Contacts of the helix formed by residues 240 - 255 (chain B) in PDB entry 4YP9
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 THR 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B GLN 5.2 10.1 - - - +
77B GLN* 6.5 0.2 - - + -
109B PRO* 6.3 3.8 - - + -
238B LYS* 3.2 11.8 + - + +
239B ALA* 1.3 84.6 - - + +
241B LYS* 1.3 60.4 + - - +
242B GLN* 4.1 6.9 + - - +
243B SER* 3.0 22.2 + - - -
244B GLY* 2.8 25.5 + - - -
267B ASP* 4.1 9.0 - - - +
268B VAL* 4.6 2.8 - - - +
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Residues in contact with LYS 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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94A TYR* 4.6 18.6 - - + +
98A ILE 5.5 3.2 + - - -
99A ASN* 5.1 7.3 + - - +
100A TYR* 5.3 11.1 - - - +
78B VAL* 3.9 24.9 - - + -
240B THR* 1.3 73.1 - - - +
242B GLN* 1.3 58.9 + - - +
244B GLY 3.1 1.4 + - - -
245B TYR* 2.9 25.7 + - - +
267B ASP* 3.4 26.5 + - + +
270B LEU* 4.2 11.7 - - + -
271B GLY* 3.3 26.2 - - - +
274B ASP* 3.2 27.4 + - - -
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Residues in contact with GLN 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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90A GLU* 5.5 2.4 + - - +
100A TYR* 3.6 17.2 + - - -
101A GLN* 3.4 29.3 + - - +
102A LEU* 3.0 49.4 + - - +
240B THR* 3.2 8.1 + - - +
241B LYS* 1.3 79.4 - - - +
243B SER* 1.3 58.4 + - - +
245B TYR* 3.3 7.7 + - - +
246B ASP* 2.9 39.3 + - - +
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Residues in contact with SER 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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237B THR* 3.5 7.7 - - - -
238B LYS* 2.8 46.5 + - - +
240B THR* 3.0 24.6 + - - -
242B GLN* 1.3 75.7 - - - +
244B GLY* 1.3 60.8 + - - +
246B ASP* 3.8 8.9 - - - +
247B ALA* 2.9 31.9 + - - +
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Residues in contact with GLY 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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204B LEU* 4.1 3.3 - - - +
237B THR* 4.2 5.3 - - - +
240B THR 2.8 14.2 + - - -
241B LYS 3.1 4.2 + - - -
243B SER* 1.3 76.6 - - - +
245B TYR* 1.3 54.9 + - - +
247B ALA* 3.7 0.9 - - - +
248B ALA* 2.8 31.9 + - - +
268B VAL* 3.8 30.7 - - - -
272B ALA 4.0 8.0 + - - -
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Residues in contact with TYR 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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66A PRO* 4.4 12.2 - - + +
101A GLN* 3.1 27.0 + - - +
241B LYS* 2.9 12.8 + - + +
242B GLN* 3.4 10.1 - - - +
244B GLY* 1.3 72.5 - - - +
246B ASP* 1.3 82.5 + - - +
248B ALA* 3.3 2.9 + - - +
249B LYS* 3.0 45.2 + - + +
271B GLY* 3.6 18.4 - - - +
274B ASP* 4.3 11.0 - - + -
275B ALA* 3.9 29.8 - - + +
278B GLU* 2.4 39.9 + - - -
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Residues in contact with ASP 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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101A GLN* 3.7 13.2 + - - -
242B GLN* 2.9 34.0 + - - +
243B SER* 3.8 7.4 - - - +
245B TYR* 1.3 92.9 - - - +
247B ALA* 1.3 57.7 + - - +
249B LYS* 3.3 6.9 + - - +
250B ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 247 (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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204B LEU* 3.9 14.1 - - + +
235B TYR* 4.7 13.6 - - + -
236B TYR 4.8 2.9 - - - +
237B THR* 3.7 22.4 - - + -
243B SER 2.9 18.1 + - - +
244B GLY 3.7 2.9 - - - +
246B ASP* 1.3 74.9 - - - +
248B ALA* 1.3 61.6 + - - +
250B ALA* 3.8 6.2 - - - +
251B SER* 2.9 31.5 + - - -
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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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204B LEU* 4.1 10.6 - - + +
244B GLY 2.8 18.5 + - - +
245B TYR 3.5 0.2 - - - +
247B ALA* 1.3 76.1 - - - +
249B LYS* 1.3 64.1 + - - +
251B SER* 3.2 4.1 + - - -
252B LEU* 2.9 33.6 + - + +
261B ILE* 5.0 9.6 - - + -
272B ALA* 3.9 18.2 - - + +
275B ALA* 3.5 24.5 - - + -
276B LEU* 5.8 0.7 - - + -
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Residues in contact with LYS 249 (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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245B TYR* 3.0 44.5 + - + +
246B ASP* 3.3 8.0 + - - +
248B ALA* 1.3 76.6 - - - +
250B ALA* 1.3 58.3 + - - +
252B LEU* 3.3 1.4 + - - +
253B ALA* 2.8 32.3 + - - +
275B ALA* 4.3 13.5 - - + -
278B GLU* 3.5 21.3 + - - +
279B LEU* 4.5 30.0 - - + +
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Residues in contact with ALA 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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235B TYR* 4.9 12.8 - - + -
246B ASP 2.9 17.0 + - - +
247B ALA* 3.8 7.4 - - - +
249B LYS* 1.3 76.5 - - - +
251B SER* 1.3 63.4 + - - +
253B ALA* 3.1 9.5 + - - +
254B LYS* 2.9 23.4 + - - +
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Residues in contact with SER 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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202B SER* 3.3 16.4 + - - -
204B LEU* 4.8 6.0 - - - +
233B SER* 3.0 23.4 + - - -
235B TYR* 3.5 23.7 - - - -
247B ALA 2.9 19.4 + - - -
248B ALA* 3.5 6.1 - - - -
250B ALA* 1.3 75.6 - - - +
252B LEU* 1.3 57.3 + - - +
254B LYS* 3.0 3.5 + - - +
255B HIS* 2.6 37.3 + - - +
261B ILE* 5.6 2.9 - - - -
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Residues in contact with LEU 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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202B SER* 6.3 0.4 - - - -
248B ALA* 2.9 24.0 + - + +
249B LYS 4.0 2.2 - - - +
251B SER* 1.3 75.8 - - - +
253B ALA* 1.3 61.1 + - - +
255B HIS 3.5 14.8 - - - +
256B PRO* 3.3 26.6 - - + +
258B VAL* 4.1 12.1 - - + -
261B ILE* 4.1 13.0 - - + -
276B LEU* 3.7 26.2 - - + +
279B LEU* 3.5 31.4 - - + -
281B ARG* 4.4 12.1 - - + +
284B ILE* 3.4 27.1 - - + -
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Residues in contact with ALA 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 LYS 2.8 13.9 + - - +
250B ALA* 3.2 14.1 - - - +
252B LEU* 1.3 80.1 - - - +
254B LYS* 1.3 61.4 + - - +
256B PRO* 4.2 5.4 - - - +
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Residues in contact with LYS 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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233B SER* 5.5 0.4 - - - -
235B TYR* 3.3 26.9 - - - +
250B ALA 2.9 14.1 + - - +
251B SER 3.8 1.3 - - - +
253B ALA* 1.3 80.0 - - - +
255B HIS* 1.3 83.6 + - + +
256B PRO* 3.8 4.9 - - - +
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Residues in contact with HIS 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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202B SER* 4.8 0.4 - - - +
232B GLN* 3.4 49.9 + - + +
233B SER* 4.0 18.0 - - - +
251B SER* 2.6 18.8 + - - +
252B LEU* 3.5 10.9 - - - +
254B LYS* 1.3 109.8 + - + +
256B PRO* 1.3 63.8 - - - +
257B ASP 3.2 3.8 - - - +
258B VAL* 3.9 14.9 - - + +
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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