Contacts of the helix formed by residues 231 - 250 (chain B) in PDB entry 6QVC
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 LYS 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER* 3.7 21.6 + - - -
135B MET* 4.6 16.6 - - - -
136B ASP* 3.9 22.2 + - - +
219B LEU* 4.6 16.6 - - + +
223B LEU* 4.6 26.2 - - + +
230B GLY* 1.3 75.4 - - - +
232B GLU* 1.3 68.1 + - + +
233B GLY 3.4 3.0 + - - -
234B PRO* 4.1 5.8 - - - +
235B PHE* 3.5 19.3 + - + +
278B CYS* 3.8 33.9 + - - -
279B PHE* 4.6 14.3 - - + -
316B PHE* 5.2 0.2 - - - -
421B ARG* 5.3 9.7 - - - +
482B GLY* 4.2 0.2 - - - -
485B MET* 4.5 18.3 - - + +
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ILE* 4.3 7.4 - - - +
231B LYS* 1.3 77.3 - - - +
233B GLY* 1.3 72.5 + - - +
235B PHE* 3.1 2.8 + - - +
236B VAL* 2.6 43.4 + - + +
275B VAL* 5.1 9.2 - - + -
278B CYS* 3.6 24.0 - - + -
279B PHE* 5.0 7.6 - - + -
288B PHE* 4.2 23.7 - - + -
482B GLY* 4.0 0.5 - - - -
483B GLY 3.4 23.0 + - - -
484B PHE* 3.7 32.3 - - + +
578B TYR* 3.4 14.2 + - - -
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Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLY* 3.8 21.7 - - - -
191B ILE* 4.3 7.9 - - - -
231B LYS 3.4 0.2 - - - -
232B GLU* 1.3 93.1 + - - +
234B PRO* 1.3 67.2 - - - +
236B VAL* 3.1 8.3 + - - +
237B HIS 3.0 21.0 + - - -
482B GLY* 4.1 5.6 - - - -
578B TYR* 5.8 0.9 - - - -
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Residues in contact with PRO 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B SER* 3.6 24.2 - - - +
215B LYS* 4.0 21.1 - - + -
219B LEU* 4.5 15.5 - - + -
231B LYS 4.1 6.1 - - - +
233B GLY* 1.3 85.1 - - - +
235B PHE* 1.3 59.5 + - - +
237B HIS* 3.4 10.8 - - + +
238B ILE* 2.9 32.8 + - - +
480B PRO* 3.6 28.5 - - + +
481B CYS 4.2 0.2 - - - -
482B GLY 4.0 15.3 - - - +
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Residues in contact with PHE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 4.1 17.3 - - + -
131B VAL* 5.0 0.4 - - + -
132B SER* 3.6 29.6 - - - -
135B MET* 3.6 39.5 - - + -
219B LEU* 5.5 5.0 - - + +
231B LYS* 3.5 19.8 + - + +
232B GLU 3.1 9.5 + - - +
234B PRO* 1.3 76.9 - - - +
236B VAL* 1.3 60.6 + - - +
238B ILE* 3.3 17.8 - - + +
239B ALA* 2.9 29.1 + - - +
274B GLY* 3.1 34.5 - - - -
277B CYS* 3.7 20.4 - - + -
278B CYS* 3.5 14.6 - - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ILE* 3.7 24.9 - - + -
194B MET* 4.4 13.0 - - + -
232B GLU* 2.6 27.2 + - - +
233B GLY 3.3 8.3 - - - +
235B PHE* 1.3 71.6 - - - +
237B HIS* 1.3 58.6 + - - +
239B ALA* 3.2 7.4 + - - +
240B SER* 2.9 28.4 + - - -
270B GLY 4.3 0.7 - - - +
271B CYS* 3.8 44.0 - - + +
274B GLY* 4.2 2.2 - - - -
275B VAL* 4.0 18.8 - - + +
288B PHE* 5.2 2.2 - - + -
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Residues in contact with HIS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA* 5.3 3.4 - - - +
189B SER* 3.3 26.5 + - - +
190B GLY 4.3 12.4 + - - +
193B GLU* 5.0 1.8 - - + +
194B MET* 5.1 12.0 - - + +
197B ILE* 6.1 0.9 - - + -
206B TYR* 3.4 48.2 + + - -
207B LEU* 5.2 6.3 - - + -
211B ALA* 6.3 1.0 - - - +
215B LYS* 4.0 18.8 - - + -
233B GLY 3.0 10.9 + - - +
234B PRO 3.4 7.6 - - - +
235B PHE 3.2 0.2 - - - -
236B VAL* 1.3 78.3 - - - +
238B ILE* 1.3 58.6 + - - +
240B SER* 3.3 6.9 + - - -
241B ILE* 3.0 62.9 + - + +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 4.4 12.6 - - - -
131B VAL* 5.0 9.6 - - + -
135B MET* 5.1 2.5 - - + -
212B PHE* 3.6 37.7 - - + +
215B LYS* 4.0 22.9 - - + -
216B VAL* 4.9 10.5 - - + -
234B PRO 2.9 19.8 + - - +
235B PHE* 3.3 42.8 - - + +
237B HIS* 1.3 73.5 - - - +
239B ALA* 1.3 61.2 + - - +
241B ILE* 3.4 13.6 - - + +
242B CYS* 2.9 33.5 + - - -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.1 1.0 - - - +
128B MET* 3.6 27.9 - - + +
235B PHE* 2.9 19.2 + - + +
236B VAL 3.5 3.1 - - - +
237B HIS 3.2 0.2 - - - -
238B ILE* 1.3 76.5 - - - +
240B SER* 1.3 58.3 + - - +
242B CYS* 3.3 2.6 + - - +
243B ALA* 2.9 27.2 + - - +
270B GLY* 3.3 24.2 - - - +
273B VAL* 4.8 0.7 - - + -
274B GLY* 3.7 15.5 - - - +
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B MET* 4.4 18.6 - - - +
207B LEU* 4.5 8.7 - - - +
236B VAL 2.9 16.2 + - - -
237B HIS* 3.8 6.5 - - - -
239B ALA* 1.3 72.4 - - - +
241B ILE* 1.3 60.8 + - - +
243B ALA* 3.3 8.2 + - - +
244B ALA* 3.0 29.3 + - - +
266B ILE* 4.6 2.3 + - - +
267B LEU* 3.9 30.1 - - - +
270B GLY* 4.2 10.5 - - - -
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B TYR 5.0 2.2 - - - +
207B LEU* 3.8 30.1 - - + +
208B THR 4.4 13.7 - - - +
209B MET* 4.7 3.8 - - + -
211B ALA* 5.6 2.5 - - + -
212B PHE* 4.0 36.1 - - + +
215B LYS* 5.9 0.7 - - - -
237B HIS* 3.0 46.2 + - + +
238B ILE* 3.4 19.3 - - + +
240B SER* 1.3 75.8 - - - +
242B CYS* 1.3 59.3 + - - +
244B ALA* 3.2 2.8 + - - +
245B VAL* 3.0 43.8 + - + +
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Residues in contact with CYS 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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124B LEU* 4.0 6.8 - - + +
127B LEU* 4.4 17.9 - - + -
128B MET* 3.8 26.7 - - + -
131B VAL* 6.2 0.4 - - - -
212B PHE* 3.6 31.9 - - - -
238B ILE* 2.9 21.4 + - - +
239B ALA 3.8 0.2 - - - +
241B ILE* 1.3 73.9 - - - +
243B ALA* 1.3 60.9 + - - +
245B VAL* 3.9 5.2 - - - +
246B LEU* 2.9 32.7 + - - +
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Residues in contact with ALA 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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120B PHE* 4.4 8.1 - - + -
124B LEU* 4.0 21.2 - - + +
239B ALA 2.9 14.5 + - - +
240B SER* 3.4 10.5 - - - +
241B ILE 3.2 0.2 - - - -
242B CYS* 1.3 76.6 - - - +
244B ALA* 1.3 56.9 + - - +
246B LEU* 3.8 1.2 - - - +
247B SER* 2.9 30.6 + - - -
266B ILE* 3.8 29.6 - - + +
269B VAL* 6.2 0.9 - - + -
270B GLY* 4.4 6.7 - - - +
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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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204B LYS* 6.1 3.6 - - - +
207B LEU* 4.6 17.9 - - + -
240B SER 3.0 17.0 + - - +
241B ILE 3.8 3.4 - - - +
243B ALA* 1.3 75.7 - - - +
245B VAL* 1.3 59.9 + - + +
247B SER* 3.3 6.2 + - - -
248B LYS* 2.9 26.7 + - - +
266B ILE* 4.0 20.1 - - + +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU 5.3 6.1 - - - +
209B MET* 4.5 24.9 - - + -
241B ILE* 3.0 31.8 + - + +
242B CYS* 4.1 5.8 - - - +
244B ALA* 1.3 78.1 - - + +
246B LEU* 1.3 58.5 + - - +
248B LYS* 3.1 12.4 + - + +
249B PHE* 2.9 26.7 + - + +
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Residues in contact with LEU 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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120B PHE* 3.6 27.6 - - + +
123B LEU* 3.7 39.7 - - + -
124B LEU* 3.9 23.3 - - + -
127B LEU* 6.5 0.4 - - + -
242B CYS 2.9 19.3 + - - +
243B ALA 4.0 1.1 - - - +
245B VAL* 1.3 75.3 - - - +
247B SER* 1.3 57.8 + - - +
249B PHE* 4.1 22.7 - - + +
250B MET* 2.6 37.4 + - + +
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Residues in contact with SER 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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120B PHE* 3.9 14.5 - - - -
243B ALA 2.9 18.3 + - - -
244B ALA* 3.5 9.4 - - - -
246B LEU* 1.3 76.8 - - - +
248B LYS* 1.3 56.6 + - - +
250B MET 2.9 18.7 - - - +
251B SER* 3.4 10.2 + - - -
252B VAL* 5.5 0.9 - - - +
266B ILE* 4.5 18.1 - - - +
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Residues in contact with LYS 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 ALA 2.9 13.7 + - - +
245B VAL* 3.1 13.7 + - + +
247B SER* 1.3 77.1 - - - +
249B PHE* 1.3 64.1 + - + +
250B MET 3.8 0.4 - - - +
252B VAL* 3.5 22.6 - - - +
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 2.9 17.2 + - + +
246B LEU* 3.1 21.7 + - + +
248B LYS* 1.3 81.9 - - + +
250B MET* 1.3 65.9 - - + +
252B VAL* 3.4 16.6 - - + +
253B PHE* 4.0 23.9 - + + +
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Residues in contact with MET 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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116B GLU 5.9 3.1 - - - +
120B PHE* 4.0 33.4 - - + -
123B LEU* 5.3 9.2 - - + -
246B LEU* 2.6 23.8 + - + +
247B SER* 2.9 13.4 - - - +
248B LYS 3.8 2.3 - - - +
249B PHE* 1.3 79.0 - - + +
251B SER* 1.3 83.2 + - - +
252B VAL* 3.1 6.8 + - - +
253B PHE* 3.8 39.3 - - + +
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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
------------------------------------------------------------
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