Contacts of the helix formed by residues 235 - 250 (chain B) in PDB entry 6Q3W
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 GLU 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B SER* 1.3 84.5 - - - +
236B TYR* 1.3 63.4 + - - +
237B PRO 3.5 0.4 - - - -
238B VAL* 3.3 22.0 + - - +
239B ARG* 3.0 48.3 + - - +
348B PHE* 3.6 36.9 - - + -
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Residues in contact with TYR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 3.9 29.8 - + - -
46B ASP* 4.4 2.8 + - - -
47B TYR* 3.3 26.2 + + - -
180B MET* 6.4 0.4 - - + -
181B PRO* 3.2 39.9 - - + -
182B CYS* 3.7 6.4 - - + +
183B GLY 3.4 15.4 + - - -
234B SER 4.7 4.7 - - - +
235B GLU* 1.3 80.0 - - - +
237B PRO* 1.4 69.4 - - + +
238B VAL 3.2 0.3 + - - -
239B ARG* 3.3 6.3 + - - +
240B ARG* 3.2 32.6 + - + +
346B GLY* 4.9 12.1 - - - -
348B PHE* 5.0 5.3 - - + -
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Residues in contact with PRO 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B PRO* 4.1 23.1 - - + -
234B SER* 3.3 24.2 - - - +
236B TYR* 1.4 97.4 - - + +
238B VAL* 1.3 58.7 + - + +
240B ARG* 3.6 10.6 - - + +
241B ARG* 3.0 28.2 + - - +
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Residues in contact with VAL 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B SER 3.3 21.1 - - - +
235B GLU* 3.4 31.2 - - - +
236B TYR 3.1 0.8 - - - -
237B PRO* 1.3 75.8 - - + +
239B ARG* 1.3 62.9 + - - +
241B ARG* 3.2 7.3 + - - +
242B GLN* 2.9 55.0 + - + +
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Residues in contact with ARG 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B HIS* 4.9 2.0 - - + +
47B TYR* 3.9 3.8 - - - +
235B GLU* 3.0 45.8 + - - +
236B TYR* 3.3 8.9 + - - +
238B VAL* 1.3 77.1 - - - +
240B ARG* 1.3 64.0 + - - +
242B GLN* 3.1 18.8 + - - +
243B CYS* 2.9 27.9 + - - -
277B ARG* 3.4 37.3 - - - +
318B TYR* 2.7 56.2 + - + +
319B GLU* 2.7 29.4 + - - +
320B VAL* 3.8 10.9 - - + +
348B PHE* 4.3 6.4 - - + -
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B TYR* 3.5 59.0 + - + +
171B GLN* 5.3 1.0 - - - +
175B HIS* 4.2 9.5 - - - -
181B PRO* 2.7 44.6 + - - +
182B CYS 3.6 15.8 + - - -
183B GLY* 4.7 0.6 - - - -
236B TYR* 3.2 23.8 + - + +
237B PRO* 3.6 11.2 - - + +
239B ARG* 1.3 78.5 - - - +
241B ARG* 1.3 62.2 + - - +
243B CYS* 3.4 2.9 + - - +
244B GLU* 3.1 41.2 + - - +
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Residues in contact with ARG 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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237B PRO 3.0 18.4 + - - +
238B VAL* 3.5 6.7 - - - +
240B ARG* 1.3 75.3 - - - +
242B GLN* 1.3 57.7 + - + +
244B GLU* 3.2 15.0 + - - +
245B GLU* 3.0 26.2 + - - +
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Residues in contact with GLN 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 2.9 39.2 + - + +
239B ARG* 3.1 19.2 + - - +
241B ARG* 1.3 76.0 - - + +
243B CYS* 1.3 61.2 + - - +
245B GLU* 3.1 18.1 + - - +
246B VAL* 3.2 18.4 + - - +
273B GLU* 3.0 30.1 + - + +
274B GLY* 5.3 4.6 - - - -
277B ARG* 2.9 41.8 + - + +
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Residues in contact with CYS 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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47B TYR* 4.4 1.6 - - + -
48B ASN* 3.2 35.0 - - - +
239B ARG 2.9 13.6 + - - +
240B ARG* 3.6 6.5 - - - +
242B GLN* 1.3 76.2 - - - +
244B GLU* 1.3 63.1 + - + +
246B VAL* 3.6 4.4 + - - +
247B ALA* 3.1 24.5 + - - +
255B LEU* 4.0 14.0 - - + +
277B ARG* 4.9 7.4 - - - -
278B ALA 6.3 0.2 - - - +
281B VAL* 3.9 12.8 - - - -
318B TYR* 3.1 33.0 - - - -
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Residues in contact with GLU 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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240B ARG* 3.1 36.0 + - - +
241B ARG* 3.4 11.9 - - - +
243B CYS* 1.3 76.5 - - + +
245B GLU* 1.3 62.4 + - - +
247B ALA* 3.6 7.4 + - - +
248B ARG* 3.2 23.2 + - - +
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Residues in contact with GLU 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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241B ARG 3.0 12.7 + - - +
242B GLN* 3.1 13.4 + - - +
244B GLU* 1.3 74.0 - - - +
246B VAL* 1.3 62.5 + - + +
248B ARG* 3.2 8.0 + - - +
249B ALA* 3.0 26.1 + - - +
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Residues in contact with VAL 246 (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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242B GLN 3.2 12.2 + - - +
243B CYS* 4.1 4.5 - - - +
245B GLU* 1.3 74.9 - - + +
247B ALA* 1.3 67.0 + - - +
249B ALA* 3.0 17.9 + - - +
250B LEU* 3.1 17.1 + - + +
255B LEU* 4.2 8.1 - - + -
258B VAL* 6.2 0.7 - - + -
263B LEU* 5.0 7.6 - - + -
270B VAL* 4.1 22.4 - - + -
271B SER* 5.3 0.7 - - - +
274B GLY* 3.2 40.2 - - - +
277B ARG* 5.8 0.7 - - + -
278B ALA* 3.7 24.7 - - + +
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Residues in contact with ALA 247 (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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243B CYS 3.1 18.6 + - - +
244B GLU* 3.7 9.2 - - - +
245B GLU 3.3 0.2 - - - -
246B VAL* 1.3 78.0 - - - +
248B ARG* 1.3 60.8 + - - +
250B LEU* 3.4 4.1 + - - +
251B GLY 3.3 3.8 + - - -
252B ALA* 3.2 43.3 + - - +
253B ALA 4.5 3.4 - - - +
254B SER* 4.4 14.1 - - - -
255B LEU* 4.2 15.7 - - + +
258B VAL* 5.7 0.2 - - - -
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Residues in contact with ARG 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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244B GLU 3.2 10.4 + - - +
245B GLU* 3.2 10.9 + - - +
246B VAL 3.1 0.6 - - - -
247B ALA* 1.3 79.3 - - - +
249B ALA* 1.3 61.8 + - - +
250B LEU 3.1 1.1 + - - -
251B GLY* 3.4 10.4 + - - +
252B ALA 5.1 0.9 - - - -
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Residues in contact with ALA 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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245B GLU 3.0 13.5 + - - +
246B VAL* 3.0 9.8 + - - +
248B ARG* 1.3 75.6 - - - +
250B LEU* 1.3 58.1 + - - +
251B GLY 3.5 0.2 - - - -
269B LEU* 4.0 26.9 - - - +
270B VAL* 3.7 24.2 - - + -
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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 VAL* 3.1 18.0 + - + +
247B ALA 4.1 2.5 - - - +
248B ARG 3.1 0.2 - - - -
249B ALA* 1.3 78.9 - - - +
251B GLY* 1.3 66.6 + - - +
252B ALA* 3.4 2.8 - - - +
258B VAL* 4.7 20.6 - - + -
266B ALA* 6.3 2.2 - - + -
269B LEU* 5.2 9.9 - - + -
270B VAL* 5.6 3.4 - - + -
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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