + - - +
199A VAL* 2.8 33.4 + - - +
219A LEU* 4.6 1.1 - - - -
223A ASN* 4.4 7.3 + - - +
224A ALA* 1.3 78.6 - - - +
226A VAL* 1.3 63.1 + - - +
227A ALA* 3.2 0.6 + - - -
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Residues in contact with VAL 226 (chain A).
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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199A VAL 3.7 5.4 - - - +
201A ILE* 4.5 5.6 - - + -
216A ILE* 4.1 17.7 - - + -
219A LEU* 3.9 22.2 - - + -
220A ASP* 6.1 0.7 - - - +
224A ALA 5.3 1.3 - - - +
225A ASN* 1.3 72.4 - - - +
227A ALA* 1.3 59.9 + - - +
228A GLY* 3.8 10.1 - - - +
229A ILE* 3.7 29.6 - - + -
244A ASP* 3.6 35.5 - - - +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 4.6 0.8 - - - -
129A ARG* 2.7 42.5 + - + +
130A GLU 3.5 25.4 - - - +
131A ILE* 4.1 13.9 - - + -
198A ASN* 4.2 4.9 - - + +
199A VAL 2.8 25.2 + - - +
200A LEU* 4.5 0.7 - - - +
225A ASN* 3.2 4.3 + - - -
226A VAL* 1.3 72.4 - - - +
228A GLY* 1.3 50.8 + - - +
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Residues in contact with GLY 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 3.9 3.8 - - - -
129A ARG* 3.8 11.0 - - - -
199A VAL 3.5 3.4 + - - +
200A LEU* 3.5 15.8 - - - +
201A ILE 3.0 22.2 + - - -
226A VAL* 3.3 6.2 - - - +
227A ALA* 1.3 81.3 - - - +
229A ILE* 1.3 68.5 + - - +
245A GLU 5.3 2.2 - - - -
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PHE* 3.5 12.8 - - - -
201A ILE* 3.3 19.3 - - + +
212A ILE* 4.0 31.4 - - + -
216A ILE* 4.1 3.8 - - + -
226A VAL* 3.7 15.5 - - + -
228A GLY* 1.3 80.6 - - - +
230A GLY* 1.3 62.0 + - - +
231A VAL* 4.1 15.3 - - + -
242A LEU* 4.3 5.4 - - + -
244A ASP* 3.9 22.4 - - + -
245A GLU 3.7 18.2 + - - +
246A TYR* 3.4 20.3 - - + +
247A MET 2.7 26.9 + - - -
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Residues in contact with GLY 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.8 19.3 - - - -
126A PHE* 4.3 8.2 - - - -
201A ILE 2.9 9.9 + - - -
202A ILE* 3.3 15.5 - - - +
203A ASP 2.9 25.1 + - - +
229A ILE* 1.3 74.3 - - - +
231A VAL* 1.3 64.5 + - - +
247A MET* 3.5 5.2 - - - -
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.9 8.0 - - - -
203A ASP* 3.0 14.6 - - + +
206A MET* 3.9 27.1 - - + +
212A ILE* 3.8 29.2 - - + -
229A ILE* 4.1 9.2 - - + -
230A GLY* 1.3 79.8 - - - +
232A LEU* 1.3 62.8 + - - +
233A VAL 4.0 17.9 - - - +
234A GLU* 4.3 0.2 - - + -
246A TYR* 4.4 2.2 - - + -
247A MET 2.8 9.3 + - - +
248A SER* 3.3 37.6 - - - -
249A LEU* 3.3 3.3 + - - +
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Residues in contact with LEU 232 (chain A).
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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87A LEU* 3.6 22.2 - - + -
91A LEU* 6.1 0.7 - - + -
108A ILE* 4.7 15.7 - - + -
109A LEU* 4.0 24.7 - - + -
114A VAL* 5.3 2.0 - - + -
115A LEU* 6.5 0.2 - - + -
118A VAL* 3.9 16.6 - - + -
122A PHE* 4.1 3.3 - - - -
144A LEU* 4.2 21.1 - - + -
203A ASP 3.1 7.5 + - - -
204A ASP 3.5 8.7 - - - +
231A VAL* 1.3 72.1 - - - +
233A VAL* 1.3 72.2 + - + +
249A LEU* 3.4 32.3 + - + -
250A LEU* 3.0 25.4 + - + +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 4.6 18.2 - - + -
105A LEU* 4.4 16.4 - - + -
204A ASP 3.0 10.9 + - - +
205A PHE* 3.2 22.0 - - + -
206A MET 2.9 23.4 + - - -
231A VAL* 4.0 5.0 - - - +
232A LEU* 1.3 95.0 - - + +
234A GLU* 1.3 63.6 + - - +
250A LEU* 3.4 20.0 - - + +
252A LEU* 3.9 32.3 - - + +
264A ILE* 6.3 0.9 - - + -
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Residues in contact with GLU 234 (chain A).
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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205A PHE* 4.3 3.8 - - - -
206A MET* 3.5 22.9 - - + +
233A VAL* 1.3 75.2 - - - +
235A ALA* 1.3 59.8 + - - +
236A GLU* 5.9 1.8 - - - -
238A VAL* 3.7 15.1 - - + +
246A TYR* 2.5 31.4 + - - -
248A SER* 2.9 26.9 + - - +
250A LEU 2.9 16.3 + - - +
251A THR* 3.2 19.8 + - + +
252A LEU 2.7 31.2 + - - -
267A GLY* 4.8 0.9 - - - -
268A ASN* 4.8 3.6 + - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PHE* 4.0 13.7 - - + -
206A MET 2.9 14.3 + - - +
207A LYS* 3.6 44.8 - - + +
234A GLU* 1.3 87.4 - - - +
236A GLU* 1.3 65.5 + - - +
237A GLY 3.6 0.9 + - - -
238A VAL* 4.2 11.8 - - - +
252A LEU* 3.5 11.7 - - + +
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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