Contacts of the helix formed by residues 238 - 253 (chain C) in PDB entry 3DM6
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C LEU 3.7 0.2 + - - -
237C PRO* 1.3 69.8 - - - +
239C LYS* 1.3 66.7 + - + +
241C PHE* 3.3 2.3 + - - +
242C GLU* 2.7 67.0 + - - +
326C GLN* 3.4 33.0 - - - +
327C SER 3.5 8.6 + - - +
328C SER* 6.4 0.4 - - - -
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Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C MET* 3.7 24.4 - - + +
219C GLU* 3.1 35.2 + - + +
222C TYR* 5.7 8.3 - - - -
237C PRO* 3.3 2.3 - - + +
238C LYS* 1.3 91.0 - - + +
240C VAL* 1.3 58.5 + - + +
242C GLU* 3.8 7.3 - - - +
243C ALA* 2.9 31.2 + - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C VAL* 5.2 5.6 - - + -
213C LEU* 4.3 14.2 - - + +
215C MET* 4.5 7.9 - - - -
219C GLU* 3.6 38.4 - - + +
220C TYR* 4.0 24.9 - - + -
236C LEU* 4.2 22.9 - - + -
237C PRO* 2.8 27.0 + - + +
239C LYS* 1.3 72.5 - - + +
241C PHE* 1.3 53.7 + - - +
243C ALA* 3.3 3.4 + - - +
244C ALA* 2.8 33.9 + - + +
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Residues in contact with PHE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LEU* 3.8 23.1 - - + +
237C PRO 2.7 19.0 + - - +
238C LYS 3.6 2.9 - - - +
240C VAL* 1.3 71.1 - - - +
242C GLU* 1.3 76.2 + - + +
244C ALA* 3.0 3.3 + - - +
245C VAL* 2.9 51.8 + - + +
262C TRP 3.8 15.5 - - - -
263C LEU* 4.7 16.4 - - + -
322C PHE* 4.4 0.4 - + - -
324C ILE* 3.1 33.9 - - + -
325C SER* 3.5 23.1 - - - -
326C GLN* 3.8 31.2 - - + -
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LYS* 2.7 49.7 + - - +
239C LYS* 3.8 7.4 + - - +
241C PHE* 1.3 85.3 - - + +
243C ALA* 1.3 60.3 + - - +
245C VAL* 3.6 6.3 + - - +
246C LYS* 3.3 22.7 + - - +
326C GLN* 4.1 11.3 + - - -
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C LEU* 4.2 20.1 - - + +
215C MET* 4.4 12.8 - - - -
239C LYS 2.9 20.7 + - - +
240C VAL 3.6 3.8 - - - +
242C GLU* 1.3 69.7 - - - +
244C ALA* 1.3 65.0 + - - +
246C LYS* 3.3 13.1 - - - +
247C SER* 2.9 25.7 + - - -
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Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C VAL* 6.2 0.2 - - + -
208C ILE* 3.7 22.4 - - + -
213C LEU* 4.5 5.3 - - + +
236C LEU* 4.2 18.2 - - + -
240C VAL* 2.8 21.1 + - + +
241C PHE* 3.6 3.6 - - + +
243C ALA* 1.3 71.9 - - - +
245C VAL* 1.3 63.9 + - + +
247C SER* 3.0 4.2 + - - -
248C ILE* 2.9 37.6 + - + +
283C ILE* 5.6 4.3 - - + -
324C ILE* 5.6 2.7 - - + -
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C PHE* 2.9 55.0 + - + +
242C GLU* 3.8 6.7 - - - +
244C ALA* 1.3 76.7 - - + +
246C LYS* 1.3 52.7 + - - +
248C ILE* 3.2 8.8 + - - +
249C LYS* 2.6 68.3 + - + +
262C TRP* 4.4 16.6 - - + -
322C PHE* 4.1 17.3 - - + -
324C ILE* 6.0 0.4 - - + -
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C GLU 3.3 12.0 + - - +
243C ALA* 3.3 15.7 - - - +
245C VAL* 1.3 79.3 - - - +
247C SER* 1.3 55.9 + - - +
249C LYS* 3.4 10.9 - - - +
250C ALA* 2.8 31.2 + - + +
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C ILE* 3.6 34.5 - - - +
213C LEU* 3.8 8.9 - - - +
243C ALA 2.9 15.1 + - - -
244C ALA 3.0 5.8 + - - -
246C LYS* 1.3 73.9 - - - +
248C ILE* 1.3 61.1 + - - +
250C ALA* 3.7 6.0 - - - +
251C ALA* 2.8 30.3 + - - +
281C PRO* 4.6 0.5 - - - +
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Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ILE* 4.7 5.8 - - + -
244C ALA* 2.9 25.3 + - + +
245C VAL* 3.8 3.1 - - + +
247C SER* 1.3 72.4 - - - +
249C LYS* 1.3 58.9 + - - +
251C ALA* 3.8 0.9 - - - +
252C SER* 2.5 34.9 + - - -
262C TRP* 3.8 18.8 - - + -
280C PHE* 3.9 11.4 - - + -
281C PRO* 3.8 33.4 - - + -
283C ILE* 4.4 10.1 - - + -
305C TYR* 3.9 13.9 - - + +
322C PHE* 3.9 24.5 - - + -
324C ILE* 4.0 18.2 - - + -
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Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C VAL* 2.6 47.0 + - + +
246C LYS* 3.4 10.5 - - - +
248C ILE* 1.3 76.5 - - - +
250C ALA* 1.3 62.7 + - - +
252C SER* 3.2 4.9 + - - -
253C SER* 3.1 24.7 + - - -
257C PHE* 6.3 0.2 - - + -
259C ASP* 6.0 4.2 - - - +
262C TRP* 3.9 38.5 - - + +
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C LYS* 2.8 22.0 + - + +
247C SER* 3.8 7.4 - - - +
249C LYS* 1.3 71.8 - - - +
251C ALA* 1.3 59.6 + - - +
252C SER 3.6 0.2 + - - -
253C SER* 3.7 17.1 + - - -
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209C ASN* 4.7 9.0 - - + +
247C SER 2.8 21.2 + - - +
248C ILE 3.8 0.7 - - - +
249C LYS 3.3 0.2 - - - -
250C ALA* 1.3 73.1 - - - +
252C SER* 1.3 59.4 + - - +
253C SER 3.5 0.4 + - - -
254C THR* 5.1 1.4 + - - -
279C ILE* 3.0 22.8 - - - +
281C PRO* 3.7 27.1 - - + -
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Residues in contact with SER 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C ILE 2.5 22.9 + - - -
249C LYS 3.2 4.0 + - - -
251C ALA* 1.3 75.6 - - - +
253C SER* 1.3 51.7 + - - +
254C THR* 2.7 18.5 + - - -
255C GLU* 3.0 17.3 + - - +
257C PHE* 4.1 6.2 - - - -
262C TRP* 3.9 6.8 - - - -
279C ILE* 3.3 39.7 - - - +
280C PHE* 3.6 24.9 - - - -
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Residues in contact with SER 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C LYS 3.1 15.7 + - - -
250C ALA* 3.7 13.1 + - - -
251C ALA 3.5 2.4 + - - -
252C SER* 1.3 71.8 - - - +
254C THR* 1.3 55.3 - - - +
255C GLU* 3.0 18.3 + - - +
257C PHE* 5.7 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