Contacts of the strand formed by residues 270 - 278 (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 VAL 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A VAL* 4.6 2.2 - - + -
228A ALA 3.6 9.6 - - - +
229A LYS* 4.0 17.7 - - + -
269A GLU* 1.3 80.6 + - - +
271A VAL* 1.3 70.9 + - - +
298A THR* 3.9 8.7 - - - +
299A PHE* 3.6 29.7 + - + +
305A LEU* 5.9 0.4 - - + -
306A ALA* 3.9 18.5 - - + +
309A LEU* 3.7 40.4 - - + -
310A ARG* 3.7 28.5 - - + +
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Residues in contact with VAL 271 (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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226A VAL 4.0 0.2 - - - +
227A VAL* 3.5 4.9 - - - +
228A ALA 3.0 39.4 + - - +
230A ILE* 3.7 33.7 - - + -
243A LEU* 5.9 0.4 - - + -
245A LEU* 4.9 4.3 - - + -
265A VAL* 5.7 1.8 - - + -
269A GLU* 3.9 2.0 + - + +
270A VAL* 1.3 81.5 - - - +
272A ARG* 1.3 59.3 + - - +
273A ILE* 4.1 15.6 + - + +
296A ILE* 3.7 27.6 - - + -
297A ILE 3.2 9.6 - - - +
298A THR* 3.6 22.4 - - + -
299A PHE* 3.9 6.1 - - - -
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Residues in contact with ARG 272 (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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59A ILE 4.6 3.8 - - - -
60A ASP* 3.0 43.3 + - - -
77A LYS* 4.7 0.6 - - - +
116A ALA* 5.9 1.1 - - - -
206A ILE* 3.8 38.1 - - - +
210A MET* 3.1 28.7 + - - +
211A TYR* 4.4 3.0 - - - +
225A ASP* 3.1 32.3 + - - +
226A VAL 3.3 7.9 - - - +
227A VAL* 4.3 4.7 - - + +
271A VAL* 1.3 75.6 - - - +
273A ILE* 1.3 65.8 + - - +
274A ARG* 3.8 7.2 + - - +
295A ASN 3.6 1.4 - - - +
296A ILE* 3.5 1.2 - - - -
297A ILE* 2.6 51.6 + - + +
299A PHE* 3.8 17.0 - - + -
2D G 4.1 3.2 + - - -
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Residues in contact with ILE 273 (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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225A ASP* 3.4 8.1 - - - +
226A VAL* 2.7 51.2 + - + +
228A ALA* 6.2 0.2 - - + -
243A LEU* 5.6 0.4 - - + -
245A LEU* 3.5 37.7 - - + -
255A THR* 4.6 10.5 - - + -
271A VAL* 4.2 12.8 - - + +
272A ARG* 1.3 77.7 - - - +
274A ARG* 1.3 63.6 + - - +
276A ALA* 4.2 12.6 - - + -
288A LEU* 4.7 4.7 - - + -
290A LEU* 3.8 25.8 - - + -
295A ASN 3.3 7.9 - - - +
296A ILE* 4.2 21.1 - - + -
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Residues in contact with ARG 274 (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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60A ASP* 2.9 43.8 + - - +
61A ALA 4.1 12.7 - - - +
62A THR* 3.2 38.4 - - + +
75A SER* 4.6 3.8 + - - -
76A LEU* 5.7 0.4 - - - +
77A LYS* 3.5 8.5 - - - +
225A ASP* 3.6 13.5 - - - -
272A ARG* 3.8 6.8 + - - +
273A ILE* 1.3 70.5 - - - +
275A SER* 1.3 72.4 + - - +
293A TYR 5.0 1.1 - - - +
294A SER* 3.2 2.1 - - - -
295A ASN* 2.8 41.4 + - + +
297A ILE* 5.1 2.9 - - + -
2D G 2.8 55.6 + - - +
3D G 2.9 24.0 + - - +
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Residues in contact with SER 275 (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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223A ASP* 2.9 22.7 + - - +
224A PHE 3.4 5.9 + - - -
225A ASP* 2.9 15.5 + - - -
273A ILE 3.6 1.0 + - - -
274A ARG* 1.3 75.9 - - - +
276A ALA* 1.3 62.3 + - - +
289A ILE 4.3 0.5 - - - +
290A LEU* 3.8 3.6 - - - +
291A SER* 4.9 1.9 + - - -
293A TYR* 3.4 21.8 + - - -
294A SER* 2.7 36.0 + - - -
3D G 3.3 21.8 - - - -
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Residues in contact with ALA 276 (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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223A ASP* 3.3 3.2 - - - -
224A PHE* 2.8 53.7 + - + +
226A VAL* 4.7 2.9 - - + -
273A ILE* 4.2 10.1 - - + -
275A SER* 1.3 76.1 + - - +
277A THR* 1.3 63.0 + - - +
288A LEU* 4.5 16.6 - - + -
289A ILE 3.3 7.0 - - - +
290A LEU* 3.8 17.5 - - + -
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Residues in contact with THR 277 (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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222A GLY* 4.2 4.9 - - - +
223A ASP* 3.7 26.7 - - + +
224A PHE* 4.0 7.6 - - - -
276A ALA* 1.3 79.1 - - - +
278A TYR* 1.3 67.6 + - - +
288A LEU* 3.4 5.4 - - - -
289A ILE* 2.8 60.4 + - - +
291A SER* 6.1 1.3 - - - +
4D G 6.2 0.2 - - - +
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Residues in contact with TYR 278 (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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217A ALA* 3.9 18.8 - - + +
218A GLN* 3.6 54.0 + - + -
220A GLN 6.1 0.2 - - - +
222A GLY 5.3 0.8 + - - -
224A PHE* 3.7 10.0 - - + -
253A PHE* 3.6 37.2 - + - -
277A THR* 1.3 75.1 - - - +
279A ASP* 1.3 80.5 + - - +
280A GLU* 3.3 24.7 + - + +
282A SER 5.2 4.3 + - - -
286A LYS* 2.8 34.2 + - + +
287A VAL 4.1 2.5 - - - -
288A LEU* 4.7 1.8 - - - -
289A ILE* 4.9 2.0 - - - +
133B ARG* 5.2 2.8 + - - -
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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