Contacts of the helix formed by residues 240 - 255 (chain B) in PDB entry 5DTI
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 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 1.3 79.1 - - - +
241B ALA* 1.3 59.2 + - - +
242B GLY* 3.7 3.7 + - - -
243B GLU* 3.2 24.6 + - - +
244B ALA* 3.0 28.4 + - - +
302B VAL* 3.8 1.1 - - - -
303B VAL* 4.7 8.1 - - - -
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Residues in contact with ALA 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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162B PRO* 3.4 26.6 - - + +
240B SER* 1.3 74.0 - - - +
242B GLY* 1.3 58.3 + - - +
244B ALA 3.4 0.3 + - - -
245B ARG* 2.9 31.4 + - - +
302B VAL* 3.7 13.4 - - + +
303B VAL 3.9 16.8 + - - +
304B ASP* 5.4 1.3 - - - -
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Residues in contact with GLY 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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240B SER* 3.2 5.4 + - - -
241B ALA* 1.3 80.0 - - - +
243B GLU* 1.3 56.6 + - - +
245B ARG* 3.5 7.5 + - - +
246B ARG* 2.9 27.7 + - - +
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Residues in contact with GLU 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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239B VAL* 4.3 7.6 - - + -
240B SER* 3.2 24.9 + - - +
242B GLY* 1.3 74.1 - - - +
244B ALA* 1.3 62.0 + - - +
246B ARG* 2.8 36.4 + - - +
247B ARG* 2.8 74.6 + - - +
290B PRO* 3.9 10.1 - - - +
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Residues in contact with ALA 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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158B PHE 5.7 1.1 - - - +
160B ALA* 3.5 18.9 + - + +
162B PRO* 4.5 1.3 - - + -
239B VAL* 3.9 14.8 - - + +
240B SER 3.0 17.9 + - - +
241B ALA* 3.7 3.1 - - - +
243B GLU* 1.3 77.4 - - - +
245B ARG* 1.3 56.3 + - - +
247B ARG* 3.3 6.6 + - - +
248B ALA* 2.9 30.8 + - - +
299B PHE* 5.2 2.5 - - - -
300B VAL 5.9 0.2 - - - +
302B VAL* 3.7 23.1 - - + -
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Residues in contact with ARG 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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160B ALA 4.0 9.8 + - - -
161B LEU* 3.5 20.3 - - + +
162B PRO* 2.9 34.1 + - + +
241B ALA 2.9 18.9 + - - +
242B GLY* 3.7 7.6 - - - +
244B ALA* 1.3 76.2 - - - +
246B ARG* 1.3 60.3 + - - +
248B ALA* 3.8 1.3 - - - +
249B THR* 2.6 42.2 + - - +
266B ASP* 2.9 42.8 + - - -
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLY 2.9 17.9 + - - +
243B GLU* 2.8 41.8 + - - +
244B ALA 3.2 0.2 - - - -
245B ARG* 1.3 78.8 - - - +
247B ARG* 1.3 61.3 + - - +
249B THR* 3.3 5.3 + - - -
250B LEU* 2.9 50.9 + - + +
288B VAL 3.3 27.1 + - - -
289B LEU 4.5 1.0 + - - -
290B PRO* 4.0 21.6 - - - +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B VAL* 3.6 30.2 - - - +
243B GLU* 2.8 50.1 + - - +
244B ALA* 3.8 6.7 - - - +
246B ARG* 1.3 81.3 - - - +
248B ALA* 1.3 61.0 + - - +
250B LEU* 3.4 3.1 + - - +
251B LEU* 2.9 29.5 + - - +
288B VAL* 3.9 29.3 - - + +
289B LEU* 4.2 10.1 - - - +
290B PRO* 3.7 18.6 - - - +
296B ARG* 6.2 2.0 - - - +
297B PHE 3.1 19.2 + - - -
298B SER* 2.8 39.2 + - - +
299B PHE* 3.9 9.8 - - + -
300B VAL* 4.8 0.2 - - - +
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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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159B LEU* 3.9 31.8 - - + +
160B ALA 3.2 27.6 - - - +
161B LEU* 4.1 14.8 - - + -
244B ALA 2.9 9.4 + - - +
245B ARG 3.8 2.9 - - - +
247B ARG* 1.3 75.8 - - - +
249B THR* 1.3 58.3 + - - +
251B LEU* 3.3 2.8 + - - +
252B ALA* 2.9 29.2 + - - +
269B LEU* 4.9 2.6 - - + +
273B LEU* 4.9 0.2 - - - +
299B PHE* 4.2 3.1 - - + -
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Residues in contact with THR 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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161B LEU* 4.1 8.3 - - - +
245B ARG* 2.6 34.1 + - - +
246B ARG* 3.7 5.3 - - - -
248B ALA* 1.3 76.4 - - - +
250B LEU* 1.3 57.5 + - - +
252B ALA* 3.4 6.6 + - - +
253B ARG* 2.9 27.3 + - + +
257B CYS 4.9 0.3 - - - +
269B LEU* 4.5 18.0 - - + +
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Residues in contact with LEU 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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246B ARG* 2.9 40.5 + - + +
247B ARG* 3.8 5.6 - - - +
249B THR* 1.3 75.2 - - - +
251B LEU* 1.3 58.5 + - - +
253B ARG* 3.2 24.0 + - - +
254B LEU* 2.9 48.8 + - + +
287B HIS 4.0 6.5 - - - +
288B VAL* 3.8 31.6 - - + -
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Residues in contact with LEU 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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155B THR* 3.7 16.2 - - + -
159B LEU* 3.6 25.8 - - + -
247B ARG 2.9 17.8 + - - +
248B ALA 3.7 2.9 - - - +
250B LEU* 1.3 76.2 - - - +
252B ALA* 1.3 63.3 + - - +
254B LEU* 3.1 14.2 + - - +
255B VAL* 3.2 14.0 + - + +
273B LEU* 4.6 4.3 - - + -
281B LEU* 3.9 28.5 - - + +
284B HIS* 3.5 43.1 - - + +
285B GLU* 3.8 11.7 - - + +
288B VAL* 3.9 7.4 - - + +
299B PHE* 4.0 8.7 - - + -
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Residues in contact with ALA 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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248B ALA 2.9 14.7 + - - +
249B THR 3.4 9.2 - - - +
251B LEU* 1.3 77.1 - - - +
253B ARG* 1.3 57.7 + - - +
255B VAL* 3.2 9.7 + - - +
257B CYS* 2.7 44.0 + - + +
269B LEU* 3.7 31.2 - - + -
273B LEU* 3.9 16.8 - - + -
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Residues in contact with ARG 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 THR* 2.9 15.0 + - + +
250B LEU* 3.4 23.5 - - - +
252B ALA* 1.3 76.5 - - - +
254B LEU* 1.3 78.5 + - - +
256B GLY* 3.1 14.0 + - - -
257B CYS 3.3 10.0 + - - +
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Residues in contact with LEU 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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250B LEU* 2.9 32.9 + - + +
251B LEU* 3.1 8.0 + - - +
253B ARG* 1.3 87.6 - - - +
255B VAL* 1.3 58.1 + - - +
256B GLY 3.4 1.0 + - - -
284B HIS* 3.7 46.7 + - + +
287B HIS* 3.8 32.1 - - + +
288B VAL* 4.2 12.8 - - + -
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Residues in contact with VAL 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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251B LEU* 3.2 13.4 + - + +
252B ALA 3.3 11.9 - - - +
254B LEU* 1.3 76.2 - - - +
256B GLY* 1.3 56.4 + - - +
257B CYS* 4.1 6.1 - - - -
273B LEU* 3.8 24.7 - - + -
276B ARG* 2.8 43.0 + - + +
280B ASP* 4.2 17.0 - - + +
281B LEU* 4.3 15.7 - - + +
284B HIS* 3.7 30.3 - - + +
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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