Contacts of the helix formed by residues 238 - 252 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D LEU 3.4 0.2 + - - -
237D PRO* 1.3 69.7 - - - +
239D LYS* 1.3 66.7 + - + +
241D PHE* 3.2 1.8 + - - +
242D GLU* 3.0 55.4 + - - +
326D GLN* 3.1 41.6 - - + +
327D SER 3.2 11.8 + - - +
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D MET* 3.6 21.6 - - + +
219D GLU* 3.9 34.4 + - - +
222D TYR* 6.5 0.9 - - + -
237D PRO* 3.1 2.7 + - + +
238D LYS* 1.3 79.8 - - + +
240D VAL* 1.3 63.4 + - + +
242D GLU* 3.3 14.1 + - - +
243D ALA* 3.1 18.4 + - - +
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D VAL* 5.2 3.6 - - + -
213D LEU* 4.1 10.3 - - + +
215D MET* 3.7 15.5 - - - -
219D GLU* 3.4 37.2 - - + +
220D TYR* 3.8 31.2 - - + +
236D LEU* 4.3 21.5 - - + -
237D PRO* 3.1 17.6 + - + +
239D LYS* 1.3 75.9 - - + +
241D PHE* 1.3 58.1 + - - +
243D ALA* 3.3 1.7 + - - +
244D ALA* 2.8 28.2 + - - +
331D THR* 5.9 0.2 - - - +
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Residues in contact with PHE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D LEU* 3.6 20.1 - - + +
237D PRO 2.9 12.5 + - - +
238D LYS* 3.5 8.1 - - - +
240D VAL* 1.3 75.3 - - - +
242D GLU* 1.3 67.5 + - + +
244D ALA* 5.4 0.2 - - + -
245D VAL* 2.9 58.0 + - + +
262D TRP 4.0 16.8 - - - -
263D LEU* 5.5 10.8 - - + -
322D PHE* 4.3 0.4 - + - -
324D ILE* 3.5 37.0 - - + -
325D SER* 3.6 20.4 - - - -
326D GLN* 3.8 32.3 - - + -
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Residues in contact with GLU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D LYS* 3.0 51.8 + - + +
239D LYS* 3.8 13.6 - - - +
241D PHE* 1.3 85.4 - - + +
243D ALA* 1.3 62.1 - - - +
245D VAL* 3.6 3.5 + - - +
246D LYS* 3.1 24.3 + - - +
326D GLN* 5.0 2.8 - - - +
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU* 4.0 15.8 - - + +
215D MET* 3.9 22.9 - - + -
239D LYS 3.1 12.9 + - - +
240D VAL 3.6 7.2 - - - +
242D GLU* 1.3 77.8 - - - +
244D ALA* 1.3 63.1 + - - +
246D LYS* 3.2 9.4 + - - +
247D SER* 3.1 23.0 + - - -
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Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D VAL* 6.0 0.7 - - + -
208D ILE* 4.7 7.4 - - + -
213D LEU* 4.2 17.4 - - + +
236D LEU* 4.0 22.0 - - + -
240D VAL 2.8 18.3 + - - +
241D PHE* 3.7 4.0 - - + +
243D ALA* 1.3 76.7 - - - +
245D VAL* 1.3 59.3 + - + +
247D SER* 3.1 4.0 + - - -
248D ILE* 2.9 43.9 + - + +
283D ILE* 6.4 0.2 - - + -
324D ILE* 5.5 1.3 - - + -
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Residues in contact with VAL 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D PHE* 2.9 57.8 + - + +
242D GLU* 4.2 3.6 - - - +
244D ALA* 1.3 75.4 - - + +
246D LYS* 1.3 58.9 + - - +
248D ILE* 3.8 6.8 - - + +
249D LYS* 2.8 56.6 + - + +
262D TRP* 4.0 18.2 - - + +
322D PHE* 4.2 14.8 - - + -
324D ILE* 5.6 0.4 - - + -
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Residues in contact with LYS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLU 3.1 16.4 + - - +
243D ALA* 3.4 12.3 - - - +
244D ALA 3.2 0.4 - - - -
245D VAL* 1.3 78.2 - - - +
247D SER* 1.3 56.6 + - - +
249D LYS* 3.4 9.1 + - - +
250D ALA* 3.0 28.3 + - + +
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Residues in contact with SER 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ILE* 3.3 32.3 + - - +
211D GLN* 4.8 12.5 + - - +
213D LEU* 4.3 8.4 - - - +
243D ALA 3.1 8.1 + - - -
244D ALA 3.6 7.0 - - - -
246D LYS* 1.3 79.0 - - - +
248D ILE* 1.3 58.7 + - - +
250D ALA* 3.3 7.4 + - - +
251D ALA* 3.0 28.9 + - - +
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Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ILE* 4.1 21.1 - - + -
244D ALA* 2.9 31.5 + - + +
245D VAL* 3.9 4.5 - - + +
247D SER* 1.3 73.2 - - - +
249D LYS* 1.3 65.1 + - - +
251D ALA* 3.3 1.7 + - - +
252D SER* 2.8 28.2 + - - +
262D TRP* 3.5 25.6 - - + -
280D PHE* 4.7 4.7 - - + -
281D PRO* 4.1 24.4 - - + +
283D ILE* 4.0 23.3 - - + -
305D TYR* 4.4 6.5 - - + +
322D PHE* 4.3 14.1 - - + -
324D ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D VAL* 2.8 39.6 + - + +
246D LYS* 3.6 8.1 - - - +
248D ILE* 1.3 78.0 - - - +
250D ALA* 1.3 62.6 + - - +
252D SER* 3.2 9.6 + - - -
253D SER* 3.0 24.5 + - - -
256D LYS* 5.2 0.9 + - - -
259D ASP* 5.2 8.1 + - - +
262D TRP* 3.7 47.8 - - + +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA* 4.9 14.7 - - - +
253A SER* 4.9 12.3 - - - +
246D LYS* 3.0 19.1 + - + +
247D SER* 3.6 7.6 - - - +
248D ILE 3.3 0.2 - - - -
249D LYS* 1.3 76.7 - - - +
251D ALA* 1.3 62.2 + - - +
253D SER* 3.3 23.7 + - - -
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLN* 3.1 15.9 + - - +
251A ALA* 6.4 2.0 - - - +
208D ILE* 5.0 2.2 - - + -
209D ASN* 4.6 9.2 - - + +
247D SER 3.0 17.2 + - - +
248D ILE 3.9 3.8 - - - +
249D LYS 3.3 0.2 - - - -
250D ALA* 1.3 77.4 - - - +
252D SER* 1.3 58.8 - - - +
253D SER* 3.4 1.0 + - - -
279D ILE 3.0 12.5 - - - +
281D PRO* 4.0 27.8 - - + -
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248D ILE 2.8 21.6 + - - -
249D LYS* 3.3 9.4 + - - -
251D ALA* 1.3 76.1 - - - +
253D SER* 1.3 60.0 + - - +
254D THR* 3.0 6.4 + - - -
255D GLU* 2.9 25.3 + - - +
257D PHE* 4.3 2.9 - - - -
262D TRP* 3.8 14.4 - - - -
279D ILE* 3.5 23.6 - - - +
280D PHE* 4.1 25.4 - - - -
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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