Contacts of the helix formed by residues 237 - 244 (chain B) in PDB entry 1QQJ
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 ARG 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B HIS* 5.0 0.6 - - - -
141B PHE* 6.0 3.1 - - + -
195B LEU* 2.9 34.4 + - + +
197B ASP* 2.8 38.2 + - + +
199B GLU* 2.6 36.2 + - - +
235B SER* 3.9 10.0 + - - +
236B ALA* 1.3 73.2 - - - +
238B ASP* 1.3 57.3 + - - +
240B GLN* 3.7 14.8 + - - +
241B GLN* 3.0 29.8 + - - +
361B SER* 3.7 9.7 + - - -
363B LEU* 3.7 33.4 - - + +
383B PHE* 4.3 8.1 - - + -
2003B CAC 2.7 32.9 + - - +
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Residues in contact with ASP 238 (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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180B MET* 2.9 36.1 - - + +
181B ARG 4.8 0.9 + - - -
193B CYS* 3.3 25.3 - - - +
194B ARG* 2.8 30.5 + - - +
195B LEU* 3.9 22.4 - - + +
236B ALA 4.0 0.2 - - - -
237B ARG* 1.3 71.3 + - - +
239B ILE* 1.3 70.9 + - - +
241B GLN* 3.5 5.1 + - - +
242B TRP* 3.5 20.4 + - - +
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Residues in contact with ILE 239 (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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336A ASN* 5.3 1.3 - - + -
176B PRO* 4.2 15.3 - - + +
177B MET 4.0 22.4 - - - +
178B GLY* 4.0 9.9 - - - +
179B GLN 3.7 25.1 - - - +
180B MET* 3.9 13.7 - - + -
193B CYS* 4.2 4.7 - - + -
236B ALA* 3.3 24.6 + - + +
238B ASP* 1.3 86.8 + - - +
240B GLN* 1.3 62.4 + - - +
242B TRP* 3.4 3.1 + - - +
243B GLU* 3.2 24.8 + - + +
251B LEU* 4.0 18.2 - - + +
252B GLY 3.8 20.2 - - - +
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Residues in contact with GLN 240 (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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235B SER* 4.3 6.4 - - - -
236B ALA 2.9 15.6 + - - +
237B ARG* 3.7 18.7 + - - +
239B ILE* 1.3 77.4 - - - +
241B GLN* 1.3 65.4 + - - +
243B GLU* 3.2 11.9 + - - +
244B TYR* 3.1 45.2 + - + +
249B PRO* 4.1 14.5 - - + +
252B GLY* 4.0 8.1 - - - +
253B LYS* 3.6 21.3 + - - +
2003B CAC 2.7 44.7 + - - +
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Residues in contact with GLN 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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141B PHE* 3.6 39.2 - - + +
237B ARG 3.0 18.6 + - - +
238B ASP* 4.0 6.1 - - - +
239B ILE 3.4 0.6 - - - -
240B GLN* 1.3 79.1 - - - +
242B TRP* 1.3 61.3 + - - +
244B TYR* 3.5 42.1 + - - -
245B VAL* 5.1 1.4 + - - +
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Residues in contact with TRP 242 (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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150A PRO* 3.5 24.2 - - + -
151A ASN* 3.0 43.5 + - + +
154A HIS* 3.8 18.8 - - + -
155A LEU* 3.5 13.7 - - + +
179B GLN* 2.8 48.8 + - + +
180B MET* 4.1 4.3 - - - -
181B ARG* 3.3 58.3 - - + +
184B ASN* 5.7 1.8 - - - -
188B PRO* 3.6 15.0 - - + +
238B ASP 3.5 12.8 + - - +
239B ILE 3.4 3.7 + - - +
240B GLN 3.3 0.4 - - - -
241B GLN* 1.3 80.2 - - - +
243B GLU* 1.3 58.2 + - - +
244B TYR 3.6 0.4 + - - -
245B VAL 5.1 0.3 + - - -
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Residues in contact with GLU 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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151A ASN* 3.3 15.0 + - - +
155A LEU* 4.7 21.0 - - + +
157A VAL* 4.5 10.9 - - - +
332A HIS* 5.1 2.9 + - + +
239B ILE* 3.2 16.1 + - + +
240B GLN* 3.2 12.8 + - - +
242B TRP* 1.3 80.2 - - + +
244B TYR* 1.3 71.0 + - + +
245B VAL 3.5 3.0 - - - +
247B LEU 5.3 0.3 + - - -
248B GLY 4.5 3.1 + - - +
249B PRO* 3.9 1.4 - - - +
250B PHE* 2.9 26.6 + - + +
251B LEU* 2.9 34.3 + - - +
252B GLY* 2.8 27.6 + - - -
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Residues in contact with TYR 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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246A PRO* 3.6 34.2 - - + +
247A LEU* 5.6 0.9 - - + -
141B PHE* 6.0 1.6 - - - +
142B ARG* 5.8 0.7 + - - -
240B GLN* 3.1 34.3 + - + +
241B GLN* 3.5 42.1 + - - -
242B TRP 3.6 0.8 - - - -
243B GLU* 1.3 77.8 - - + +
245B VAL* 1.3 82.1 + - + +
246B PRO 3.6 1.0 - - - -
247B LEU 3.3 0.9 + - - -
248B GLY* 2.6 51.2 + - - +
249B PRO* 4.0 10.3 - - + -
2000B ACT 4.4 20.2 + - + +
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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