Contacts of the strand formed by residues 224 - 235 (chain A) in PDB entry 1PH3
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 PHE 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A THR* 3.6 24.5 - - - +
213A ALA 6.0 0.2 - - - -
214A LEU* 5.0 0.9 - - + -
217A ALA* 3.5 38.1 - - + -
220A GLN* 3.5 31.0 - - + +
222A GLY 3.7 3.1 - - - -
223A ASP* 1.3 77.5 - - - +
225A ASP* 1.3 79.1 + - - +
226A VAL* 3.6 20.6 - - + -
275A SER* 3.4 0.2 - - - -
276A ALA* 2.8 47.3 + - + +
277A THR* 4.0 0.7 - - - -
278A TYR* 3.7 18.2 - - + -
288A LEU* 3.8 21.1 - - + -
2D G 3.9 5.6 - - - +
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Residues in contact with ASP 225 (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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210A MET 3.4 23.2 - - - +
211A TYR* 3.8 3.5 - - - +
212A THR* 2.9 24.3 + - - +
224A PHE* 1.3 77.8 - - - +
226A VAL* 1.3 70.4 + - - +
272A ARG* 3.1 24.9 + - - +
273A ILE 3.4 8.1 - - - +
274A ARG* 3.6 1.4 - - - -
275A SER 2.9 17.2 + - - -
2D G 2.6 48.8 + - - +
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Residues in contact with VAL 226 (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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211A TYR* 4.1 2.5 - - - -
212A THR 4.5 5.4 - - - +
214A LEU* 3.7 31.6 - - + -
224A PHE* 3.6 24.2 - - + -
225A ASP* 1.3 81.6 - - - +
227A VAL* 1.3 78.6 + - - +
228A ALA* 4.1 13.0 - - + +
245A LEU* 5.3 0.9 - - + -
247A ASP* 5.2 0.4 - - + -
272A ARG* 3.3 5.5 - - - +
273A ILE* 2.7 55.5 + - + +
276A ALA* 4.7 5.8 - - + -
288A LEU* 4.2 11.2 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ILE* 3.8 18.6 - - + -
211A TYR* 3.5 48.3 - - + -
212A THR 5.1 0.4 + - - -
226A VAL* 1.3 84.4 - - - +
228A ALA* 1.3 59.7 + - - +
247A ASP* 3.3 17.5 + - - +
248A ALA 4.7 0.9 + - - -
270A VAL* 4.6 5.6 - - + -
271A VAL 3.5 8.3 - - - +
272A ARG* 4.3 11.0 - - + -
299A PHE* 4.8 3.8 - - + -
305A LEU* 4.4 13.0 - - + -
309A LEU* 3.7 29.3 - - + +
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Residues in contact with ALA 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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214A LEU* 4.2 1.3 - - + -
226A VAL* 4.1 14.8 - - + +
227A VAL* 1.3 75.6 - - - +
229A LYS* 1.3 60.1 + - - +
245A LEU* 4.1 14.1 - - + -
246A LYS 3.3 29.8 - - - +
247A ASP* 3.6 9.4 - - + +
270A VAL* 3.6 7.4 - - - +
271A VAL* 3.0 37.2 + - + +
273A ILE* 6.2 0.6 - - + +
309A LEU* 5.6 0.2 - - - -
313A ILE* 4.8 2.2 - - - -
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Residues in contact with LYS 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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228A ALA* 1.3 74.5 - - - +
230A ILE* 1.3 66.5 + - - +
231A LEU* 3.3 25.6 + - + +
245A LEU* 3.5 4.9 - - - -
246A LYS 3.0 34.1 + - - +
268A GLY* 3.4 29.8 - - - +
269A GLU 3.5 9.9 - - - +
270A VAL* 4.0 9.6 - - + -
309A LEU 4.3 2.5 - - - +
310A ARG* 2.6 33.4 + - - +
313A ILE* 3.0 38.9 + - + +
314A GLN* 4.5 5.5 + - - +
315A ASP 5.5 1.2 - - - +
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Residues in contact with ILE 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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229A LYS* 1.3 72.3 - - - +
231A LEU* 1.3 58.3 + - - +
232A GLN 3.8 12.3 - - - +
233A VAL* 3.6 27.6 - - + -
243A LEU* 4.4 10.3 - - + -
244A LYS 3.8 4.3 - - - +
245A LEU* 4.1 14.8 - - + -
265A VAL* 4.1 18.4 - - + -
266A ARG 3.6 33.0 - - - +
267A THR* 4.0 1.8 - - - -
268A GLY* 2.7 33.8 + - - -
269A GLU* 2.8 15.7 + - + +
271A VAL* 3.7 31.2 - - + -
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Residues in contact with LEU 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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229A LYS* 3.3 37.4 + - + +
230A ILE* 1.3 73.7 - - - +
232A GLN* 1.3 62.5 + - - +
244A LYS* 2.8 29.0 + - + +
245A LEU 5.0 0.7 - - - -
246A LYS* 3.6 40.6 - - + +
252A VAL* 4.7 1.8 - - + -
267A THR* 3.3 16.3 - - - +
268A GLY* 4.9 0.7 - - - +
313A ILE* 4.3 4.5 - - + -
315A ASP* 3.6 31.1 - - - +
316A ASP* 3.7 23.3 - - + +
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Residues in contact with GLN 232 (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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230A ILE* 3.4 4.9 - - - +
231A LEU* 1.3 82.2 - - - +
233A VAL* 1.3 76.3 + - - +
234A HIS* 4.2 15.6 - - + +
242A GLU* 3.6 0.9 - - - +
243A LEU* 3.4 5.5 - - - -
244A LYS* 2.9 55.6 + - + +
254A TYR* 4.7 6.4 - - - -
267A THR* 4.2 5.8 - - - -
320A GLU* 4.5 9.2 + - - +
332A ALA* 4.4 16.2 - - - +
334A VAL* 3.3 38.6 - - + +
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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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230A ILE* 3.6 20.6 - - + -
232A GLN* 1.3 81.9 - - - +
234A HIS* 1.3 57.5 + - - +
235A GLU 3.9 1.7 + - - -
241A ASN* 4.0 34.1 - - + +
242A GLU 3.8 2.5 - - - -
243A LEU* 4.3 9.9 - - + -
265A VAL* 4.4 17.7 - - + +
266A ARG* 4.3 3.1 - - - -
267A THR* 3.8 23.5 + - - +
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Residues in contact with HIS 234 (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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232A GLN* 3.9 15.9 - - + +
233A VAL* 1.3 73.5 - - - +
235A GLU* 1.3 74.9 + - - +
236A LEU* 2.9 25.1 + - + +
241A ASN* 4.4 2.0 - - - -
242A GLU* 2.7 60.8 + - + +
332A ALA* 3.8 17.2 - - + +
334A VAL* 5.6 5.4 - - + +
472A ASN* 4.9 1.0 + - - -
474A TYR* 3.4 55.4 + + - +
149B GLN* 5.4 0.4 + - - -
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Residues in contact with GLU 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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233A VAL 3.9 3.8 + - - -
234A HIS* 1.3 83.5 + - - +
236A LEU* 1.3 62.3 + - - +
237A ASP 3.5 9.3 - - - +
238A GLU* 4.9 0.5 - - - -
241A ASN* 3.6 12.2 + - - +
259A LYS* 2.5 39.6 + - - +
372A GLN* 5.5 4.3 + - - -
420A ALA* 3.5 29.0 - - + +
421A SER* 4.5 8.1 + - - -
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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