Contacts of the helix formed by residues 277 - 282 (chain A) in PDB entry 1JQP
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 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP* 3.4 33.0 - - + -
63A ILE* 4.6 16.2 - - + -
64A TYR* 3.4 51.4 - + + -
66A GLN* 3.3 31.6 - - + -
80A PHE* 5.8 1.8 - + - -
234A TYR* 3.9 5.1 - - - +
269A TYR 5.3 1.6 + - - -
270A ALA* 5.2 0.8 - - - +
271A GLN* 5.6 0.7 - - - -
276A GLY* 1.3 81.0 - - - -
278A PRO* 1.3 75.9 - - + +
279A TYR* 3.2 4.9 - - + +
280A LEU* 2.9 26.2 + - + +
281A ILE* 3.2 13.7 + - - +
322A TYR* 5.3 1.6 - - - +
378A THR* 4.8 6.1 - - - -
428A ILE* 5.3 7.4 - - + -
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Residues in contact with PRO 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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234A TYR* 4.1 16.4 - - + +
237A ALA* 4.6 1.1 - - + -
238A SER* 3.1 22.6 - - - +
276A GLY 4.3 0.9 - - - +
277A PHE* 1.3 88.5 - - + +
279A TYR* 1.3 64.1 + - - +
281A ILE 2.8 0.9 + - - -
282A ALA* 2.8 25.4 + - + +
283A GLY 3.2 3.1 + - - -
346A ALA* 3.6 31.9 - - + -
347A VAL 5.6 1.8 - - - +
348A ALA* 6.1 3.4 - - + -
381A ALA* 4.3 18.2 - - + -
430A MET* 3.7 13.0 - - + -
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Residues in contact with TYR 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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59A TYR* 3.3 18.7 + - - -
61A THR* 3.5 10.3 - - + +
63A ILE* 4.0 32.5 - - + -
69A GLU* 2.6 35.1 + - + -
277A PHE* 3.2 2.8 + - + +
278A PRO* 1.3 77.8 - - - +
280A LEU* 1.3 63.2 + - + +
283A GLY* 3.3 6.1 - - - -
284A LYS* 3.0 20.3 + - + -
320A TYR* 3.8 25.0 + + - -
321A TYR* 4.1 15.5 - - - -
322A TYR* 3.3 51.5 - + + +
430A MET* 3.5 22.9 - - + +
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Residues in contact with LEU 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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63A ILE* 4.0 29.2 - - + -
78A PHE* 3.6 44.4 - - + -
80A PHE* 3.9 12.1 - - + -
269A TYR* 3.5 33.3 - - + +
277A PHE* 2.9 18.3 + - + +
279A TYR* 1.3 81.0 - - + +
281A ILE* 1.3 62.1 + - + +
284A LYS* 3.8 26.2 - - + -
285A TYR* 2.7 28.3 + - - +
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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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234A TYR* 3.8 22.9 - - + +
235A SER* 5.0 2.0 - - - -
238A SER* 3.5 23.6 - - - +
239A LEU* 5.1 4.9 - - + -
263A VAL* 3.8 37.9 - - + -
267A SER* 3.4 25.8 - - - +
269A TYR* 4.4 2.9 - - + -
270A ALA* 3.8 14.1 - - + -
277A PHE 3.2 10.5 + - - +
278A PRO 2.8 3.8 + - - -
280A LEU* 1.3 84.7 - - + +
282A ALA* 1.3 67.1 + - - +
283A GLY 3.0 0.7 - - - -
285A TYR* 3.6 8.3 - - + +
286A ALA* 2.9 26.2 + - - +
291A VAL* 5.0 1.5 - - + +
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Residues in contact with ALA 282 (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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238A SER* 3.3 36.8 + - - +
239A LEU* 6.1 0.4 - - - -
241A MET* 3.7 25.6 - - + -
242A LEU* 4.0 9.8 - - + +
278A PRO* 2.8 11.2 + - + +
281A ILE* 1.3 76.3 - - - +
283A GLY* 1.3 56.1 + - - +
286A ALA* 3.3 6.1 - - - +
317A SER* 2.8 26.2 + - - -
430A MET* 4.3 2.7 - - - -
432A ALA* 3.4 7.6 - - + +
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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