Contacts of the helix formed by residues 243 - 262 (chain A) in PDB entry 2NUN
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 SER 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A ASP 4.2 0.8 + - - -
242A LEU* 1.3 75.5 - - - +
244A GLN* 1.3 61.4 + - - +
245A ALA* 3.6 8.6 + - - +
246A GLU* 3.0 37.5 + - - +
247A LEU* 2.8 25.5 + - - +
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Residues in contact with GLN 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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242A LEU 3.8 0.8 + - - +
243A SER* 1.3 72.8 - - - +
245A ALA* 1.3 56.9 + - - +
247A LEU* 3.7 11.2 - - + +
248A ILE* 2.9 39.4 + - + +
285A ILE* 3.2 37.6 - - + +
313A ARG* 4.9 11.7 + - - +
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Residues in contact with ALA 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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243A SER* 3.0 9.2 - - - +
244A GLN* 1.3 77.6 - - - +
246A GLU* 1.3 57.5 + - + +
248A ILE* 4.1 4.0 - - - +
249A SER* 2.7 33.9 + - - -
313A ARG* 5.6 4.9 - - - +
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Residues in contact with GLU 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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241A ASP 4.2 4.2 - - - +
242A LEU* 3.9 24.3 - - + +
243A SER* 3.0 34.6 + - - +
245A ALA* 1.3 79.0 - - + +
247A LEU* 1.3 61.2 + - - +
249A SER* 3.5 6.7 + - - -
250A LEU* 3.2 29.0 + - + +
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Residues in contact with LEU 247 (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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237A ALA* 4.0 8.7 - - + +
242A LEU* 4.3 17.2 - - + +
243A SER 2.8 16.0 + - - +
244A GLN* 3.7 11.7 - - + +
245A ALA 3.2 0.2 - - - -
246A GLU* 1.3 75.9 - - - +
248A ILE* 1.3 66.4 + - + +
250A LEU* 3.2 6.9 + - + +
251A ILE* 3.1 40.8 + - + +
279A ILE* 5.1 1.3 - - + -
283A HIS* 3.4 52.0 - - + +
285A ILE* 3.5 35.4 - - + -
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Residues in contact with ILE 248 (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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244A GLN* 2.9 33.1 + - + +
245A ALA* 4.1 4.3 - - - +
246A GLU 3.5 0.2 - - - -
247A LEU* 1.3 76.0 - - + +
249A SER* 1.3 63.1 + - - +
251A ILE* 3.3 16.3 + - + +
252A ALA* 3.0 21.8 + - - +
285A ILE* 4.2 28.5 - - + -
287A LEU* 4.4 11.2 - - + -
309A VAL 6.0 1.3 - - - +
312A TYR* 4.4 18.5 - - + -
313A ARG* 3.9 46.0 - - + +
316A LEU* 6.4 0.7 - - + -
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Residues in contact with SER 249 (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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245A ALA 2.7 20.2 + - - -
246A GLU* 3.6 10.1 - - - -
247A LEU 3.2 0.4 - - - -
248A ILE* 1.3 79.1 - - - +
250A LEU* 1.3 58.3 + - - +
252A ALA* 3.3 3.9 + - - +
253A ARG* 3.0 39.7 + - - +
309A VAL* 4.0 24.4 - - - +
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Residues in contact with LEU 250 (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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233A LEU* 4.1 24.6 - - + +
236A GLN* 3.9 28.9 - - + +
237A ALA* 3.8 28.5 - - + +
242A LEU* 3.7 34.8 - - + -
246A GLU* 3.2 11.8 + - + +
247A LEU* 3.2 8.8 + - - +
249A SER* 1.3 79.7 - - - +
251A ILE* 1.3 58.2 + - - +
253A ARG* 3.3 11.2 + - - +
254A THR* 2.9 34.6 + - - -
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Residues in contact with ILE 251 (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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247A LEU* 3.1 35.4 + - + +
248A ILE* 3.6 18.8 - - + +
250A LEU* 1.3 78.4 - - + +
252A ALA* 1.3 56.5 + - - +
254A THR* 3.4 6.9 + - - -
255A HIS* 2.9 28.1 + - - +
276A ALA* 3.4 32.3 - - + +
279A ILE* 4.4 19.5 - - + -
280A ALA* 3.5 30.5 - - + -
287A LEU* 4.4 7.9 - - + -
312A TYR* 4.2 15.0 - - + +
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Residues in contact with ALA 252 (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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248A ILE* 3.0 15.7 + - + +
249A SER* 3.6 6.7 - - - +
251A ILE* 1.3 76.9 - - - +
253A ARG* 1.3 52.5 + - - +
255A HIS* 3.3 0.7 + - - +
256A TRP* 2.8 30.3 + - - +
308A PHE* 3.3 13.5 - - + -
309A VAL* 4.0 17.3 - - + +
312A TYR* 3.5 45.1 - - + -
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Residues in contact with ARG 253 (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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229A HIS* 6.3 0.2 - - - -
233A LEU* 4.2 24.7 - - + -
249A SER* 3.0 21.7 + - - +
250A LEU* 3.5 18.3 - - - +
252A ALA* 1.3 74.9 - - - +
254A THR* 1.3 60.1 + - - +
256A TRP* 3.0 7.2 + - - +
257A TRP* 2.8 37.4 + - + -
305A GLU* 2.3 43.5 + - - +
306A GLU* 2.9 39.5 + - - -
309A VAL* 3.6 22.0 - - + +
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Residues in contact with THR 254 (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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88A PHE* 3.6 31.4 - - + -
230A LEU* 3.5 14.2 - - + +
233A LEU* 3.7 23.8 + - + +
234A TYR 6.0 0.4 - - - +
237A ALA* 5.2 1.4 - - - +
250A LEU 2.9 18.9 + - - -
251A ILE* 3.7 7.2 - - - -
253A ARG* 1.3 75.1 - - - +
255A HIS* 1.3 59.6 + - - +
258A ALA* 3.0 33.5 + - + +
272A ALA 5.9 0.2 - - - +
275A ALA* 5.2 0.7 - - + -
276A ALA* 5.0 8.1 - - - +
279A ILE* 4.0 22.0 - - + +
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Residues in contact with HIS 255 (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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251A ILE 2.9 18.2 + - - +
252A ALA 3.5 5.2 - - - +
254A THR* 1.3 77.6 - - - +
256A TRP* 1.3 57.0 + - - +
258A ALA* 4.7 2.5 - - - -
259A ALA* 2.9 36.8 + - + +
269A ALA 5.0 0.8 + - - -
272A ALA* 4.1 19.1 - - + +
273A GLU* 3.7 27.0 + - + +
276A ALA* 3.8 14.6 - - + +
290A PHE* 3.7 14.1 - + - -
296A SER* 3.6 34.1 + - - -
297A ASP 4.8 0.6 + - - -
300A ALA* 5.8 0.2 - - + -
308A PHE* 4.5 5.8 - + + -
312A TYR* 2.8 28.8 + + + +
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Residues in contact with TRP 256 (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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164A GLN* 3.6 13.2 + - - -
165A THR 3.8 9.2 - - - -
166A ALA* 3.5 25.8 - - + -
175A LEU* 3.6 10.1 - - + -
252A ALA 2.8 18.6 + - - +
253A ARG* 3.0 11.6 + - - +
255A HIS* 1.3 73.9 - - - +
257A TRP* 1.3 103.1 + + - +
259A ALA* 4.1 0.2 - - - +
260A SER* 2.8 37.3 + - - -
300A ALA* 3.3 21.7 + - + -
303A SER 3.0 25.5 + - - -
304A GLY 3.8 0.6 - - - -
305A GLU* 3.4 49.3 - - + +
308A PHE* 3.5 36.1 - + + -
309A VAL* 5.9 0.2 - - + -
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Residues in contact with TRP 257 (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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166A ALA* 3.6 26.0 - - + -
167A TYR 3.6 17.9 - - - -
168A LEU* 3.8 22.2 - - + -
173A ILE* 4.9 3.6 - - + -
175A LEU* 5.1 4.2 - - + +
226A ILE* 4.2 33.4 - - + +
229A HIS* 3.5 29.5 - + + -
230A LEU* 3.8 21.1 - - + -
233A LEU* 3.8 14.8 - - + +
253A ARG 2.8 32.6 + - - +
256A TRP* 1.3 90.0 - + - +
258A ALA* 1.3 57.5 + - - +
260A SER* 3.8 1.7 - - - -
261A ALA* 2.8 34.1 + - - +
305A GLU* 3.1 39.5 + - - -
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Residues in contact with ALA 258 (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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88A PHE* 4.2 6.3 - - + -
92A TRP* 4.1 15.3 - - + -
230A LEU* 3.9 20.2 - - + +
254A THR* 3.0 20.2 + - + +
255A HIS* 4.0 1.1 - - - +
257A TRP* 1.3 78.0 - - - +
259A ALA* 1.3 61.8 + - - +
261A ALA* 4.6 1.1 - - - -
262A MET* 3.1 17.8 + - - -
263A PRO* 3.3 14.3 - - - +
268A SER* 5.0 0.3 - - - -
272A ALA* 3.9 22.8 - - + +
275A ALA* 5.9 0.2 - - + -
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Residues in contact with ALA 259 (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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255A HIS* 2.9 24.5 + - + +
256A TRP 4.1 1.1 - - - +
258A ALA* 1.3 77.1 - - - +
260A SER* 1.3 63.6 + - - +
262A MET* 3.4 12.4 + - - +
268A SER* 5.2 3.5 - - - -
269A ALA* 5.6 1.6 - - - +
272A ALA* 3.8 16.3 - - + +
297A ASP* 3.9 34.1 - - + +
300A ALA* 4.2 7.2 - - + -
301A MET* 3.8 15.7 - - - +
1503A TRS 5.2 1.6 + - - -
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Residues in contact with SER 260 (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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164A GLN* 2.9 26.7 + - - -
175A LEU* 3.6 19.1 - - - -
176A ASN* 2.9 20.4 + - - +
218A THR* 2.7 20.7 + - - -
256A TRP* 2.8 29.9 + - - -
257A TRP* 4.1 1.8 - - - -
259A ALA* 1.3 77.8 - - - +
261A ALA* 1.3 60.5 + - - +
262A MET* 4.4 0.2 - - - +
300A ALA* 3.8 13.5 + - - +
301A MET* 4.1 3.1 + - - +
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Residues in contact with ALA 261 (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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117A ARG* 2.9 21.3 + - - -
175A LEU* 5.3 0.6 - - - +
218A THR* 3.8 10.9 - - - -
223A LEU* 4.0 9.1 - - + +
226A ILE* 3.6 34.8 - - + -
257A TRP 2.8 20.1 + - - +
258A ALA* 3.9 4.0 - - - +
260A SER* 1.3 75.5 - - - +
262A MET* 1.3 70.2 + - - +
263A PRO* 4.1 12.1 - - + -
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Residues in contact with MET 262 (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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117A ARG* 2.8 59.1 + - - +
122A ASP* 4.8 7.6 - - - +
123A ALA* 5.0 0.9 - - - -
217A HIS* 3.6 46.2 - - + -
258A ALA 3.1 4.0 + - - -
259A ALA 3.4 10.0 + - - +
260A SER 3.3 3.3 - - - +
261A ALA* 1.3 80.1 - - - +
263A PRO* 1.3 69.6 - - - +
264A ASP 3.4 8.6 + - - +
265A GLN 4.7 7.9 - - - +
268A SER* 3.5 23.1 - - - +
301A MET* 4.6 4.0 - - + -
1503A TRS 4.4 22.0 - - - +
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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