Contacts of the helix formed by residues 252 - 262 (chain X) in PDB entry 3OEF
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 252 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250X ILE* 3.4 4.0 - - - +
251X SER* 1.3 78.0 - - - +
253X GLU* 1.3 59.0 + - - +
254X SER* 2.9 14.9 + - - -
255X ALA* 2.8 34.3 + - - +
256X ARG* 3.0 30.8 + - - +
1100X BOG 4.7 2.0 + - - -
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Residues in contact with GLU 253 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251X SER 3.3 6.2 + - - +
252X SER* 1.3 71.4 - - - +
254X SER* 1.3 58.5 + - - +
256X ARG* 3.1 18.1 + - - +
257X ASN* 2.8 48.2 + - - +
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Residues in contact with SER 254 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252X SER* 2.9 14.8 + - - -
253X GLU* 1.3 79.1 - - - +
255X ALA* 1.3 51.6 + - - +
257X ASN* 3.2 11.6 + - - +
258X TYR* 2.7 36.0 + - - +
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Residues in contact with ALA 255 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250X ILE* 4.4 4.9 - - + -
252X SER* 2.8 29.8 + - - +
254X SER* 1.3 76.0 + - - +
256X ARG* 1.3 57.9 + - - +
258X TYR* 3.2 7.5 + - - +
259X ILE* 2.8 37.2 + - - +
1100X BOG 4.0 32.8 - - + -
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Residues in contact with ARG 256 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247X LEU* 2.9 63.9 + - + +
248X LYS* 3.6 14.8 + - - +
250X ILE* 3.4 26.6 + - + -
251X SER 5.2 1.6 + - - -
252X SER 3.0 17.9 + - - +
253X GLU* 3.5 19.0 + - - +
255X ALA* 1.3 76.8 - - - +
257X ASN* 1.3 62.3 + - - +
259X ILE* 3.7 9.6 + - - +
260X GLN* 2.9 36.9 + - - +
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Residues in contact with ASN 257 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253X GLU* 2.8 37.4 + - - +
254X SER* 3.4 11.7 - - - +
256X ARG* 1.3 77.2 - - - +
258X TYR* 1.3 62.1 + - - +
260X GLN* 3.2 20.1 + - - +
261X SER* 3.1 21.8 + - - -
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Residues in contact with TYR 258 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X ILE* 3.8 22.2 - - + +
254X SER 2.7 20.6 + - - +
255X ALA* 3.2 7.8 + - - +
257X ASN* 1.3 69.7 - - - +
259X ILE* 1.3 65.6 + - + +
261X SER* 2.8 29.3 + - - -
262X LEU* 3.5 30.4 + - + +
1100X BOG 3.9 26.0 - - + -
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Residues in contact with ILE 259 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236X LEU* 4.5 8.8 - - + +
241X THR* 5.7 0.2 - - - -
242X PRO* 3.3 42.6 - - + -
247X LEU* 4.0 16.6 - - + -
250X ILE* 4.6 9.0 - - + -
255X ALA 2.8 22.2 + - - +
256X ARG* 3.8 8.3 - - - +
258X TYR* 1.3 73.2 - - - +
260X GLN* 1.3 70.2 + - + +
261X SER 3.1 0.9 + - - -
262X LEU* 3.2 10.7 + - - +
263X THR* 3.1 22.4 - - + -
1000X BOG 5.1 6.3 - - + -
1100X BOG 3.6 42.0 - - + -
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Residues in contact with GLN 260 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241X THR* 6.1 1.8 - - - -
247X LEU* 5.8 11.9 - - + +
256X ARG* 2.9 38.7 + - - +
257X ASN* 3.2 21.7 + - - +
259X ILE* 1.3 81.3 - - + +
261X SER* 1.3 58.8 + - - +
262X LEU 3.4 0.2 - - - -
263X THR* 3.3 26.4 + - + +
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Residues in contact with SER 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257X ASN 3.1 10.0 + - - -
258X TYR* 2.8 30.5 + - - -
259X ILE 3.0 1.0 - - - -
260X GLN* 1.3 76.7 - - - +
262X LEU* 1.3 62.5 + - - +
263X THR 3.2 5.1 + - - -
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Residues in contact with LEU 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229X ILE* 3.9 15.0 - - + -
233X LYS* 4.0 34.3 - - + +
236X LEU* 4.2 17.6 - - + +
237X ARG* 5.1 9.7 + - - +
258X TYR* 3.6 35.0 - - + +
259X ILE* 3.2 6.3 + - - +
261X SER* 1.3 81.4 - - - +
263X THR* 1.3 58.7 + - - +
1100X BOG 3.4 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