Contacts of the helix formed by residues 234 - 251 (chain B) in PDB entry 5KAL
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 GLY 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B PRO 4.0 0.2 - - - +
6B ALA 5.3 0.4 - - - -
9B GLY* 3.1 28.4 + - - -
13B VAL* 4.0 11.9 - - - -
230B PRO* 4.3 6.8 - - - +
232B ASP* 3.1 8.8 + - - -
233B GLU* 1.3 79.2 - - - +
235B LEU* 1.3 64.5 + - - +
236B GLU 3.5 2.0 - - - -
237B LEU* 3.4 11.1 + - - +
238B GLY 3.1 11.6 + - - -
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Residues in contact with LEU 235 (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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5B PRO* 4.1 12.8 - - + +
6B ALA* 3.7 37.2 - - + +
232B ASP* 3.3 22.8 + - + +
233B GLU 3.7 0.6 - - - -
234B GLY* 1.3 74.0 - - - +
236B GLU* 1.3 68.8 + - - +
238B GLY* 3.1 3.1 + - - -
239B THR* 2.9 29.1 + - - +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASN* 5.7 1.7 + - - +
160B PRO* 5.4 12.5 - - - +
161B CYS* 5.6 1.4 - - - -
232B ASP* 2.7 22.9 + - - +
235B LEU* 1.3 74.0 - - - +
237B LEU* 1.3 62.9 + - - +
239B THR* 3.4 6.8 + - - -
240B GLN* 2.9 58.4 + - + +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLY* 5.2 0.2 - - - -
12B LEU* 3.8 29.6 - - + -
13B VAL* 5.1 8.7 - - + -
16B PHE* 5.5 3.4 - - + -
163B TRP* 4.2 30.5 - - + -
164B LEU* 4.5 13.2 - - + +
167B SER* 4.3 13.5 - - - +
230B PRO* 5.0 12.8 - - + -
232B ASP* 5.3 0.4 + - - -
234B GLY* 3.4 14.2 + - - +
235B LEU 3.1 0.8 - - - -
236B GLU* 1.3 79.2 - - - +
238B GLY* 1.3 58.0 + - - +
240B GLN* 3.2 9.5 + - + +
241B VAL* 2.9 45.5 + - + +
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Residues in contact with GLY 238 (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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5B PRO* 3.8 20.9 - - - -
8B VAL* 4.1 20.6 - - - -
9B GLY* 4.4 1.9 - - - -
12B LEU* 4.9 0.2 - - - -
234B GLY 3.1 9.1 + - - -
235B LEU 3.7 2.2 - - - -
237B LEU* 1.3 78.6 - - - +
239B THR* 1.3 63.0 + - - +
241B VAL* 3.2 2.7 + - - +
242B LEU* 2.9 30.2 + - - +
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Residues in contact with THR 239 (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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5B PRO* 3.4 24.4 - - + +
235B LEU* 2.9 19.7 + - - +
236B GLU* 3.6 11.3 - - - -
238B GLY* 1.3 76.0 - - - +
240B GLN* 1.3 59.0 + - + +
242B LEU* 4.0 3.0 - - - +
243B ASP* 3.0 34.2 + - + +
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Residues in contact with GLN 240 (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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158B ASN* 5.9 0.4 - - - +
161B CYS* 4.4 24.6 - - - +
164B LEU* 4.1 32.7 - - + +
198B TYR* 3.7 14.3 + - + +
199B LEU* 5.3 6.6 - - + +
204B HIS* 5.4 14.3 + - + +
236B GLU* 2.9 50.6 + - + +
237B LEU* 3.6 7.8 - - - +
239B THR* 1.3 78.3 - - + +
241B VAL* 1.3 58.3 + - - +
243B ASP* 3.4 1.1 + - - -
244B PHE* 2.9 31.0 + - - +
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Residues in contact with VAL 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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8B VAL* 5.0 7.2 - - + -
12B LEU* 4.3 10.3 - - + -
164B LEU* 3.6 20.0 - - + -
167B SER* 5.2 7.4 - - - -
168B ILE* 5.1 9.9 - - + -
237B LEU* 2.9 41.0 + - + +
238B GLY* 3.2 6.3 + - - +
240B GLN* 1.3 75.1 - - - +
242B LEU* 1.3 71.4 + - + +
244B PHE* 3.0 6.2 + - - +
245B LEU* 3.0 37.7 + - + +
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Residues in contact with LEU 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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3B PRO 4.2 18.2 - - - +
5B PRO* 4.2 26.7 - - + -
8B VAL* 4.5 17.7 - - + -
238B GLY 2.9 19.5 + - - +
239B THR* 4.0 3.1 - - - +
241B VAL* 1.3 84.4 - - + +
243B ASP* 1.3 62.4 + - - +
245B LEU* 3.3 13.6 + - + +
246B HIS* 2.9 24.8 + - - +
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Residues in contact with ASP 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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198B TYR* 2.5 21.7 + - - +
202B ARG* 2.9 42.0 + - - +
204B HIS* 5.7 0.3 + - - -
239B THR* 3.0 22.3 + - + +
240B GLN* 3.8 1.6 - - - +
242B LEU* 1.3 76.9 - - - +
244B PHE* 1.3 58.1 + - - +
246B HIS* 3.8 9.0 - - - +
247B PHE* 2.9 28.1 + - - +
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Residues in contact with PHE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 4.8 9.2 - - + -
168B ILE* 4.0 33.2 - - + -
171B TRP* 6.1 3.4 - + - -
191B PHE* 5.9 1.1 - + - -
194B MET* 4.6 13.2 - - + -
195B VAL* 4.1 33.9 - - + -
198B TYR* 3.7 34.2 + + + -
240B GLN 2.9 14.6 + - - +
241B VAL* 3.0 12.1 + - - +
243B ASP* 1.3 72.5 - - - +
245B LEU* 1.3 81.8 + - + +
247B PHE* 3.1 4.0 + - - +
248B PHE* 3.0 56.6 + + + -
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Residues in contact with LEU 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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168B ILE* 5.7 3.4 - - + -
171B TRP* 5.2 19.1 - - + -
241B VAL* 3.0 30.6 + - + +
242B LEU* 3.8 15.9 - - + +
244B PHE* 1.3 92.7 - - + +
246B HIS* 1.3 64.3 + - - +
248B PHE* 3.3 3.6 + - + +
249B LEU* 2.9 40.3 + - + +
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Residues in contact with HIS 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 LEU 2.9 16.7 + - - +
243B ASP* 3.8 11.4 - - - +
245B LEU* 1.3 76.2 - - - +
247B PHE* 1.3 63.4 + - - +
249B LEU* 3.7 6.7 - - - +
250B HIS* 2.9 59.4 + + + +
251B GLU* 3.8 23.0 + - + +
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Residues in contact with PHE 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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197B TYR* 4.0 23.8 - + - -
198B TYR* 3.8 20.0 - + + -
201B GLN* 4.1 22.0 - - + -
202B ARG* 3.7 25.8 - - - +
243B ASP 2.9 18.2 + - - +
244B PHE 3.1 4.5 + - - +
246B HIS* 1.3 76.3 - - - +
248B PHE* 1.3 98.6 + + - +
251B GLU* 3.0 52.4 + - + -
252B PHE* 3.1 25.1 + + + -
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Residues in contact with PHE 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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194B MET* 3.6 35.0 - - + -
197B TYR* 4.3 8.3 - + - -
198B TYR* 3.8 13.5 - - + -
244B PHE* 3.0 57.2 + + + +
245B LEU* 3.7 3.8 - - - +
247B PHE* 1.3 96.5 - + - +
249B LEU* 1.3 62.0 + - - +
252B PHE* 4.1 21.2 - + + +
259B ILE* 4.0 25.6 - - + -
293B TRP* 4.0 33.1 - + + -
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Residues in contact with LEU 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 LEU* 2.9 32.6 + - + +
246B HIS* 3.7 5.8 - - - +
248B PHE* 1.3 83.4 - - - +
250B HIS* 1.3 87.1 + - + +
251B GLU 3.9 0.2 - - - -
252B PHE 5.1 4.3 - - - +
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Residues in contact with HIS 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 HIS* 2.9 45.1 + + + +
249B LEU* 1.3 106.4 - - + +
251B GLU* 1.3 65.0 + - + +
252B PHE 4.9 1.8 - - - -
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Residues in contact with GLU 251 (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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202B ARG* 2.6 44.9 + - - -
246B HIS* 3.8 22.3 + - + +
247B PHE* 3.0 29.7 + - + +
250B HIS* 1.3 81.9 - - - +
252B PHE* 1.3 65.3 + - - +
253B ASP* 3.4 5.5 + - - +
257B GLN* 4.0 6.2 + - - +
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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