Contacts of the helix formed by residues 237 - 252 (chain A) in PDB entry 2Y4T
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 ASP 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A ARG* 2.4 44.5 + - - -
232A TYR* 3.1 43.0 + - + +
235A LEU* 3.7 2.8 - - - +
236A GLY* 1.3 79.1 - - - +
238A HIS* 1.3 61.2 + - - +
239A GLU 3.5 2.7 - - - +
240A LEU* 4.4 11.5 - - + +
241A SER* 3.2 23.5 + - - -
304A TYR* 4.5 0.9 - - - -
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Residues in contact with HIS 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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236A GLY 3.0 18.7 + - - -
237A ASP* 1.3 71.2 - - - +
239A GLU* 1.3 76.9 + - + +
241A SER* 4.1 1.3 - - - -
242A LEU* 2.9 27.1 + - - +
265A VAL* 3.5 21.2 - - + +
268A LEU* 5.1 3.4 - - + -
269A ASN* 2.9 34.4 + - - -
272A ILE* 3.5 50.1 - - + +
273A GLU* 4.5 10.8 - - - -
304A TYR* 3.9 18.8 - + + +
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Residues in contact with GLU 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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237A ASP 3.5 0.2 - - - -
238A HIS* 1.3 91.0 + - + +
240A LEU* 1.3 69.4 + - + +
242A LEU* 3.4 6.4 + - - +
243A SER* 3.2 17.8 + - - -
269A ASN* 4.5 13.0 - - - +
273A GLU* 3.8 15.9 - - - +
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Residues in contact with LEU 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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232A TYR* 3.4 48.5 - - + +
237A ASP* 4.0 12.5 + - + +
238A HIS 3.4 0.4 - - - -
239A GLU* 1.3 79.5 - - + +
241A SER* 1.3 55.6 + - - +
243A SER* 2.6 35.8 + - - +
244A GLU* 2.7 18.4 + - + +
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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
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229A SER* 2.6 52.4 + - - +
232A TYR* 3.8 6.1 - - - +
233A TYR* 3.6 12.3 - - - +
237A ASP 3.2 20.5 + - - -
238A HIS 3.3 5.4 + - - -
240A LEU* 1.3 76.2 - - - +
242A LEU* 1.3 56.8 + - - +
244A GLU* 3.8 1.1 - - - -
245A VAL* 3.0 15.9 + - - +
261A HIS* 3.0 18.5 + - - -
265A VAL* 3.8 6.6 - - - +
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Residues in contact with LEU 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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238A HIS 2.9 16.7 + - - +
239A GLU* 3.6 4.9 - - + +
240A LEU 2.8 3.4 + - - -
241A SER* 1.3 74.6 + - - +
243A SER* 1.3 58.9 + - - +
245A VAL* 3.1 6.2 + - + +
246A ARG* 2.9 36.0 + - + +
262A TYR* 3.8 32.8 - - + -
265A VAL* 3.6 22.0 - - + +
266A LYS* 4.1 16.8 - - + -
269A ASN* 3.4 39.9 - - + +
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Residues in contact with SER 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 GLU 3.2 9.0 + - - -
240A LEU* 2.6 24.2 + - - +
242A LEU* 1.3 78.3 - - - +
244A GLU* 1.3 69.1 + - - +
246A ARG* 3.3 13.4 + - - +
247A GLU* 3.3 24.6 + - - +
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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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212A LYS* 3.4 36.9 + - - +
225A PHE* 3.4 34.2 - - + +
228A ILE* 3.8 32.5 - - + -
229A SER* 4.2 11.0 - - - -
232A TYR* 4.3 8.3 - - + -
240A LEU* 2.7 21.0 + - - +
241A SER 3.9 4.5 - - - +
243A SER* 1.3 85.5 + - - +
245A VAL* 1.3 55.5 + - - +
247A GLU* 3.3 28.8 - - - +
248A CYS 3.6 3.1 + - - -
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Residues in contact with VAL 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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226A TYR* 5.0 1.1 - - + -
229A SER* 3.3 19.2 - - - +
241A SER 3.0 16.0 + - - +
242A LEU* 3.1 21.3 - - - +
244A GLU* 1.3 72.2 - - - +
246A ARG* 1.3 67.3 + - - +
247A GLU 3.0 1.3 - - - -
248A CYS* 3.0 13.6 + - - +
249A LEU* 3.0 14.3 + - + +
258A CYS* 3.2 45.5 - - + +
261A HIS* 4.1 9.6 - - + -
262A TYR* 4.1 16.2 - - + -
265A VAL* 4.1 13.5 - - + -
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Residues in contact with ARG 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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242A LEU* 2.9 25.5 + - + +
243A SER* 3.3 15.9 + - - +
245A VAL* 1.3 77.9 - - - +
247A GLU* 1.3 56.6 + - - +
249A LEU* 3.2 7.4 + - + +
250A LYS* 2.9 58.5 + - - +
262A TYR* 4.0 31.6 + - + -
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Residues in contact with GLU 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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225A PHE* 3.5 26.4 - - + -
243A SER 3.3 14.8 + - - +
244A GLU* 3.3 28.5 - - - +
245A VAL 3.0 0.2 - - - -
246A ARG* 1.3 73.8 - - - +
248A CYS* 1.3 66.6 + - - +
250A LYS* 2.9 47.0 + - - +
251A LEU* 3.1 17.9 + - - +
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Residues in contact with CYS 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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222A THR* 3.2 40.5 - - - +
225A PHE* 4.1 19.9 - - + +
226A TYR 4.6 0.9 - - - +
244A GLU 3.6 2.8 + - - -
245A VAL* 3.0 14.0 + - - +
247A GLU* 1.3 77.6 - - - +
249A LEU* 1.3 57.6 + - - +
251A LEU* 3.0 3.9 + - - -
252A ASP* 2.9 22.2 + - - -
255A HIS* 3.8 6.5 - - - -
258A CYS* 2.1 49.8 - - - -
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Residues in contact with LEU 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 VAL 3.0 15.2 + - - +
246A ARG* 3.8 5.6 - - + +
248A CYS* 1.3 75.3 - - - +
250A LYS* 1.3 63.6 + - - +
251A LEU 3.0 1.8 - - - -
252A ASP 3.2 33.7 + - - +
253A GLN* 3.3 27.7 + - + +
255A HIS 4.0 7.0 - - - +
258A CYS* 4.3 9.6 - - + +
259A PHE* 3.7 32.8 - - + +
262A TYR* 3.7 44.2 - - + -
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Residues in contact with LYS 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 ARG* 2.9 49.7 + - - +
247A GLU* 2.9 44.1 + - - +
249A LEU* 1.3 76.5 - - - +
251A LEU* 1.3 63.9 + - + +
253A GLN 5.3 0.2 + - - -
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Residues in contact with LEU 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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219A ASN 3.9 3.8 - - - +
220A ASP* 3.5 49.1 - - + +
222A THR* 3.2 24.9 - - + +
225A PHE* 3.9 26.9 - - + -
247A GLU* 3.1 10.6 + - - +
248A CYS 3.0 2.5 + - - +
250A LYS* 1.3 81.8 - - + +
252A ASP* 1.3 60.1 + - - +
253A GLN 4.2 0.2 - - - -
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Residues in contact with ASP 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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222A THR* 4.0 15.3 + - + +
248A CYS 2.9 5.9 + - - -
249A LEU* 3.2 20.9 + - - +
251A LEU* 1.3 80.0 - - - +
253A GLN* 1.3 62.8 + - - +
254A ASP* 3.0 19.2 + - - +
255A HIS* 3.2 43.2 + - + +
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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