Contacts of the helix formed by residues 250 - 261 (chain D) in PDB entry 6CAJ
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 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D ILE* 5.1 5.2 - - - +
219D ASP* 5.3 4.5 - - - -
222D ILE* 4.3 10.1 - - - +
249D THR* 1.3 78.6 + - - +
251D THR* 1.3 61.2 + - - +
252D HIS 3.4 2.7 - - - -
253D THR* 3.5 14.7 - - - -
254D LEU* 3.4 16.6 + - - +
314D ASP* 2.9 7.7 + - - +
388E ILE* 6.4 0.7 - - - -
389E PRO* 3.5 22.7 + - - +
392E SER* 6.0 0.9 - - - -
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Residues in contact with THR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ILE* 3.7 21.3 - - - +
234D ILE* 3.3 28.7 - - + +
245D LEU* 5.0 0.2 - - + -
247D ALA* 3.7 18.4 - - + -
248D VAL 3.3 18.4 - - - +
249D THR 3.4 2.0 - - - -
250D GLY* 1.3 75.1 - - - +
252D HIS* 1.3 63.1 + - - +
253D THR 3.2 0.7 - - - -
254D LEU* 3.6 9.1 - - - +
255D ALA* 2.9 27.2 + - - +
265D LEU* 5.6 0.2 - - - +
314D ASP* 2.9 14.8 + - - +
316D VAL* 3.8 13.3 - - + +
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Residues in contact with HIS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D THR* 1.3 78.2 - - - +
253D THR* 1.3 56.8 + - - +
255D ALA* 3.3 3.3 + - - +
256D LEU* 2.9 52.5 + - + +
314D ASP* 2.9 15.5 + - + +
315D TYR* 3.0 27.3 + + - +
316D VAL* 3.8 8.4 - - + -
317D PRO* 3.5 31.3 - - + +
320D LEU* 3.6 16.3 - - + +
392E SER* 3.1 27.8 - - - +
429E ALA* 5.7 0.2 - - - +
430E HIS* 4.2 15.8 + + - -
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Residues in contact with THR 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ILE* 4.8 4.5 - - + -
250D GLY* 3.5 17.4 + - - -
251D THR 3.2 0.2 - - - -
252D HIS* 1.3 78.8 - - - +
254D LEU* 1.3 56.7 + - - +
256D LEU* 3.3 4.2 + - - +
257D ALA* 2.9 29.2 + - + +
388E ILE* 4.8 8.3 + - + +
389E PRO* 5.5 0.2 - - - +
392E SER* 3.9 17.8 + - - -
422E GLN* 3.4 43.1 - - + +
425E LEU* 5.7 0.2 - - - +
426E VAL* 3.7 26.9 - - + +
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Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D MET* 3.7 32.5 - - + +
167D THR 4.7 8.3 - - - +
168D ILE* 4.3 17.7 - - + -
222D ILE* 3.8 23.5 - - + +
226D MET* 4.0 12.6 - - - -
232D VAL* 3.7 31.4 - - + -
234D ILE* 3.8 17.3 - - + -
250D GLY 3.4 5.3 + - - +
251D THR* 3.4 16.5 + - - +
252D HIS 3.3 0.2 - - - -
253D THR* 1.3 78.4 - - - +
255D ALA* 1.3 57.0 + - - +
257D ALA* 3.5 0.9 + - - -
258D ALA* 2.9 30.3 + - - +
265D LEU* 5.3 0.4 - - - -
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Residues in contact with ALA 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ILE* 6.3 0.4 - - + -
251D THR 2.9 17.4 + - - +
252D HIS 3.6 6.3 - - - +
254D LEU* 1.3 75.9 - - - +
256D LEU* 1.3 59.3 + - - +
258D ALA* 3.4 1.4 + - - +
259D LYS* 2.9 29.6 + - - +
265D LEU* 3.9 24.4 - - + +
316D VAL* 4.2 11.2 - - + -
320D LEU* 3.8 31.9 - - + +
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Residues in contact with LEU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D HIS* 2.9 47.2 + - + +
253D THR* 3.3 4.2 + - - +
255D ALA* 1.3 73.7 - - - +
257D ALA* 1.3 60.4 + - - +
259D LYS* 3.3 5.5 + - + +
260D HIS* 2.9 28.1 + - - +
320D LEU* 3.8 23.8 - - + -
425E LEU* 4.1 10.1 - - + +
426E VAL* 3.9 28.7 - - + -
429E ALA* 3.7 33.4 - - + -
430E HIS* 5.1 0.4 - - - +
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Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D ILE* 4.6 4.5 - - + -
223D PHE* 3.8 24.0 - - + -
226D MET* 3.8 22.4 - - + -
253D THR* 2.9 18.9 + - + +
254D LEU* 3.9 5.8 - - - +
256D LEU* 1.3 75.7 - - - +
258D ALA* 1.3 58.4 + - - +
260D HIS* 3.4 1.1 + - - +
261D HIS* 2.9 34.3 + - - +
425E LEU* 3.9 12.7 - - + +
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Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D MET* 3.7 12.7 - - + +
232D VAL* 3.8 7.2 - - + -
254D LEU 2.9 18.4 + - - +
255D ALA 3.8 1.1 - - - +
257D ALA* 1.3 76.3 - - - +
259D LYS* 1.3 59.0 + - - +
262D SER* 2.8 24.0 + - - +
263D THR* 2.8 35.0 + - - +
265D LEU* 3.7 24.9 - - + -
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Residues in contact with LYS 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ALA 2.9 17.7 + - - +
256D LEU* 3.3 5.6 + - + +
258D ALA* 1.3 73.0 - - - +
260D HIS* 1.3 65.9 + - - +
262D SER* 3.6 13.5 + - - +
263D THR 5.4 0.7 - - - -
265D LEU* 5.0 2.1 - - + +
319D GLU* 4.2 18.8 + - - +
320D LEU* 3.7 27.4 - - + +
495F GLU* 4.2 23.0 + - - +
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Residues in contact with HIS 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C HIS 3.8 7.1 - - - +
262C SER* 2.3 57.1 + - - -
223D PHE* 3.8 24.3 - + + -
256D LEU 2.9 17.2 + - - +
257D ALA 3.5 5.4 - - - +
258D ALA 3.3 0.2 - - - -
259D LYS* 1.3 79.9 - - - +
261D HIS* 1.3 58.5 + + - +
262D SER 3.5 0.5 + - - -
425E LEU* 3.6 34.5 - - + +
493E PRO* 5.0 8.5 - - + -
495E GLU* 4.9 10.6 + - - +
496E LEU* 4.9 9.3 - - + +
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Residues in contact with HIS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C HIS* 3.5 25.3 + - - +
262C SER* 3.4 30.5 + - - -
263C THR* 5.7 0.8 - - - +
223D PHE* 3.3 34.1 + + - -
226D MET* 3.5 33.0 - - + +
227D SER* 4.0 30.1 + - - -
257D ALA 2.9 25.2 + - - +
258D ALA* 3.5 1.3 - - - +
260D HIS* 1.3 77.2 - + - +
262D SER* 1.3 68.1 + - - +
263D THR* 3.3 15.0 + - + +
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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