Contacts of the helix formed by residues 242 - 253 (chain B) in PDB entry 2VN9
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 THR 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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299A LYS 6.1 0.9 - - - +
300A LEU* 5.9 1.8 - - + -
110B GLU* 2.8 35.0 + - - +
240B THR 3.9 1.5 + - - +
241B VAL* 1.3 76.6 - - - +
243B PRO* 1.3 72.7 - - + +
244B GLU* 3.3 13.9 + - - +
245B ALA* 3.3 20.8 + - - +
246B LYS* 3.3 12.6 + - - +
271B TRP* 3.7 5.9 + - - -
278B VAL 3.7 17.3 - - - +
280B SER* 3.8 16.8 - - - -
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Residues in contact with PRO 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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241B VAL 3.6 2.2 - - - +
242B THR* 1.3 86.2 - - + +
244B GLU* 1.3 73.3 + - - +
246B LYS* 3.2 15.0 + - + +
247B ASP* 2.9 29.6 + - - +
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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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242B THR* 3.3 20.1 - - - +
243B PRO* 1.3 88.6 - - - +
245B ALA* 1.3 64.3 + - - +
247B ASP* 3.4 5.9 + - - +
248B LEU* 3.1 18.5 + - - +
269B HIS* 3.2 20.3 - - + -
270B PRO* 5.3 6.3 - - + -
271B TRP* 4.3 7.9 - - + -
278B VAL* 3.6 34.9 - - + +
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Residues in contact with ALA 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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110B GLU* 4.1 1.8 - - - +
204B LEU* 4.6 1.4 - - - +
208B LEU* 3.7 25.6 - - + -
241B VAL* 3.7 6.5 - - + -
242B THR* 3.3 22.4 + - - +
244B GLU* 1.3 77.9 - - - +
246B LYS* 1.3 61.8 + - - +
248B LEU* 3.2 5.9 + - - +
249B ILE* 3.0 27.0 + - - +
271B TRP* 3.6 27.0 - - + +
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Residues in contact with LYS 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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233B PHE* 3.8 39.1 + - + +
238B TRP* 2.9 48.3 + - + +
239B ASP* 4.6 5.1 + - - +
241B VAL* 3.5 22.8 + - + +
242B THR 3.3 9.6 + - - +
243B PRO* 3.2 14.5 + - + +
245B ALA* 1.3 76.2 - - - +
247B ASP* 1.3 57.1 + - - +
249B ILE* 3.3 5.4 + - - +
250B ASN* 2.9 37.5 + - - +
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Residues in contact with ASP 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 PRO 2.9 17.0 + - - +
244B GLU* 3.6 9.0 - - - +
245B ALA 3.2 0.2 - - - -
246B LYS* 1.3 74.8 - - - +
248B LEU* 1.3 65.1 + - - +
250B ASN* 3.2 12.5 + - - +
251B LYS* 2.4 62.5 + - - +
269B HIS* 3.1 14.3 + - - +
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Residues in contact with LEU 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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117B ILE* 5.0 0.4 - - + -
204B LEU* 3.8 13.5 - - + -
244B GLU 3.1 13.7 + - - +
245B ALA* 3.6 9.4 - - - +
247B ASP* 1.3 76.6 - - - +
249B ILE* 1.3 62.9 + - - +
251B LYS* 3.1 4.5 + - - +
252B MET* 3.1 52.2 + - + +
261B ILE* 4.1 16.4 - - + -
266B ALA* 4.2 4.5 - - + +
269B HIS* 3.6 36.0 + - + +
271B TRP* 3.8 18.4 - - + -
272B ILE* 3.8 29.4 - - + -
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Residues in contact with ILE 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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201B GLY* 4.5 2.7 - - - +
204B LEU* 3.7 24.0 - - + -
205B TYR* 4.1 16.4 - - + +
208B LEU* 3.8 20.4 - - + -
231B TYR* 4.2 3.1 - - + -
233B PHE* 4.0 18.8 - - + -
238B TRP* 3.6 33.0 - - + -
245B ALA 3.0 15.6 + - - +
246B LYS* 3.6 6.5 - - - +
248B LEU* 1.3 73.7 - - - +
250B ASN* 1.3 53.1 + - - +
252B MET* 3.2 5.7 + - - +
253B LEU* 2.7 59.7 + - + +
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Residues in contact with ASN 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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231B TYR* 2.8 23.6 + - - +
233B PHE* 3.4 22.3 - - - -
246B LYS* 2.9 24.3 + - - +
247B ASP* 3.4 15.7 + - - +
249B ILE* 1.3 77.4 - - - +
251B LYS* 1.3 59.6 + - + +
253B LEU 3.5 11.1 - - - +
254B THR* 3.0 16.5 + - - -
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Residues in contact with LYS 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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247B ASP* 2.4 56.0 + - - +
248B LEU 3.1 5.3 + - - +
250B ASN* 1.3 78.1 - - + +
252B MET* 1.3 57.9 + - - +
254B THR* 3.2 13.4 + - - -
259B LYS 4.8 0.3 - - - +
260B ARG* 3.5 2.1 - - - +
261B ILE* 3.0 55.5 + - + +
269B HIS* 4.2 12.5 + - + -
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Residues in contact with MET 252 (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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117B ILE* 4.8 2.9 - - + -
121B LEU* 4.1 13.5 - - + -
197B MET* 3.4 33.9 - - + +
198B TRP* 3.7 6.9 - - - -
200B CYS* 3.8 9.9 - - + +
201B GLY* 3.5 31.2 - - - -
204B LEU* 4.2 12.3 - - + -
248B LEU* 3.1 40.9 + - + +
249B ILE 3.6 3.1 - - - +
251B LYS* 1.3 74.6 - - - +
253B LEU* 1.3 59.3 + - - +
254B THR 3.0 10.2 + - - -
260B ARG* 3.1 28.3 + - - -
261B ILE* 3.6 13.2 - - + -
266B ALA* 3.9 8.7 - - + -
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Residues in contact with LEU 253 (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 TRP* 3.4 58.5 - - + +
201B GLY* 3.8 11.7 - - - +
202B VAL* 3.7 13.7 - - + +
205B TYR* 4.7 0.9 - - + -
213B PRO* 4.6 9.4 - - + -
214B PHE* 4.5 8.1 - - + -
229B GLY* 5.7 0.7 - - - -
231B TYR* 3.8 45.6 + - + +
249B ILE* 2.7 42.5 + - + +
250B ASN 3.5 8.3 - - - +
252B MET* 1.3 69.9 - - - +
254B THR* 1.3 58.5 + - - +
255B ILE* 4.0 2.3 + - - +
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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
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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