Contacts of the helix formed by residues 252 - 265 (chain f) in PDB entry 5T0J
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 ALA 252 (chain f).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247f GLY 4.9 2.2 - - - +
249f LEU 3.6 1.6 + - - +
250f SER* 3.1 18.2 + - - +
251f ALA* 1.3 77.2 - - - +
253f ALA* 1.3 62.8 + - - +
256f GLY* 3.1 22.7 + - - -
333f SER* 4.1 8.9 - - - -
334f ASN* 3.7 22.2 - - + +
335f ARG* 5.8 0.9 - - - +
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Residues in contact with ALA 253 (chain f).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247f GLY 3.4 22.1 + - - +
248f MET* 4.7 3.6 - - - -
252f ALA* 1.3 78.8 - - - +
254f SER* 1.3 60.5 + - - +
256f GLY* 4.2 2.0 - - - +
257f MET* 2.8 45.8 + - + +
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Residues in contact with SER 254 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222f VAL* 4.0 16.3 + - - +
223f ASN* 3.8 27.9 - - - +
248f MET* 2.4 32.9 + - - +
251f ALA* 3.7 17.4 + - - -
252f ALA 3.3 0.4 - - - +
253f ALA* 1.3 80.3 - - - +
255f LEU* 1.3 64.7 + - - +
257f MET* 4.0 2.5 - - - +
258f ILE* 3.3 26.3 + - - +
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Residues in contact with LEU 255 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222f VAL 6.0 0.2 - - - +
223f ASN 4.1 8.3 - - - +
225f ALA 5.1 7.4 - - - +
226f PHE* 5.7 8.1 - - - +
251f ALA* 3.3 39.6 + - + +
254f SER* 1.3 80.5 - - - +
256f GLY* 1.3 59.1 + - - +
257f MET 3.4 0.2 - - - -
258f ILE* 3.5 24.2 - - + +
259f LEU* 3.2 26.0 + - - +
331f ALA 4.9 3.8 - - - +
332f GLY 3.6 23.1 - - - +
333f SER* 3.8 11.7 - - - +
334f ASN* 4.6 1.1 - - - +
368f VAL* 6.0 5.4 - - + -
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Residues in contact with GLY 256 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252f ALA 3.1 19.8 + - - -
253f ALA* 3.3 2.4 + - - -
254f SER 3.1 0.8 - - - -
255f LEU* 1.3 77.2 - - - +
257f MET* 1.3 69.0 + - - +
259f LEU* 3.7 4.3 + - - +
260f LEU* 3.4 30.0 + - - +
333f SER* 4.4 12.1 - - - -
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Residues in contact with MET 257 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253f ALA* 2.8 30.0 + - + +
254f SER* 4.0 2.9 - - - +
256f GLY* 1.3 83.5 - - - +
258f ILE* 1.3 62.1 + - + +
260f LEU* 3.5 21.2 + - + +
261f TRP* 3.0 26.6 + - - +
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Residues in contact with ILE 258 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223f ASN* 3.3 44.6 - - + +
224f ALA* 5.4 1.3 - - - -
254f SER 3.5 11.2 - - - +
255f LEU* 3.5 30.7 - - + +
257f MET* 1.3 77.2 - - + +
259f LEU* 1.3 63.7 + - + +
261f TRP* 3.5 11.2 - - + +
262f ASP* 3.0 36.7 + - - +
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Residues in contact with LEU 259 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255f LEU 3.2 20.2 + - - +
256f GLY* 4.1 4.9 - - - +
257f MET 3.3 0.2 - - - -
258f ILE* 1.3 77.1 - - + +
260f LEU* 1.3 63.9 + - + +
262f ASP* 3.1 12.1 + - - +
263f VAL* 3.0 34.6 + - + +
298f ASN* 5.2 9.9 - - + +
299f GLU* 3.3 28.0 - - - +
332f GLY* 4.5 24.0 - - - +
333f SER* 5.1 3.1 - - - +
657f TYR* 4.4 31.4 - - + +
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Residues in contact with LEU 260 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256f GLY 3.4 18.6 + - - +
257f MET* 3.5 21.7 + - + +
259f LEU* 1.3 80.1 - - + +
261f TRP* 1.3 59.0 + - - +
263f VAL* 3.3 16.6 + - + +
264f ASP* 2.9 26.9 + - - +
299f GLU* 6.0 1.6 - - - +
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Residues in contact with TRP 261 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257f MET 3.0 18.3 + - - +
258f ILE* 3.5 11.7 - - + +
259f LEU 3.2 0.2 - - - -
260f LEU* 1.3 75.9 - - - +
262f ASP* 1.3 85.5 + - - +
264f ASP* 3.4 18.6 + - - +
265f GLY* 3.0 26.2 + - - -
659f LEU* 3.6 25.4 - - + -
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Residues in contact with ASP 262 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258f ILE* 3.0 20.5 + - - +
259f LEU* 3.1 11.3 + - - +
261f TRP* 1.3 99.4 - - - +
263f VAL* 1.3 55.1 + - - +
265f GLY* 3.5 2.6 - - - +
266f GLY* 2.7 31.5 + - - -
657f TYR* 2.8 48.3 - - + +
658f VAL* 4.9 0.6 - - - -
659f LEU* 4.0 12.2 - - - +
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Residues in contact with VAL 263 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259f LEU* 3.0 20.3 + - + +
260f LEU* 3.3 19.9 + - + +
262f ASP* 1.3 73.2 - - - +
264f ASP* 1.3 67.6 + - - +
266f GLY* 3.2 13.7 + - - -
267f LEU* 3.7 28.4 - - + +
297f ARG* 5.6 4.7 - - - +
657f TYR* 3.9 26.7 - - + +
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Residues in contact with ASP 264 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260f LEU 2.9 15.1 + - - +
261f TRP* 3.4 24.4 + - - +
262f ASP 3.3 0.2 - - - -
263f VAL* 1.3 78.2 - - - +
265f GLY* 1.3 58.6 + - - +
266f GLY 3.1 9.5 + - - +
618f THR* 5.3 1.0 - - - +
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Residues in contact with GLY 265 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261f TRP* 3.0 16.0 + - - -
262f ASP* 3.5 4.3 - - - -
264f ASP* 1.3 77.6 - - - +
266f GLY* 1.3 60.9 + - - +
615f GLY 4.9 1.9 + - - +
618f THR* 3.3 24.2 - - - +
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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