Contacts of the helix formed by residues 240 - 247 (chain B) in PDB entry 1QI9
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASP* 3.5 26.5 - - + -
63B LEU* 4.7 0.2 - - - -
238B VAL 3.9 3.0 + - - -
239B ASP* 1.3 71.7 + - - +
241B ASP* 1.3 71.8 + - - +
243B TRP* 3.2 36.9 + + - +
244B LEU* 2.9 39.7 + - + -
355B GLY 5.6 0.2 - - - -
358B HIS* 4.0 25.8 - + - +
359B LEU* 3.9 30.7 - - + -
395B GLU* 4.9 11.5 + - - +
397B THR* 4.3 7.4 - - + +
399B LEU* 3.9 11.8 - - + +
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Residues in contact with ASP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASP* 3.1 11.3 + - - +
240B PHE* 1.3 87.5 - - - +
242B GLU* 1.3 58.1 + - + +
244B LEU* 3.2 8.3 + - - +
245B ASN* 2.9 31.0 + - - +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 5.6 0.7 - - - -
237B MET* 4.4 20.0 + - + +
238B VAL 5.2 0.2 + - - -
239B ASP* 3.0 35.7 + - - +
240B PHE 3.2 0.2 - - - -
241B ASP* 1.3 76.7 - - + +
243B TRP* 1.3 63.0 + - - +
245B ASN* 3.4 9.3 + - - +
246B ILE* 3.1 28.5 + - + +
253B ALA* 4.0 28.0 - - + +
392B PRO* 6.1 0.7 - - - +
405B GLN* 4.6 4.0 - - - +
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Residues in contact with TRP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU 4.8 2.7 - - - -
64B GLY* 4.1 22.9 - - - -
237B MET* 3.9 32.2 - - + +
239B ASP 3.0 13.6 + - - +
240B PHE* 3.5 44.0 - + - +
242B GLU* 1.3 78.3 - - - +
244B LEU* 1.3 80.3 + - + +
246B ILE* 3.4 2.1 + - - +
247B GLN* 3.0 59.0 + - + +
351B GLU* 3.0 26.2 + - + -
352B ALA* 4.3 7.0 - - - -
355B GLY* 3.4 29.4 - - - -
359B LEU* 5.1 0.4 - - + -
399B LEU* 3.7 25.2 - - + +
400B LEU 6.1 0.2 - - - -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 4.4 1.3 - - + -
61B ASP 3.9 14.8 - - - +
62B ASP* 3.8 30.7 - - + +
64B GLY* 4.4 12.8 - - - +
240B PHE* 2.9 41.2 + - + +
241B ASP* 3.2 9.4 + - - +
243B TRP* 1.3 85.9 - - + +
245B ASN* 1.3 62.0 + - - +
247B GLN* 3.1 5.8 + - + +
248B ASN* 2.9 51.3 + - - +
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Residues in contact with ASN 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ASN* 3.8 12.1 + - - -
95B GLU* 4.7 1.4 - - - +
241B ASP 2.9 16.4 + - - +
242B GLU* 3.5 9.4 + - - +
244B LEU* 1.3 75.3 - - - +
246B ILE* 1.3 66.5 + - - +
248B ASN* 3.1 14.6 + - - +
250B GLY* 3.0 40.7 + - - -
251B PRO* 2.9 31.6 + - - +
252B PRO 5.1 0.6 - - - -
253B ALA* 5.3 2.0 - - - +
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Residues in contact with ILE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 3.4 39.3 - - - +
99B VAL* 5.3 2.2 - - + -
237B MET* 3.6 23.3 - - + -
242B GLU* 3.1 15.1 + - + +
243B TRP 3.6 7.2 - - - +
245B ASN* 1.3 75.6 - - - +
247B GLN* 1.3 63.1 + - - +
249B GLY* 3.0 13.3 + - - -
250B GLY 3.7 19.9 - - - +
251B PRO 4.0 3.6 - - - +
252B PRO* 3.9 19.5 - - + -
253B ALA 5.1 1.6 - - - +
351B GLU* 3.8 1.3 - - - +
405B GLN 3.7 24.0 - - - +
406B GLU* 3.5 13.2 - - - +
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 3.8 17.1 - - - +
57B SER 2.9 22.3 + - - -
60B HIS* 3.2 29.1 - - + +
64B GLY* 5.9 1.6 - - - +
237B MET* 3.7 6.3 - - - +
243B TRP* 3.0 59.8 + - + +
244B LEU* 3.1 10.1 + - + +
246B ILE* 1.3 76.1 - - - +
248B ASN* 1.3 57.1 + - - +
249B GLY 3.2 0.2 - - - -
351B GLU* 2.9 41.6 + - - +
352B ALA* 4.2 13.1 - - + +
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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