Contacts of the helix formed by residues 238 - 252 (chain B) in PDB entry 2VKM
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 238 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B TYR* 6.2 0.2 - - - -
236B LEU 3.4 0.4 + - - -
237B PRO* 1.3 70.3 - - - +
239B LYS* 1.3 67.6 + - + +
241B PHE* 3.3 0.8 + - - +
242B GLU* 3.0 44.1 + - + +
326B GLN* 3.5 38.8 - - - +
327B SER 3.2 11.7 + - - +
328B SER* 6.2 0.7 - - - -
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Residues in contact with LYS 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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215B MET* 3.9 16.5 - - + +
219B GLU* 3.4 37.4 + - - +
222B TYR* 6.5 0.4 - - + -
237B PRO* 3.0 3.3 + - + +
238B LYS* 1.3 82.1 - - + +
240B VAL* 1.3 63.8 + - + +
242B GLU* 3.5 6.5 + - - +
243B ALA* 3.2 22.3 + - - +
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Residues in contact with VAL 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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206B VAL* 5.2 3.6 - - + -
213B LEU* 4.1 15.0 - - + -
215B MET* 3.8 17.3 - - + -
219B GLU* 3.3 30.3 - - + +
220B TYR* 3.7 31.2 - - + -
236B LEU* 4.2 23.6 - - + -
237B PRO* 2.9 21.1 + - + +
239B LYS* 1.3 70.7 - - + +
241B PHE* 1.3 55.7 + - - +
243B ALA* 3.4 1.2 + - - +
244B ALA* 2.7 33.4 + - - +
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Residues in contact with PHE 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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236B LEU* 3.8 21.7 - - + +
237B PRO 2.9 12.3 + - - +
238B LYS* 3.6 7.0 - - - +
240B VAL* 1.3 74.5 - - - +
242B GLU* 1.3 90.7 + - - +
244B ALA* 3.8 0.6 - - + +
245B VAL* 2.9 54.9 + - + +
262B TRP 3.8 17.3 - - - -
263B LEU* 4.6 17.3 - - + -
322B PHE* 4.5 0.2 - + - -
324B ILE* 3.4 33.4 - - + -
325B SER* 3.6 20.6 - - - -
326B GLN* 3.7 22.4 - - + -
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Residues in contact with GLU 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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238B LYS* 3.0 36.6 + - + +
239B LYS* 3.8 7.0 - - - +
241B PHE* 1.3 93.2 - - - +
243B ALA* 1.3 63.5 + - - +
245B VAL* 3.5 3.6 + - - +
246B LYS* 3.1 24.1 + - - +
326B GLN* 3.0 25.6 - - - +
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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
----------------------------------------------------------
213B LEU* 4.0 15.1 - - + +
215B MET* 3.9 22.0 - - + -
239B LYS 3.2 14.9 + - - +
240B VAL 3.7 3.6 - - - +
242B GLU* 1.3 79.3 - - - +
244B ALA* 1.3 62.9 + - - +
246B LYS* 3.3 9.3 + - - +
247B SER* 3.2 22.2 + - - -
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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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206B VAL* 5.9 1.1 - - + -
208B ILE* 4.5 10.9 - - + +
213B LEU* 4.1 20.3 - - + +
236B LEU* 4.0 20.6 - - + -
240B VAL 2.7 22.2 + - - +
241B PHE 3.8 2.7 - - - +
243B ALA* 1.3 73.6 - - - +
245B VAL* 1.3 58.6 + - + +
247B SER* 3.2 3.8 + - - -
248B ILE* 2.9 40.0 + - + +
324B ILE* 5.5 2.0 - - + -
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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
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241B PHE* 2.9 57.8 + - + +
242B GLU* 4.2 3.8 - - - +
244B ALA* 1.3 77.3 - - + +
246B LYS* 1.3 58.6 + - - +
248B ILE* 3.8 7.1 - - + +
249B LYS* 2.9 45.3 + - - +
262B TRP* 3.9 29.2 - - + -
322B PHE* 4.2 13.5 - - + -
324B ILE* 5.5 0.7 - - + -
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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
----------------------------------------------------------
242B GLU 3.1 19.2 + - - +
243B ALA* 3.6 8.1 - - - +
244B ALA 3.2 0.2 - - - -
245B VAL* 1.3 77.6 - - - +
247B SER* 1.3 58.2 + - - +
249B LYS* 3.5 10.3 + - - +
250B ALA* 3.0 26.8 + - + +
254C THR* 6.2 4.5 - - - +
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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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208B ILE* 3.3 32.6 + - - +
211B GLN* 4.3 17.7 + - - +
213B LEU* 4.2 6.9 - - - +
243B ALA 3.2 10.3 + - - -
244B ALA 3.2 7.9 + - - -
246B LYS* 1.3 79.9 - - - +
248B ILE* 1.3 60.3 + - - +
250B ALA* 3.3 7.7 + - - +
251B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 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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208B ILE* 4.0 19.3 - - + -
244B ALA* 2.9 30.1 + - + +
245B VAL* 3.9 5.2 - - + +
247B SER* 1.3 75.6 - - - +
249B LYS* 1.3 53.7 + - - +
251B ALA* 3.4 2.1 + - - +
252B SER* 2.7 33.9 + - - +
262B TRP* 3.5 26.0 - - + -
280B PHE* 4.7 3.8 - - + -
281B PRO* 4.1 23.3 - - + -
283B ILE* 3.9 22.9 - - + -
305B TYR* 4.3 6.7 - - + +
322B PHE* 4.0 14.8 - - + -
324B ILE* 4.0 15.5 - - + -
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Residues in contact with LYS 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 35.2 + - + +
246B LYS* 3.6 9.2 - - - +
248B ILE* 1.3 75.8 - - - +
250B ALA* 1.3 65.2 + - - +
252B SER* 3.3 7.2 + - - -
253B SER* 3.0 25.6 + - - -
256B LYS* 5.2 0.9 + - - -
259B ASP* 4.3 13.7 + - - +
262B TRP* 3.3 53.1 - - + +
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Residues in contact with ALA 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 LYS* 3.0 16.2 + - + +
247B SER* 3.6 7.6 - - - +
249B LYS* 1.3 81.2 - - - +
251B ALA* 1.3 58.6 + - - +
253B SER* 3.1 23.9 + - - -
250C ALA* 4.5 16.7 - - - +
253C SER* 4.5 15.5 - - - +
254C THR* 6.4 1.8 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ILE* 5.0 1.8 - - + -
209B ASN* 4.7 7.4 - - + +
247B SER 3.0 16.2 + - - +
248B ILE 3.7 5.2 - - - +
250B ALA* 1.3 76.7 - - - +
252B SER* 1.3 59.5 + - - +
253B SER* 3.5 0.6 + - - -
254B THR 5.4 0.2 + - - -
279B ILE 3.0 12.8 - - - +
281B PRO* 3.8 30.1 - - + -
211C GLN* 3.2 14.9 - - - +
251C ALA* 6.3 3.1 - - - +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE 2.7 21.2 + - - -
249B LYS* 3.3 4.9 + - - -
251B ALA* 1.3 76.6 - - - +
253B SER* 1.3 57.0 + - - +
254B THR* 2.9 12.8 + - - -
255B GLU* 2.9 20.0 + - - +
257B PHE* 4.4 3.0 - - - -
262B TRP* 3.7 19.8 - - - -
279B ILE* 3.5 28.6 - - - +
280B PHE* 4.1 21.5 - - - -
211C GLN* 4.9 0.2 - - - -
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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