Contacts of the helix formed by residues 271 - 281 (chain B) in PDB entry 2OUC
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 GLY 271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASN* 3.3 11.3 - - - +
240B THR 2.7 18.3 + - - -
241B ASN* 3.7 18.6 - - - -
270B LYS* 1.3 75.1 - - - +
272B GLY* 1.3 68.6 + - - +
274B SER* 3.3 21.0 + - - -
275B SER* 3.3 14.9 - - - -
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Residues in contact with GLY 272 (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 ASP* 3.2 20.6 - - - -
239B ASN* 4.1 5.6 - - - -
240B THR 3.4 2.0 + - - -
269B LEU* 2.8 38.0 + - - +
270B LYS 3.3 1.0 - - - -
271B GLY* 1.3 83.0 - - - +
273B LEU* 1.3 61.7 + - - -
275B SER* 3.9 0.9 - - - -
276B PHE 3.2 13.3 + - - -
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Residues in contact with LEU 273 (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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178B ARG* 3.5 38.1 - - - +
186B SER* 4.0 20.4 - - - +
187B HIS* 4.5 1.1 - - - -
188B ILE* 4.0 21.5 - - + +
236B TYR* 4.1 11.1 - - + -
237B ASP 3.0 15.3 + - - +
238B GLU* 3.5 12.3 + - - +
269B LEU* 4.8 0.2 - - - -
272B GLY* 1.3 67.7 - - - -
274B SER* 1.3 60.7 + - - +
275B SER 3.1 2.2 - - - -
276B PHE* 2.9 7.1 + - + -
277B LYS* 2.8 46.7 + - + +
284B CYS* 3.8 26.7 - - - -
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Residues in contact with SER 274 (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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238B GLU* 3.1 21.5 + - - -
239B ASN* 3.7 10.9 - - - +
271B GLY 3.3 10.4 + - - -
273B LEU* 1.3 75.3 - - - +
275B SER* 1.3 60.8 + - - +
277B LYS* 3.3 32.4 - - - +
278B GLN* 3.0 27.4 + - - +
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Residues in contact with SER 275 (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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152B PRO* 3.4 25.9 - - - +
241B ASN* 5.8 0.2 - - - -
270B LYS 3.7 4.7 + - - -
271B GLY* 3.3 31.2 + - - -
272B GLY 3.9 0.9 - - - -
273B LEU 3.1 0.4 - - - -
274B SER* 1.3 78.9 + - - +
276B PHE* 1.3 61.9 + - - +
278B GLN* 3.3 28.7 + - - +
279B ASN* 4.8 2.3 + - - -
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Residues in contact with PHE 276 (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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152B PRO* 3.6 39.0 - - + -
155B LEU* 3.6 23.3 - - + -
156B ALA 4.4 1.8 - - - -
159B MET* 3.9 15.3 - - - -
188B ILE* 3.7 28.9 - - + -
269B LEU* 4.0 8.3 - - + -
272B GLY 3.2 14.0 + - - +
273B LEU* 2.9 9.9 + - + +
275B SER* 1.3 76.2 - - - +
277B LYS* 1.3 57.6 + - - +
278B GLN 3.0 5.3 + - - -
279B ASN 3.5 1.7 + - - -
280B HIS* 3.0 51.4 + + + +
283B LEU* 3.8 29.6 - - + -
284B CYS* 3.9 12.3 - - - -
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Residues in contact with LYS 277 (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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238B GLU* 4.1 13.1 + - - -
273B LEU* 2.8 35.2 + - + +
274B SER* 3.3 33.2 - - - +
276B PHE* 1.3 72.2 - - - +
278B GLN* 1.3 66.1 + - + +
279B ASN 3.4 0.4 + - - -
280B HIS 4.5 0.7 - - - -
281B GLU* 3.4 46.1 - - - +
284B CYS* 4.6 5.4 - - - -
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Residues in contact with GLN 278 (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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153A ASN* 3.5 7.3 - - - +
274B SER* 3.0 25.5 + - - +
275B SER* 3.3 26.3 - - - +
276B PHE 3.0 1.0 - - - -
277B LYS* 1.3 81.3 - - + +
279B ASN* 1.3 75.0 + - - +
281B GLU* 5.7 0.2 - - - +
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Residues in contact with ASN 279 (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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153A ASN* 3.0 26.6 + - - +
279A ASN* 3.1 45.9 + - + +
280A HIS* 3.1 25.3 + - - -
153B ASN* 5.2 1.6 + - - +
275B SER 4.8 1.6 + - - -
276B PHE 3.5 2.0 + - - -
278B GLN* 1.3 87.7 + - - +
280B HIS* 1.3 69.2 + - + +
281B GLU 3.5 3.7 + - - -
282B ASN* 3.3 1.7 - - - +
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Residues in contact with HIS 280 (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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279A ASN* 2.8 27.7 - - + +
280A HIS* 3.7 15.8 + + - -
282A ASN* 4.1 4.6 + - - -
152B PRO* 3.7 24.5 - - + -
153B ASN* 2.6 26.6 + - - -
156B ALA* 3.4 27.6 - - + +
276B PHE* 3.0 38.3 + + + +
277B LYS* 4.5 0.2 - - - -
279B ASN* 1.3 83.4 - - + +
281B GLU* 1.3 51.8 + - - +
282B ASN* 2.7 15.1 + - - +
283B LEU* 2.7 33.0 + - + +
284B CYS* 3.9 1.2 + - - -
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Residues in contact with GLU 281 (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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153A ASN* 6.2 1.5 - - + +
157A LYS* 3.4 36.3 - - + +
186B SER* 4.9 1.0 + - - -
277B LYS* 3.4 43.8 + - - +
278B GLN 5.7 0.2 - - - +
279B ASN 3.5 3.5 + - - -
280B HIS* 1.3 76.8 - - - +
282B ASN* 1.3 56.4 + - - +
283B LEU 3.0 5.2 + - - -
284B CYS* 3.1 25.0 + - - +
286B ASN* 3.1 33.9 + - - +
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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