Contacts of the helix formed by residues 230 - 250 (chain A) 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 SER 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 3.8 4.3 + - - +
229A HIS* 1.3 72.5 - - - +
231A LEU* 1.3 70.7 + - - +
232A ALA 3.1 0.2 - - - -
233A SER* 3.0 19.1 + - - -
234A SER* 3.3 14.1 + - - -
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A HIS* 3.1 7.3 - - + -
230A SER* 1.3 81.1 + - - +
232A ALA* 1.3 60.0 + - - +
233A SER 3.0 0.4 - - - -
234A SER* 3.6 12.8 - - - +
235A GLU* 2.7 37.0 + - + +
236A TYR 3.7 1.0 + - - -
348A PHE* 3.7 39.0 - - + -
228D ARG* 3.2 33.2 - - + +
229D HIS 3.9 7.6 - - - +
230D SER 3.5 32.8 - - - +
231D LEU* 3.7 11.9 - - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A MET* 4.0 5.9 - - - +
228A ARG* 3.7 31.4 + - + +
229A HIS 3.1 14.1 + - - +
230A SER 3.1 0.6 - - - -
231A LEU* 1.3 78.1 - - - +
233A SER* 1.3 59.5 + - - +
236A TYR* 3.6 20.3 - - - +
346A GLY 6.0 0.9 - - - -
347A GLY 3.7 20.2 - - - +
348A PHE* 3.7 16.5 - - + +
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLY 5.7 0.9 - - - +
180A MET* 3.9 19.5 - - - +
228A ARG* 3.2 25.5 + - - -
230A SER* 3.0 9.7 + - - -
231A LEU 3.0 0.4 - - - -
232A ALA* 1.3 81.3 - - - +
234A SER* 1.3 58.7 + - - +
235A GLU 3.6 0.2 - - - -
237A PRO* 3.2 22.3 - - - +
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A SER* 3.3 7.2 + - - -
231A LEU* 3.3 25.2 + - - +
233A SER* 1.3 79.5 - - - +
235A GLU* 1.3 63.1 + - - +
236A TYR 3.4 0.2 - - - -
237A PRO* 3.2 14.4 - - - +
238A VAL* 3.4 14.7 - - - +
228D ARG* 4.4 4.8 + - - +
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Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 2.7 29.4 + - + +
234A SER* 1.3 73.7 + - - +
236A TYR* 1.3 64.0 + - - +
238A VAL* 3.1 9.5 + - - +
239A ARG* 2.7 57.4 + - + +
242A GLN* 5.1 0.7 + - - -
277A ARG* 4.9 1.0 + - - -
348A PHE* 3.7 28.0 - - + -
228D ARG 3.8 5.4 - - - +
229D HIS* 2.9 56.2 + - - +
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Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A HIS* 3.8 29.4 - + - -
46A ASP* 4.4 1.9 + - - -
47A TYR* 3.4 19.1 + + - -
180A MET* 3.9 20.9 - - - -
181A PRO* 3.3 31.6 - - + -
182A CYS* 3.5 6.9 - - + +
183A GLY 3.3 23.9 + - - -
231A LEU 3.7 3.6 + - - -
232A ALA 3.6 19.9 + - - +
233A SER 4.3 1.3 - - - +
235A GLU* 1.3 77.5 - - - +
237A PRO* 1.4 70.1 - - + +
239A ARG* 3.1 17.9 + - - +
240A ARG* 3.3 20.6 + - + +
346A GLY* 4.8 13.7 - - - -
348A PHE* 5.0 4.0 - - + -
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Residues in contact with PRO 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLY 5.7 1.3 - - - +
181A PRO* 4.0 28.3 - - + -
233A SER 3.2 22.0 - - - +
234A SER* 3.2 13.9 - - - +
236A TYR* 1.4 96.8 - - + +
238A VAL* 1.3 60.1 + - + +
240A ARG* 3.3 8.1 + - + +
241A ARG* 3.1 22.0 + - - +
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A SER 3.4 19.1 - - - +
235A GLU* 3.1 27.5 + - - +
237A PRO* 1.3 75.5 - - + +
239A ARG* 1.3 65.5 + - - +
241A ARG* 3.2 7.8 + - + +
242A GLN* 3.0 48.1 + - + +
229D HIS* 3.8 28.5 - - + -
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Residues in contact with ARG 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A HIS* 4.7 4.3 - - + +
47A TYR* 3.6 6.5 - - - +
235A GLU* 2.7 54.8 + - + +
236A TYR* 3.1 9.2 + - - +
238A VAL* 1.3 82.8 - - - +
240A ARG* 1.3 62.8 + - - +
242A GLN* 3.2 19.6 + - - +
243A CYS* 3.0 28.1 + - - -
277A ARG* 3.0 40.3 - - - +
318A TYR* 2.8 50.6 + - + +
319A GLU* 3.2 24.4 + - - +
320A VAL* 3.6 11.2 - - + +
348A PHE* 4.4 0.8 - - + -
229D HIS 5.0 2.6 + - - -
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TYR* 3.5 58.2 + - + +
171A GLN* 4.9 1.8 - - - +
175A HIS* 3.8 11.1 - - - -
181A PRO* 2.7 46.8 + - - +
182A CYS 3.3 17.8 + - - -
183A GLY* 4.6 0.4 - - - -
236A TYR* 3.8 19.7 - - + +
237A PRO* 3.3 8.7 + - + +
238A VAL 3.3 0.6 - - - -
239A ARG* 1.3 76.8 - - - +
241A ARG* 1.3 58.1 + - - +
243A CYS* 3.4 3.3 + - - +
244A GLU* 3.0 51.8 + - - +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PRO 3.1 13.8 + - - +
238A VAL* 3.2 9.4 + - + +
240A ARG* 1.3 76.5 - - - +
242A GLN* 1.3 59.8 + - + +
244A GLU* 3.3 15.6 + - - +
245A GLU* 2.9 30.1 + - - +
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Residues in contact with GLN 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A GLU* 5.1 0.8 + - - -
238A VAL* 3.0 36.6 + - + +
239A ARG* 3.2 21.9 + - - +
241A ARG* 1.3 77.8 - - + +
243A CYS* 1.3 60.9 + - - +
245A GLU* 3.5 7.7 + - - +
246A VAL* 3.1 29.1 + - - +
273A GLU* 3.7 31.2 + - - +
274A GLY* 5.3 5.1 - - - -
277A ARG* 3.1 40.4 + - + +
229D HIS* 5.7 2.2 + - - -
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Residues in contact with CYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TYR* 4.3 2.5 - - + -
48A ASN* 3.2 33.9 - - - +
239A ARG 3.0 13.6 + - - +
240A ARG* 3.7 5.8 - - - +
242A GLN* 1.3 76.3 - - - +
244A GLU* 1.3 61.2 + - + +
246A VAL* 3.3 5.1 + - - +
247A ALA* 2.9 29.9 + - - +
255A LEU* 3.9 13.6 - - + +
277A ARG* 4.8 7.2 - - - -
278A ALA 6.3 0.2 - - - +
281A VAL* 4.0 12.3 - - - -
318A TYR* 3.1 32.5 - - - -
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ARG* 3.0 44.0 + - - +
241A ARG* 3.5 16.7 - - - +
243A CYS* 1.3 77.4 - - + +
245A GLU* 1.3 57.3 + - - +
247A ALA* 3.3 7.2 + - - +
248A ARG* 2.8 31.7 + - - +
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Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ARG 2.9 17.4 + - - +
242A GLN* 3.7 8.3 - - - +
244A GLU* 1.3 77.6 - - - +
246A VAL* 1.3 56.7 + - + +
248A ARG* 3.3 6.9 + - - +
249A ALA* 3.0 30.0 + - - +
270A VAL* 5.6 0.2 - - - -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLN 3.1 16.5 + - - +
243A CYS* 3.7 8.7 - - - +
244A GLU 3.3 0.2 - - - -
245A GLU* 1.3 75.7 - - + +
247A ALA* 1.3 63.6 + - - +
249A ALA 3.3 1.4 + - - -
250A LEU* 3.3 30.0 + - + +
255A LEU* 3.8 10.8 - - + -
263A LEU* 4.4 10.3 - - + -
270A VAL* 4.1 26.7 - - + -
274A GLY* 3.5 34.1 - - - +
277A ARG* 5.7 0.4 - - + -
278A ALA* 3.7 23.6 - - + +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A CYS 2.9 17.2 + - - +
244A GLU* 3.6 7.0 - - - +
246A VAL* 1.3 77.0 - - - +
248A ARG* 1.3 59.8 + - - +
250A LEU* 3.4 2.5 + - - -
251A GLY 3.2 2.9 + - - -
252A ALA* 2.9 47.0 + - - +
253A ALA 4.7 2.0 - - - +
254A SER* 4.1 17.3 - - - -
255A LEU* 4.0 17.7 - - + +
258A VAL* 5.6 0.2 - - - -
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Residues in contact with ARG 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLU 2.8 17.7 + - - +
245A GLU* 3.7 7.0 - - - +
247A ALA* 1.3 76.4 - - - +
249A ALA* 1.3 64.8 + - - +
251A GLY* 3.2 13.0 + - - +
252A ALA 4.8 2.2 - - - +
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A GLU 3.0 17.5 + - - +
246A VAL 3.3 6.2 + - - +
248A ARG* 1.3 75.2 - - - +
250A LEU* 1.3 67.2 + - + +
251A GLY 3.4 0.6 + - - -
269A LEU* 3.8 31.7 - - + +
270A VAL* 4.1 4.7 - - + -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL* 3.3 22.8 + - + +
247A ALA* 3.4 4.0 + - - +
248A ARG 3.1 0.8 - - - -
249A ALA* 1.3 83.7 - - + +
251A GLY* 1.3 64.0 + - - +
252A ALA* 3.3 8.7 - - + +
258A VAL* 4.0 32.1 - - + -
262A GLU* 4.6 4.0 - - + +
263A LEU* 4.4 19.7 - - + -
266A ALA* 4.0 29.4 - - + +
269A LEU* 4.7 1.8 - - + -
270A VAL* 3.8 22.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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