Contacts of the strand formed by residues 274 - 281 (chain A) in PDB entry 1PT6
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 ILE 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ARG* 3.8 36.8 - - + +
234A PHE* 4.1 16.2 - - + -
246A LYS* 3.6 24.7 - - + +
248A MET* 3.9 26.9 - - + +
269A CYS* 3.1 27.3 + - + +
270A GLU* 5.2 0.2 - - - +
272A GLU* 3.8 14.6 - - + +
273A ASN* 1.3 79.2 - - - +
275A GLN* 1.3 69.7 + - - +
276A ARG* 2.9 31.1 + - + +
304A SER* 4.1 0.2 + - - -
260B HIS* 5.5 1.1 - - - -
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 2.7 44.8 + - - +
246A LYS 3.1 12.2 + - - +
247A VAL* 3.3 12.9 - - + +
248A MET 2.8 32.1 + - - +
273A ASN 4.0 1.4 - - - -
274A ILE* 1.3 72.3 - - - +
276A ARG* 1.3 52.5 + - - +
277A PHE* 3.6 21.3 - - + -
304A SER* 3.6 4.5 - - - -
309A LYS* 3.9 9.7 + - - -
310A HIS* 3.1 34.5 + - + +
330A ARG 4.8 1.2 - - - +
331A ILE 4.8 3.8 + - - -
260B HIS* 3.6 35.3 + - + +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 5.2 0.2 - - - -
248A MET* 3.3 19.5 - - + +
250A ILE* 4.3 15.0 - - + -
266A ILE* 3.6 33.0 - - - +
269A CYS* 3.6 31.2 - - - +
270A GLU* 3.0 34.1 + - - +
274A ILE* 2.9 30.6 + - + +
275A GLN* 1.3 73.3 - - - +
277A PHE* 1.3 61.9 + - - +
302A ILE 2.7 30.8 + - - +
303A ALA* 3.6 13.7 + - - -
304A SER* 2.9 41.0 + - - +
310A HIS* 3.3 12.0 - - - +
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Residues in contact with PHE 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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247A VAL* 3.7 25.4 - - + -
248A MET 2.8 9.7 + - - +
249A VAL* 3.3 10.0 - - + -
250A ILE* 2.8 28.8 + - - +
275A GLN* 3.6 28.9 - - - -
276A ARG* 1.3 76.9 - - - +
278A SER* 1.3 61.0 + - - +
279A ILE* 5.6 0.7 - - + -
309A LYS* 3.8 11.2 - - - -
310A HIS* 3.2 32.8 - + - +
312A PHE* 4.2 4.9 - + + -
327A LEU* 4.0 23.6 - - + -
330A ARG* 3.7 38.4 - - + -
331A ILE* 3.7 21.8 - - + -
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.3 9.6 - - - -
276A ARG 4.1 0.4 + - - -
277A PHE* 1.3 74.1 - - - +
279A ILE* 1.3 64.7 + - - +
280A ALA 4.2 0.4 - - - -
299A ILE* 2.6 36.9 + - - -
302A ILE* 4.1 12.3 - - - -
303A ALA* 3.3 20.5 - - - +
310A HIS 2.9 7.4 + - - +
311A PHE* 3.4 8.3 - - - -
312A PHE* 2.9 24.8 + - - +
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Residues in contact with ILE 279 (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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164A PHE* 3.9 10.3 - - + -
249A VAL* 3.7 29.4 - - + -
250A ILE 2.7 9.9 + - - +
251A VAL* 3.6 19.3 - - + +
252A THR* 3.0 31.4 + - - +
277A PHE* 5.2 0.9 - - + -
278A SER* 1.3 81.3 - - - +
280A ALA* 1.3 61.1 + - - +
281A ILE* 4.5 1.8 - - + -
299A ILE* 3.9 2.5 - - - -
312A PHE* 3.3 18.8 - - + +
314A VAL* 3.7 29.4 - - + -
320A LEU* 3.8 16.6 - - + -
323A ILE* 3.9 15.9 - - + -
327A LEU* 4.1 7.6 - - + -
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Residues in contact with ALA 280 (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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252A THR 3.5 4.9 - - - -
279A ILE* 1.3 71.4 - - - +
281A ILE* 1.3 61.0 + - - +
282A LEU* 3.8 12.1 - - + +
295A PHE* 3.9 9.0 - - + -
296A VAL* 4.9 3.6 - - + -
299A ILE* 3.7 22.5 - - + +
311A PHE* 3.7 26.7 - - + -
312A PHE 2.9 5.9 + - - -
314A VAL* 2.9 29.1 + - - +
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Residues in contact with ILE 281 (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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155A ILE* 5.4 7.2 - - + -
161A VAL* 5.4 4.3 - - + -
251A VAL* 3.8 18.2 - - + -
252A THR* 2.8 19.8 + - - +
253A ASP* 3.3 32.4 - - + +
279A ILE* 4.5 3.6 - - + -
280A ALA* 1.3 73.9 - - - +
282A LEU* 1.3 63.9 + - - +
283A GLY 3.8 10.3 - - - +
284A SER 4.8 0.5 + - - -
295A PHE* 3.3 6.3 - - - -
314A VAL* 3.4 5.6 - - + +
316A ASP 4.0 4.5 - - - -
317A GLU* 3.9 38.4 - - + +
320A LEU* 3.7 42.8 - - + -
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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