Contacts of the helix formed by residues 236 - 245 (chain B) in PDB entry 6V96
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 ASP 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASP* 4.0 6.1 - - - +
228B THR* 4.4 3.8 - - - +
229B SER* 3.2 30.6 - - - +
230B SER* 2.6 38.3 + - - -
232B ASP 3.0 21.3 + - - +
235B LYS* 1.3 88.4 - - - +
237B ILE* 1.3 71.0 + - - +
238B ILE 3.4 0.7 - - - -
239B PRO* 3.5 3.3 - - - +
240B TYR* 3.2 23.4 + - - +
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA* 3.9 18.6 - - + -
211B PHE* 4.3 8.3 - - + -
216B LEU* 4.9 2.0 - - + -
219B ALA* 3.9 23.6 - - + +
220B LEU* 4.5 5.8 - - + -
223B ASP* 3.5 37.9 - - + +
232B ASP 3.1 12.0 + - - +
233B PHE* 3.9 25.1 - - + -
236B ASP* 1.3 76.5 - - - +
238B ILE* 1.3 73.6 + - + +
240B TYR* 3.4 4.9 + - - +
241B ILE* 3.3 32.0 + - + +
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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
----------------------------------------------------------
156B VAL* 4.4 7.4 - - + -
158B ILE* 3.4 35.9 - - + -
174B MET* 4.4 12.1 - - + -
185B PHE* 4.9 4.0 - - + -
209B TYR* 4.1 20.0 - - + -
211B PHE* 4.1 10.3 - - + -
233B PHE* 3.1 38.4 + - + +
234B GLY* 4.3 4.9 - - - +
237B ILE* 1.3 83.0 - - + +
239B PRO* 1.3 76.2 - - + +
241B ILE* 3.0 8.1 + - + +
242B VAL* 2.8 32.3 + - + +
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Residues in contact with PRO 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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185B PHE* 3.4 32.1 - - + -
234B GLY 3.3 14.4 - - - +
235B LYS 3.4 20.6 - - - +
236B ASP* 3.5 14.8 - - - +
238B ILE* 1.3 92.0 - - + +
240B TYR* 1.3 55.0 + - - +
242B VAL* 3.3 8.7 + - + +
243B GLU* 2.8 28.8 + - - +
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Residues in contact with TYR 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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222B ARG* 3.5 37.7 + - - -
236B ASP 3.2 17.6 + - - +
237B ILE* 3.5 5.8 - - - +
238B ILE 3.1 0.4 - - - -
239B PRO* 1.3 79.8 - - - +
241B ILE* 1.3 64.0 + - + +
243B GLU* 3.1 7.2 + - + +
244B HIS* 2.8 68.4 + + + +
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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
----------------------------------------------------------
155B ASP* 3.8 10.3 - - + -
156B VAL* 3.7 22.7 - - + -
211B PHE* 3.7 29.6 - - + -
215B PHE* 3.7 24.9 - - + -
219B ALA* 5.4 2.7 - - + -
222B ARG* 6.0 0.9 - - - +
237B ILE* 3.3 21.7 + - + +
238B ILE* 3.0 8.0 + - - +
240B TYR* 1.3 79.2 - - + +
242B VAL* 1.3 64.0 + - - +
245B GLY* 2.6 38.5 + - - +
246B LYS 3.6 29.8 - - - +
247B ALA 4.0 0.4 - - - +
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Residues in contact with VAL 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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158B ILE* 5.5 0.2 - - + -
174B MET* 5.5 0.2 - - - -
182B ILE* 3.4 35.1 - - + +
183B ILE* 3.7 23.4 - - - +
184B ASP* 3.7 11.4 - - - +
185B PHE* 4.6 5.8 - - + +
238B ILE* 2.8 32.6 + - + +
239B PRO* 3.6 9.6 - - + +
241B ILE* 1.3 76.0 - - - +
243B GLU* 1.3 63.0 + - - +
245B GLY 4.4 4.8 - - - +
247B ALA* 3.6 24.7 - - + +
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Residues in contact with GLU 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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239B PRO 2.8 13.4 + - - +
240B TYR* 3.2 12.3 - - - +
242B VAL* 1.3 82.2 - - - +
244B HIS* 1.3 91.3 + - + +
245B GLY 4.6 1.2 - - - +
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Residues in contact with HIS 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 TYR* 2.8 64.3 + + + +
243B GLU* 1.3 100.1 - - + +
245B GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASP* 3.2 13.7 - - - -
215B PHE* 6.2 0.2 - - - -
241B ILE* 2.6 30.1 + - - +
242B VAL 4.4 5.2 - - - +
243B GLU 4.6 0.9 - - - +
244B HIS* 1.3 77.5 - - - +
246B LYS* 1.3 60.3 + - - +
247B ALA 4.2 0.5 + - - -
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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