Contacts of the helix formed by residues 244 - 255 (chain B) in PDB entry 4AY1
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 ASN 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B PHE* 3.5 14.7 - - - -
229B PRO* 3.5 13.2 - - + +
230B LEU 3.7 1.0 + - - +
231B SER 3.5 19.5 - - - +
232B LYS* 3.5 24.2 - - - +
236B ASP* 5.2 0.3 - - - +
240B SER 5.0 0.3 - - - +
241B SER 3.0 25.3 - - - +
242B TYR 3.0 3.3 + - - +
243B TYR* 1.3 75.9 - - - +
245B VAL* 1.3 64.4 + - - +
246B GLU* 3.4 13.5 - - - +
247B TYR* 2.7 37.2 + - - +
248B ALA 3.2 17.2 + - - -
322B GLN* 5.2 0.2 - - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B SER* 3.8 17.5 - - - +
214B PHE* 3.7 9.8 - - + -
228B SER* 3.7 22.2 - - - +
229B PRO 3.0 23.3 + - - +
230B LEU* 3.8 18.8 - - + +
244B ASN* 1.3 70.4 - - - +
246B GLU* 1.3 58.6 + - - +
248B ALA* 3.1 2.8 + - - +
249B VAL* 2.9 32.7 + - + +
264B MET* 3.4 41.7 - - + -
265B GLY 5.2 2.0 - - - +
345B LYS* 4.4 9.2 - - + -
348B PHE* 4.4 0.9 - - + -
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Residues in contact with GLU 246 (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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230B LEU* 2.9 17.9 + - + +
231B SER* 3.0 27.0 + - - -
232B LYS 5.0 0.3 + - - -
244B ASN* 3.5 5.8 - - - +
245B VAL* 1.3 76.2 - - - +
247B TYR* 1.3 62.7 + - - +
249B VAL* 3.5 1.9 + - - +
250B GLY* 3.1 19.8 + - - -
348B PHE* 3.7 35.2 - - + -
352B LEU* 5.9 1.6 - - + +
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG* 2.7 44.4 + - + -
241B SER* 4.2 6.7 - - - -
242B TYR* 3.4 54.5 - + + +
244B ASN* 2.7 27.3 - - - +
246B GLU* 1.3 73.0 - - - +
248B ALA* 1.3 60.6 + - - +
250B GLY* 3.2 2.2 + - - -
251B TYR* 2.8 50.1 + + + -
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Residues in contact with ALA 248 (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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186B ALA* 3.2 46.2 - - + +
191B ILE* 5.4 0.9 - - - -
209B LEU* 4.3 9.2 - - + -
211B SER* 5.2 0.2 - - - -
214B PHE* 4.1 2.9 - - + -
242B TYR 4.7 0.6 + - - +
244B ASN 3.2 10.2 + - - +
245B VAL* 3.1 7.9 + - - +
247B TYR* 1.3 82.8 - - - +
249B VAL* 1.3 63.6 + - - +
251B TYR* 3.3 3.9 + - - +
252B TRP* 3.1 29.8 + - + -
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.7 22.9 - - + -
245B VAL* 2.9 19.1 + - + +
246B GLU 3.9 3.1 - - - +
248B ALA* 1.3 77.9 - - - +
250B GLY* 1.3 63.6 + - - +
252B TRP* 3.5 4.4 + - - +
253B ILE* 3.2 30.5 + - + +
262B VAL* 4.6 5.1 - - + +
264B MET* 4.2 10.8 - - + -
348B PHE* 4.0 22.4 - - + -
352B LEU* 4.3 6.1 - - + -
354B LEU* 3.8 44.2 - - + -
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Residues in contact with GLY 250 (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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246B GLU 3.1 15.0 + - - -
247B TYR* 3.6 2.9 - - - -
249B VAL* 1.3 78.6 - - - +
251B TYR* 1.3 56.5 + - - +
253B ILE* 3.4 8.0 + - - +
254B HIS* 2.9 30.8 + - - +
352B LEU* 5.5 5.4 - - - +
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Residues in contact with TYR 251 (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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188B ARG* 3.3 45.4 + - + -
191B ILE* 3.9 29.6 - - + -
192B ASP* 2.4 36.0 + - - -
247B TYR* 2.8 40.6 + + + +
248B ALA* 3.8 5.6 - - - +
250B GLY* 1.3 75.6 - - - +
252B TRP* 1.3 60.7 + - - +
254B HIS* 3.3 24.6 + + - +
255B LYS* 2.9 52.6 + - + +
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Residues in contact with TRP 252 (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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184B VAL* 3.2 32.5 - - + -
185B SER 3.0 18.1 + - - -
191B ILE* 3.3 21.7 - - + +
195B TYR* 3.4 44.4 - + + -
197B VAL* 3.6 35.9 - - + +
200B LEU* 5.1 3.6 - - + -
207B ILE* 3.8 22.9 - - + -
209B LEU* 3.3 21.6 - - + +
248B ALA 3.1 24.0 + - - +
249B VAL* 3.8 5.2 - - - +
251B TYR* 1.3 75.4 - - - +
253B ILE* 1.3 62.9 + - - +
255B LYS* 3.3 11.7 + - - +
256B GLY 3.3 0.9 + - - -
257B MET* 3.0 41.9 + - + +
262B VAL* 4.6 6.3 - - + -
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Residues in contact with ILE 253 (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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249B VAL* 3.2 22.6 + - + +
250B GLY* 3.7 8.3 - - - +
252B TRP* 1.3 72.0 - - - +
254B HIS* 1.3 69.2 + - - +
256B GLY* 2.9 15.6 + - - -
257B MET 3.4 20.6 + - - +
258B PRO* 6.0 0.2 - - + -
259B SER* 3.7 32.1 - - - +
262B VAL* 4.3 6.5 - - + -
352B LEU* 4.7 10.8 - - + +
354B LEU* 4.0 17.0 - - + -
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Residues in contact with HIS 254 (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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250B GLY 2.9 17.9 + - - +
251B TYR* 3.5 31.1 - + + +
253B ILE* 1.3 79.3 - - - +
255B LYS* 1.3 70.1 + - + +
256B GLY 3.3 1.6 + - - -
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Residues in contact with LYS 255 (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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191B ILE* 4.9 4.0 - - + -
192B ASP* 3.1 29.4 + - - +
195B TYR 5.1 6.1 + - - -
197B VAL* 3.5 41.4 - - + +
198B GLU* 3.5 19.4 - - - +
251B TYR* 2.9 48.7 + - + +
252B TRP* 3.8 4.9 - - - +
253B ILE 3.1 0.4 - - - -
254B HIS* 1.3 85.5 - - + +
256B GLY* 1.3 57.1 + - - +
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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