Contacts of the helix formed by residues 240 - 255 (chain D) in PDB entry 1C2O
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239D VAL* 1.3 79.7 - - - +
241D ALA* 1.3 65.2 + - - +
242D GLY* 3.8 4.4 + - - -
243D GLU* 3.3 22.8 + - - +
244D ALA* 3.0 21.8 + - - +
302D VAL* 3.8 2.2 - - - -
303D VAL* 4.7 8.3 - - - +
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Residues in contact with ALA 241 (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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162D PRO* 3.6 33.8 - - + +
240D SER* 1.3 72.0 - - - +
242D GLY* 1.3 57.0 + - - +
244D ALA* 2.8 4.5 + - - +
245D ARG* 2.7 32.7 + - - +
302D VAL* 3.8 10.0 - - + +
303D VAL 4.2 13.2 + - - +
304D ASP* 5.7 1.1 - - - -
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Residues in contact with GLY 242 (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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240D SER* 3.4 5.8 + - - -
241D ALA* 1.3 79.2 - - - +
243D GLU* 1.3 56.9 + - - +
245D ARG* 3.4 7.3 + - - +
246D ARG* 2.9 28.1 + - - +
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Residues in contact with GLU 243 (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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239D VAL* 4.4 6.5 - - + -
240D SER* 3.3 25.6 + - - +
241D ALA 3.2 0.6 - - - -
242D GLY* 1.3 72.7 - - - +
244D ALA* 1.3 59.5 - - - +
246D ARG* 2.6 46.3 + - - +
247D ARG* 2.5 83.5 + - - +
290D PRO* 3.8 7.6 - - - +
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Residues in contact with ALA 244 (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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160D ALA* 3.8 19.0 - - + +
162D PRO* 4.1 4.0 - - + -
239D VAL* 4.1 10.3 - - + +
240D SER 3.0 14.4 + - - +
241D ALA* 2.8 9.8 + - - +
243D GLU* 1.3 74.1 - - - +
245D ARG* 1.3 69.5 + - - +
247D ARG* 2.8 8.3 + - - +
248D ALA* 2.7 22.9 + - - +
299D PHE* 5.0 3.8 - - - -
302D VAL* 3.8 21.3 - - + -
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Residues in contact with ARG 245 (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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160D ALA 3.9 9.8 + - - -
161D LEU* 3.2 37.4 - - - +
162D PRO* 4.1 14.1 - - + +
241D ALA 2.7 14.5 + - - +
242D GLY* 3.5 11.9 - - - +
244D ALA* 1.3 73.4 - - - +
246D ARG* 1.3 65.6 + - - +
248D ALA* 2.8 13.6 + - - -
249D THR* 3.0 35.1 + - + +
264D GLY* 6.2 1.4 - - - -
266D ASP* 3.1 25.8 + - - -
269D LEU* 5.5 0.4 - - - +
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Residues in contact with ARG 246 (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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242D GLY 2.9 18.1 + - - +
243D GLU* 2.6 54.3 + - - +
245D ARG* 1.3 77.8 - - - +
247D ARG* 1.4 65.9 + - - +
249D THR* 3.3 5.5 + - - -
250D LEU* 3.1 51.7 + - + +
288D VAL 2.8 30.9 + - - -
289D LEU 4.0 6.5 + - - -
290D PRO* 3.5 20.1 - - - +
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Residues in contact with ARG 247 (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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239D VAL* 3.9 21.6 - - - +
243D GLU* 2.5 53.0 + - - +
244D ALA* 2.8 6.0 + - - +
246D ARG* 1.4 90.3 - - - +
248D ALA* 1.3 62.2 + - - +
250D LEU* 3.9 0.9 - - - +
251D LEU* 3.0 27.9 + - - +
288D VAL* 3.4 29.9 - - + +
289D LEU* 3.5 16.0 - - - +
290D PRO* 3.6 19.8 - - - +
296D ARG* 5.6 4.6 - - - +
297D PHE 3.0 26.3 + - - -
298D SER 3.0 25.2 + - - -
299D PHE* 3.5 11.3 - - + -
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Residues in contact with ALA 248 (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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159D LEU* 4.0 17.3 - - + +
160D ALA 3.4 26.9 - - - +
161D LEU* 3.6 21.5 - - + -
244D ALA 2.7 12.2 + - - +
245D ARG* 2.8 5.4 + - - +
247D ARG* 1.3 70.1 - - - +
249D THR* 1.3 56.0 + - - +
251D LEU* 2.9 5.2 + - - +
252D ALA* 2.6 36.4 + - - +
269D LEU* 5.6 0.4 - - - -
273D LEU* 5.6 0.4 - - - -
299D PHE* 4.3 8.4 - - - -
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Residues in contact with THR 249 (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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161D LEU* 5.0 0.6 - - + +
245D ARG* 3.4 43.8 + - + +
246D ARG* 3.3 11.3 + - - -
248D ALA* 1.3 79.8 - - + +
250D LEU* 1.3 76.6 + - - +
252D ALA* 3.0 8.9 + - - +
253D ARG* 2.7 44.8 + - - +
269D LEU* 4.3 18.6 - - + -
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Residues in contact with LEU 250 (chain D).
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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246D ARG* 3.1 43.5 + - + +
249D THR* 1.3 84.7 + - - +
251D LEU* 1.3 65.6 + - - +
253D ARG* 3.2 30.9 + - + +
254D LEU* 2.9 36.4 + - + +
287D HIS 3.8 11.2 - - - +
288D VAL* 3.6 23.1 - - + -
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Residues in contact with LEU 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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155D THR* 3.9 18.4 - - + -
159D LEU* 4.0 10.5 - - + -
247D ARG 3.0 19.7 + - - +
248D ALA* 2.9 3.9 + - - +
250D LEU* 1.3 75.7 - - - +
252D ALA* 1.3 69.9 + - - +
254D LEU* 3.1 14.8 + - - +
255D VAL* 3.3 9.6 + - + +
273D LEU* 4.1 3.4 - - + -
281D LEU* 3.6 36.1 - - + +
284D HIS* 3.5 42.8 - - + +
285D GLU* 3.7 8.7 - - - +
288D VAL* 3.6 9.1 - - + +
299D PHE* 4.2 13.0 - - + -
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Residues in contact with ALA 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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248D ALA 2.6 16.7 + - - +
249D THR* 3.4 7.9 - - - +
251D LEU* 1.3 74.2 - - - +
253D ARG* 1.3 54.0 + - - +
255D VAL* 2.7 26.6 + - - +
257D CYS* 2.9 30.5 + - + +
269D LEU* 3.2 29.6 - - + -
273D LEU* 3.8 21.3 - - + -
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Residues in contact with ARG 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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305C GLY 5.6 0.7 - - - +
309C SER* 3.9 17.4 - - - +
249D THR* 2.7 38.2 + - - +
250D LEU* 3.4 42.4 - - + +
252D ALA* 1.3 71.9 - - - +
254D LEU* 1.3 64.4 + - + +
256D GLY* 2.9 14.9 + - - -
257D CYS 3.0 11.3 + - - +
258D PRO* 5.3 6.7 - - + +
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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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216C LEU* 4.9 4.2 - - - +
309C SER* 3.9 22.3 + - - +
310C ASP* 5.3 12.3 - - + +
315C LEU* 5.6 5.8 - - + -
318C THR* 5.9 2.5 - - - +
250D LEU* 2.9 39.4 + - + +
251D LEU* 3.1 7.8 + - - +
253D ARG* 1.3 75.5 - - + +
255D VAL* 1.3 57.9 + - - +
256D GLY 3.3 1.1 + - - -
284D HIS* 3.7 50.3 + - + +
287D HIS* 3.9 23.6 - - + +
288D VAL* 4.8 3.6 - - + -
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Residues in contact with VAL 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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216C LEU* 4.8 8.8 - - + +
309C SER* 5.5 0.2 - - - -
251D LEU* 3.6 7.4 - - + +
252D ALA 2.7 17.4 + - - +
254D LEU* 1.3 73.4 - - - +
256D GLY* 1.3 56.9 + - - +
257D CYS* 4.0 4.0 - - - +
273D LEU* 4.0 20.2 - - + -
276D ARG* 2.8 51.8 + - + +
280D ASP* 3.8 42.0 - - + +
281D LEU* 4.1 9.6 - - + -
284D HIS* 4.2 10.5 - - + -
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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