Contacts of the helix formed by residues 236 - 251 (chain D) in PDB entry 6V3O
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 THR 236 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D GLN* 4.5 6.5 - - + +
235D PRO* 1.3 76.9 - - - +
237D PRO* 1.3 74.0 - - - +
238D GLN* 3.5 12.8 + - - +
239D ASP* 3.2 33.5 + - - +
240D GLU* 3.0 20.4 + - - +
298D ARG* 3.8 3.1 - - - +
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Residues in contact with PRO 237 (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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236D THR* 1.3 89.5 - - - +
238D GLN* 1.3 66.0 + - - +
240D GLU* 3.4 21.6 + - + +
241D MET* 3.4 14.7 + - - +
289D MET* 5.1 0.3 - - - +
290D GLY* 5.0 10.2 + - - +
298D ARG* 3.7 52.2 - - + +
299D VAL* 4.8 7.9 - - + -
303D VAL* 3.8 24.9 - - + -
307D VAL* 4.6 4.5 - - - +
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Residues in contact with GLN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D THR* 3.1 11.5 + - - +
237D PRO* 1.3 83.9 - - - +
239D ASP* 1.3 68.2 + - - +
241D MET* 3.3 19.2 - - - +
242D ARG* 3.4 15.4 + - - +
302D GLU* 5.7 0.2 - - - +
303D VAL* 3.8 29.3 - - - +
306D ASP* 2.7 44.3 + - + +
307D VAL* 4.5 9.9 - - + -
310D LEU* 4.2 16.7 - - + +
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Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D PRO* 5.3 6.3 - - + +
236D THR* 3.2 27.1 + - - +
238D GLN* 1.3 76.0 - - - +
240D GLU* 1.3 66.3 + - - +
241D MET 3.1 2.2 - - - -
242D ARG* 3.5 27.4 + - - +
243D TYR* 2.9 49.5 + - + +
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Residues in contact with GLU 240 (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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176D ALA* 3.8 30.4 - - + +
177D HIS 5.2 4.0 - - - +
235D PRO* 4.8 13.7 - - + +
236D THR 3.0 11.3 + - - +
237D PRO* 3.5 14.6 - - - +
239D ASP* 1.3 77.9 - - - +
241D MET* 1.3 55.8 + - - +
243D TYR* 3.5 8.6 - - - +
244D GLY* 3.0 17.5 + - - -
289D MET* 3.6 17.3 - - + +
298D ARG* 3.4 25.1 + - - -
757D GLY 5.5 0.2 - - - +
758D SER* 3.9 13.0 + - - -
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Residues in contact with MET 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D PRO 3.4 6.8 + - - +
238D GLN 3.3 12.8 - - - +
239D ASP 3.1 0.6 - - - -
240D GLU* 1.3 75.1 - - - +
242D ARG* 1.3 59.9 + - + +
243D TYR 3.1 1.6 - - - -
244D GLY* 2.8 1.5 + - - -
245D MET* 2.6 73.1 + - + +
287D SER* 5.7 1.6 - - - -
289D MET* 3.5 39.9 - - + +
307D VAL* 3.4 48.9 - - + +
310D LEU* 4.7 5.4 - - + -
311D ALA* 4.5 14.1 - - + +
314D MET* 4.6 9.0 - - + -
451D VAL* 5.8 2.0 - - + -
453D LEU* 6.1 0.7 - - - -
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Residues in contact with ARG 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ARG* 3.3 19.3 + - - +
238D GLN* 3.4 11.3 + - - +
239D ASP* 3.2 32.6 + - - +
241D MET* 1.3 80.2 - - + +
243D TYR* 1.3 70.8 + - + +
245D MET 3.4 0.6 + - - +
246D SER* 3.3 17.3 + - - -
310D LEU* 3.7 39.3 - - - +
314D MET* 3.8 32.0 - - + +
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Residues in contact with TYR 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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181D SER* 3.3 36.8 - - - -
182D ALA* 3.3 30.0 - - + +
183D ARG* 3.6 40.1 + - + +
235D PRO* 6.0 4.5 - - + -
239D ASP* 2.9 41.7 + - + +
240D GLU* 3.5 7.6 - - - +
242D ARG* 1.3 86.9 - - + +
244D GLY* 1.3 57.3 + - - +
246D SER* 2.3 26.4 + - - -
247D TYR* 4.2 6.1 - - - -
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Residues in contact with GLY 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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174D PHE* 5.2 3.1 - - - -
240D GLU 3.0 13.0 + - - -
241D MET 2.8 10.1 + - - -
243D TYR* 1.3 79.1 - - - +
245D MET* 1.3 63.8 + - - -
246D SER 3.3 0.7 + - - -
247D TYR* 3.7 12.9 + - - +
248D ILE* 3.3 14.2 - - - +
289D MET* 4.1 16.6 - - - -
677D ILE* 4.7 9.0 - - - +
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Residues in contact with MET 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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174D PHE* 5.1 1.8 - - + -
184D ARG* 4.1 4.0 - - - +
241D MET* 2.6 46.6 + - + +
242D ARG 3.4 5.6 + - - +
243D TYR 3.3 0.4 - - - -
244D GLY* 1.3 74.1 - - - +
246D SER* 1.3 64.7 + - - +
247D TYR 3.2 0.2 - - - -
248D ILE* 3.2 27.0 + - + +
249D HIS* 3.1 19.9 + - - +
287D SER* 4.5 4.5 - - - +
289D MET* 4.4 14.6 - - + -
311D ALA* 5.6 2.2 - - - -
314D MET* 3.7 22.7 - - + +
450D LEU* 4.4 22.6 - - + +
451D VAL* 3.8 34.1 - - + -
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Residues in contact with SER 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ALA 3.2 14.1 + - - -
184D ARG* 3.4 43.3 - - - +
187D LEU* 4.6 6.5 - - - +
242D ARG 3.3 7.8 + - - -
243D TYR* 2.3 28.8 + - - -
245D MET* 1.3 75.6 - - - +
247D TYR* 1.3 63.0 + - - +
249D HIS* 3.2 3.6 + - - +
250D GLU* 2.9 34.5 + - - +
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Residues in contact with TYR 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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174D PHE* 5.5 2.5 - - + -
180D GLN* 5.6 2.3 + - - -
182D ALA* 3.7 31.6 - - + +
187D LEU* 3.6 25.0 - - + +
243D TYR 4.2 4.7 - - - -
244D GLY* 3.7 4.7 + - - +
245D MET 3.2 0.8 - - - -
246D SER* 1.3 86.9 + - - +
248D ILE* 1.3 59.6 + - + +
250D GLU* 4.4 0.9 - - - +
251D THR* 2.9 34.9 + - - +
252D VAL* 3.3 6.7 + - + +
677D ILE* 3.4 41.3 - - + +
678D GLU* 2.8 50.9 + - - +
681D PHE* 4.0 24.7 - - + -
682D GLY* 4.1 4.9 - - - -
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Residues in contact with ILE 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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174D PHE* 3.8 32.1 - - + -
244D GLY 3.3 22.9 - - - +
245D MET* 3.2 31.0 + - + +
247D TYR* 1.3 75.7 - - + +
249D HIS* 1.3 63.1 + - - +
252D VAL* 3.5 13.9 + - + -
253D TRP* 2.9 35.6 + - + +
285D PHE* 5.5 0.9 - - + -
318D LEU* 5.4 0.2 - - + -
446D PHE* 3.9 28.9 - - + -
450D LEU* 4.3 24.7 - - + -
451D VAL* 4.8 7.4 - - + -
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Residues in contact with HIS 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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184D ARG* 4.1 29.3 - - - +
245D MET 3.1 12.3 + - - +
246D SER* 3.2 11.2 + - - +
248D ILE* 1.3 79.9 - - - +
250D GLU* 1.3 74.6 + - + +
251D THR* 3.6 0.3 + - - -
253D TRP* 4.1 12.8 - - - +
254D LYS* 5.3 4.9 + - - +
318D LEU* 4.0 33.4 - - + +
321D ASP* 5.8 1.2 + - - -
450D LEU* 5.9 0.4 - - - +
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Residues in contact with GLU 250 (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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184D ARG* 4.2 19.8 - - + +
187D LEU* 3.6 36.7 - - + +
188D GLN* 2.9 51.7 + - - +
191D ALA* 5.1 1.6 - - - +
246D SER 2.9 23.4 + - - +
247D TYR 4.3 1.3 - - - +
249D HIS* 1.3 86.3 + - - +
251D THR* 1.3 71.7 + - + +
254D LYS* 5.6 4.4 - - - +
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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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247D TYR* 2.9 16.4 + - - -
249D HIS 3.5 0.4 - - - -
250D GLU* 1.3 88.1 - - + +
252D VAL* 1.3 63.5 + - - +
253D TRP 3.3 2.0 + - - -
254D LYS* 3.6 6.1 + - - +
255D GLY* 2.9 25.5 + - - -
681D PHE* 2.7 31.1 + - - +
682D GLY 4.0 13.7 - - - +
683D GLU 4.1 1.1 - - - -
684D GLU* 4.0 24.7 - - + +
687D CYS* 4.2 12.9 - - - -
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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