Contacts of the helix formed by residues 238 - 251 (chain A) in PDB entry 2YNU
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ALA* 3.4 24.7 - - - +
195A GLY 3.0 9.7 + - - -
198A GLU* 5.1 4.0 - - - +
236A ASP 4.0 1.6 + - - -
237A ALA* 1.3 72.5 + - - +
239A ILE* 1.3 65.6 + - - +
240A SER* 3.2 9.0 - - - -
241A SER* 2.9 29.4 + - - -
242A TRP* 2.9 13.4 + - - +
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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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231A LEU* 4.1 20.9 - - + -
234A VAL* 3.7 38.6 - - + +
237A ALA* 3.6 8.4 + - + -
238A SER* 1.3 73.3 - - - +
240A SER* 1.3 64.4 + - - +
241A SER 3.2 0.5 + - - -
242A TRP* 3.4 16.8 + - + +
243A ALA* 4.3 3.5 + - - +
290A ALA* 4.5 6.1 - - - +
293A ALA* 3.9 30.5 - - + +
294A SER* 3.9 23.3 + - - +
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Residues in contact with SER 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A SER* 3.9 11.6 - - - -
239A ILE* 1.3 77.0 + - - +
241A SER* 1.3 59.0 + - - -
243A ALA* 4.9 4.2 + - - +
244A ASP* 4.6 8.7 + - - +
294A SER* 4.5 9.0 + - - +
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A GLY* 5.9 0.2 - - - -
194A ALA* 3.6 12.3 + - - +
238A SER* 2.9 24.6 + - - -
240A SER* 1.3 75.5 - - - +
242A TRP* 1.3 66.0 + - - +
243A ALA 3.2 3.1 - - - -
244A ASP* 3.1 14.8 + - - +
245A SER* 3.0 26.7 + - - -
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Residues in contact with TRP 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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194A ALA 3.5 9.4 - - - -
195A GLY* 3.5 16.8 - - - -
196A HIS* 3.7 28.7 - - + -
221A CYS 3.9 12.6 - - - -
222A LEU* 2.8 43.5 + - + +
224A ARG* 4.5 6.5 - - + -
231A LEU* 3.9 57.4 - - + -
234A VAL* 4.2 4.7 - - + -
237A ALA* 4.2 15.0 - - + -
238A SER 2.9 12.8 + - - +
239A ILE* 3.4 12.3 + - + +
241A SER* 1.3 76.4 - - - +
243A ALA* 1.3 62.4 + - - +
245A SER* 3.6 1.4 + - - -
246A ILE* 3.1 23.6 + - + +
286A THR* 3.6 12.8 - - + +
290A ALA* 4.6 8.3 - - + -
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Residues in contact with ALA 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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239A ILE 4.3 3.7 + - - +
240A SER 4.9 3.1 + - - +
241A SER 3.2 0.6 - - - +
242A TRP* 1.3 76.0 - - - +
244A ASP* 1.3 67.7 + - - +
246A ILE* 3.2 8.9 + - - +
247A LYS* 3.1 32.0 + - - +
287A ILE* 4.2 7.0 - - + +
290A ALA* 4.1 16.1 - - + +
291A GLU* 3.9 33.4 - - + +
294A SER* 5.9 1.1 - - - +
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Residues in contact with ASP 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 SER 4.6 9.3 + - - +
241A SER* 3.1 14.9 + - - +
243A ALA* 1.3 79.6 - - - +
245A SER* 1.3 61.8 + - - +
247A LYS* 3.3 25.6 + - - +
248A ASN* 2.9 29.8 + - - +
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Residues in contact with SER 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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192A PRO* 3.3 28.1 - - - +
193A GLY* 3.0 25.0 - - - -
194A ALA 2.5 31.1 + - - -
222A LEU* 4.5 7.0 - - - -
241A SER* 3.0 10.6 + - - -
242A TRP 3.8 4.7 - - - -
243A ALA 3.2 0.2 - - - -
244A ASP* 1.3 76.2 - - - +
246A ILE* 1.3 62.6 + - - +
248A ASN* 3.1 18.2 + - - +
249A ILE* 3.3 5.5 + - - +
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Residues in contact with ILE 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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222A LEU* 4.0 11.9 - - + +
223A VAL* 5.2 4.3 - - + -
242A TRP* 3.1 26.7 - - + +
243A ALA* 3.2 6.5 + - - +
245A SER* 1.3 75.0 - - - +
247A LYS* 1.3 60.5 + - - +
249A ILE* 2.9 12.7 + - + +
250A VAL* 2.9 26.2 + - + +
283A LEU* 4.0 29.2 - - + +
286A THR* 3.1 41.5 - - + -
287A ILE* 3.5 29.8 - - + +
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Residues in contact with LYS 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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243A ALA* 3.1 20.8 + - - +
244A ASP* 3.3 26.8 + - - +
246A ILE* 1.3 78.6 - - - +
248A ASN* 1.3 56.5 + - - +
250A VAL* 3.4 11.1 + - + +
251A SER* 2.7 31.6 + - - -
287A ILE* 3.8 22.9 - - + -
291A GLU* 3.0 27.6 + - - -
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Residues in contact with ASN 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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190A TYR* 3.4 22.9 + - - +
192A PRO* 2.7 26.0 + - + +
244A ASP* 2.9 19.6 + - - +
245A SER* 3.1 12.0 - - - +
246A ILE 3.1 0.2 - - - -
247A LYS* 1.3 78.9 - - - +
249A ILE* 1.3 61.6 + - - +
251A SER* 3.4 16.5 + - - -
252A LYS* 3.4 14.7 + - - +
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Residues in contact with ILE 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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190A TYR* 4.3 2.0 - - + -
192A PRO* 3.8 13.9 - - + -
202A VAL* 3.8 32.8 - - + -
217A LEU* 4.1 24.5 - - + -
222A LEU* 3.9 17.5 - - + -
223A VAL* 5.4 2.2 - - + -
245A SER 3.3 11.6 + - - +
246A ILE* 2.9 14.3 + - + +
248A ASN* 1.3 75.6 - - - +
250A VAL* 1.3 69.7 + - - +
252A LYS* 2.9 23.6 + - - +
253A LYS 3.9 1.2 + - - -
254A TYR* 4.3 21.2 + - + -
256A ILE* 5.3 1.5 - - + +
283A LEU* 4.5 22.0 - - + -
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Residues in contact with VAL 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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246A ILE* 2.9 23.8 + - + +
247A LYS* 3.6 13.0 - - + +
249A ILE* 1.3 77.7 - - - +
251A SER* 1.3 56.2 + - - +
253A LYS* 2.9 29.3 + - + +
254A TYR 4.7 0.6 + - - +
256A ILE* 6.5 0.2 - - - -
283A LEU* 4.4 23.1 - - + -
284A ASP* 5.7 4.9 - - - +
287A ILE* 4.9 7.0 - - + -
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Residues in contact with SER 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 LYS 2.7 27.2 + - - -
248A ASN* 3.7 12.2 + - - -
249A ILE 3.1 0.8 + - - -
250A VAL* 1.3 69.2 - - - +
252A LYS* 1.3 61.5 + - - +
253A LYS* 2.9 26.5 + - - +
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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