Contacts of the helix formed by residues 235 - 245 (chain B) in PDB entry 3N1Y
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 LEU 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 4.2 20.0 - - + -
165B TRP* 4.4 11.9 - - + -
230B VAL* 4.7 1.1 - - + +
231B GLU* 3.1 38.1 + - + +
234B LEU* 1.3 84.7 - - + +
236B GLN* 1.3 67.2 + - - +
239B GLY* 3.1 21.7 + - - -
254B ALA* 3.5 25.8 - - + +
257B GLN* 3.4 31.0 - - + +
258B LYS* 4.1 33.9 - - + +
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Residues in contact with GLN 236 (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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231B GLU 2.9 7.3 + - - +
232B GLU* 3.3 37.5 - - - +
235B LEU* 1.3 76.3 - - - +
237B GLN* 1.3 69.6 + - - +
240B SER* 2.7 55.7 + - - -
258B LYS* 3.6 24.2 + - - +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 2.9 23.3 + - - +
233B ALA* 3.3 14.1 + - - +
236B GLN* 1.3 86.6 - - - +
238B LEU* 1.3 67.3 + - - +
240B SER* 3.4 8.6 + - - -
241B LEU* 3.1 23.0 + - - +
304B CYS* 4.4 2.2 - - - -
307B LEU* 4.5 14.9 - - + +
313B ALA* 3.5 38.8 + - + +
316B GLU* 3.4 35.2 + - - +
317B ALA* 4.3 7.0 - - + +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TRP* 4.2 17.9 - - + -
120B THR* 5.0 2.7 - - + +
121B LEU* 5.8 0.4 - - + -
124B PHE* 3.6 30.7 - - + +
125B TYR* 3.9 28.9 - - + +
233B ALA 3.1 10.8 + - - +
234B LEU* 3.3 22.2 + - + +
236B GLN 3.6 0.2 - - - -
237B GLN* 1.3 77.9 - - - +
239B GLY* 1.3 57.2 + - - +
241B LEU* 3.4 7.3 + - + +
242B ALA* 2.8 27.2 + - - +
250B LEU* 4.2 11.2 - - + -
303B TYR* 3.6 18.6 - - + +
307B LEU* 4.4 15.2 - - + +
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Residues in contact with GLY 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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234B LEU 4.2 1.0 + - - -
235B LEU 3.1 21.9 + - - -
238B LEU* 1.3 76.1 - - - +
240B SER* 1.3 64.0 + - - +
242B ALA* 3.2 8.2 + - - +
243B GLN* 3.1 20.4 + - - +
250B LEU* 4.7 2.2 - - - -
251B GLY* 3.7 14.8 - - - -
254B ALA* 4.2 14.1 - - - -
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Residues in contact with SER 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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236B GLN* 2.7 38.9 + - - -
237B GLN* 3.8 8.4 + - - -
239B GLY* 1.3 74.6 - - - +
241B LEU* 1.3 63.1 + - - +
243B GLN* 3.3 7.3 + - - +
244B SER* 3.2 21.5 + - - -
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Residues in contact with LEU 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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117B TRP* 3.6 24.2 - - + -
120B THR* 4.8 1.8 - - + -
237B GLN 3.1 16.9 + - - +
238B LEU* 3.5 7.4 - - + +
240B SER* 1.3 78.6 - - - +
242B ALA* 1.3 62.0 + - - +
244B SER* 2.8 27.7 + - - +
245B GLU* 2.9 26.2 + - + +
307B LEU* 4.0 22.0 - - + -
308B PRO* 3.6 45.3 - - + +
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Residues in contact with ALA 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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117B TRP* 3.4 27.1 - - + -
238B LEU 2.8 21.0 + - - +
239B GLY 3.3 7.0 - - - +
241B LEU* 1.3 73.3 - - - +
243B GLN* 1.3 60.7 + - - +
245B GLU* 3.1 7.1 + - - +
246B GLY 3.2 0.2 + - - -
247B ASP* 2.8 37.9 + - + +
250B LEU* 3.9 22.4 - - + -
251B GLY 4.1 1.6 - - - +
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Residues in contact with GLN 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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239B GLY 3.1 13.2 + - - +
240B SER* 3.8 8.7 - - - +
242B ALA* 1.3 75.9 - - - +
244B SER* 1.3 63.3 + - - +
246B GLY* 3.2 12.0 + - - -
247B ASP 3.8 8.9 + - - +
248B THR* 4.9 15.6 - - - +
251B GLY* 4.7 7.4 - - - -
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Residues in contact with SER 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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240B SER 3.2 10.6 + - - -
241B LEU* 2.8 31.8 + - - +
243B GLN* 1.3 78.7 - - - +
245B GLU* 1.3 65.1 + - - +
246B GLY 3.3 1.4 + - - -
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Residues in contact with GLU 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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113B LEU* 5.1 2.4 - - - +
114B THR* 4.7 16.3 + - - +
116B GLU* 5.4 4.7 - - - +
117B TRP* 3.4 52.7 + - + +
241B LEU* 2.9 27.9 + - + +
242B ALA 3.6 4.3 - - - +
243B GLN 3.1 0.6 - - - -
244B SER* 1.3 85.4 + - - +
246B GLY* 1.3 58.7 + - - +
247B ASP 3.4 1.0 + - - -
308B PRO* 6.6 0.2 - - - -
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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