Contacts of the helix formed by residues 236 - 246 (chain A) in PDB entry 1QIB
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 GLN 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LEU 5.1 1.4 - - - +
235A SER* 1.3 73.6 - - - +
237A ASP* 1.3 56.6 + - - +
239A ILE* 3.1 23.3 + - - +
240A LYS* 2.8 35.0 + - + +
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Residues in contact with ASP 237 (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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212A SER* 2.6 36.5 + - - -
214A ASP* 3.5 25.5 + - + +
217A ALA* 4.0 3.4 - - + +
235A SER* 3.1 7.3 - - - +
236A GLN* 1.3 79.6 - - - +
238A ASP* 1.3 61.4 + - - +
240A LYS* 3.8 13.1 - - - +
241A GLY* 3.3 17.7 + - - -
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Residues in contact with ASP 238 (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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124A TRP* 4.3 11.0 - - + -
209A LEU* 4.9 4.0 - - - +
217A ALA* 3.7 6.4 - - - +
218A LEU* 2.9 26.4 + - - +
219A MET* 3.4 32.2 + - - +
234A LEU* 3.4 23.0 - - + +
235A SER* 2.9 29.1 + - - +
237A ASP* 1.3 76.6 - - - +
239A ILE* 1.3 65.0 + - - +
241A GLY* 3.3 2.3 + - - -
242A ILE* 3.2 25.4 + - - +
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Residues in contact with ILE 239 (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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127A VAL* 4.4 20.6 - - + -
234A LEU* 4.1 30.7 - - + +
235A SER 3.1 15.4 + - - +
236A GLN* 3.6 27.6 - - - +
238A ASP* 1.3 76.4 - - - +
240A LYS* 1.3 61.9 + - - +
242A ILE* 3.6 6.4 - - - +
243A GLN* 3.1 58.4 + - + +
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Residues in contact with LYS 240 (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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236A GLN* 2.8 17.3 + - + +
237A ASP* 3.8 12.8 - - - +
239A ILE* 1.3 80.1 - - - +
241A GLY* 1.3 60.0 + - - +
243A GLN* 4.3 5.8 - - - +
244A GLU* 3.4 26.5 + - - +
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Residues in contact with GLY 241 (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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209A LEU* 3.8 19.7 - - - +
237A ASP 3.3 8.8 + - - -
238A ASP* 3.3 6.0 + - - -
240A LYS* 1.3 79.8 - - - +
242A ILE* 1.3 62.7 + - - +
244A GLU* 3.4 17.8 + - - +
245A LEU* 3.6 9.2 + - - +
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Residues in contact with ILE 242 (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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124A TRP* 4.0 26.7 - - + -
127A VAL* 3.9 17.9 - - + -
128A THR* 3.7 25.8 - - + +
130A LEU* 5.0 2.2 - - + -
207A MET* 3.9 31.4 - - + -
209A LEU* 4.0 21.8 - - + +
238A ASP 3.2 15.1 + - - +
239A ILE* 3.6 11.0 - - - +
241A GLY* 1.3 73.6 - - - +
243A GLN* 1.3 65.0 + - + +
245A LEU* 3.3 7.4 + - + +
246A TYR* 3.1 39.4 + - + +
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Residues in contact with GLN 243 (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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127A VAL* 3.1 31.2 - - - +
239A ILE* 3.1 39.2 + - + +
240A LYS* 4.5 5.4 - - - +
242A ILE* 1.3 77.4 - - + +
244A GLU* 1.3 63.2 + - - +
245A LEU 3.1 0.2 - - - -
247A GLY* 2.7 41.7 + - - +
248A ALA* 3.7 20.6 - - - +
249A SER* 4.4 0.7 + - - -
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Residues in contact with GLU 244 (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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240A LYS* 3.4 17.1 + - - +
241A GLY* 3.4 14.3 + - - +
242A ILE 3.2 0.4 - - - -
243A GLN* 1.3 80.9 - - - +
245A LEU* 1.3 61.4 + - + +
247A GLY 4.7 0.7 + - - -
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Residues in contact with LEU 245 (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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89A LYS* 4.8 20.9 - - + +
90A PRO 5.2 0.9 - - - +
91A LYS* 2.9 52.9 + - + +
207A MET 4.1 12.6 - - - +
208A GLY* 3.9 29.6 - - - +
209A LEU* 4.2 16.6 - - + -
241A GLY 3.6 4.7 + - - +
242A ILE* 3.3 9.8 + - + +
243A GLN 3.1 0.2 - - - -
244A GLU* 1.3 84.1 - - + +
246A TYR* 1.3 71.6 + - + +
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Residues in contact with TYR 246 (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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91A LYS* 3.5 16.7 - - + +
92A TRP* 3.1 53.3 + + + -
94A LYS 5.4 0.9 - - - -
95A ASN* 4.0 12.8 + - - +
128A THR* 4.5 2.7 - - - -
129A PRO* 3.2 25.4 - - + +
130A LEU* 3.6 47.3 - - + -
207A MET* 2.8 30.7 + - + -
242A ILE* 3.1 25.5 + - + +
245A LEU* 1.3 90.9 - - + +
247A GLY* 1.3 61.0 + - - +
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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