Contacts of the helix formed by residues 225 - 242 (chain D) in PDB entry 3SDI
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 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D ILE* 3.4 5.1 + - - +
224D TYR* 1.3 76.6 - - - +
226D ASN* 1.3 65.9 + - - +
227D GLU* 3.7 26.2 + - - +
228D LYS* 3.2 23.2 + - - +
229D THR* 3.3 10.1 + - - -
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Residues in contact with ASN 226 (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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52D LYS* 5.3 7.9 + - - +
61D SER* 5.7 0.9 + - - -
62D ASP* 4.7 16.3 - - - +
209D GLU* 3.2 52.2 + - + +
210D ALA 5.2 2.2 + - - -
211D GLN* 5.7 4.4 + - - +
224D TYR 4.9 2.8 + - - -
225D ASP* 1.3 74.7 - - - +
227D GLU* 1.3 68.5 + - - +
229D THR* 3.4 4.5 + - - +
230D ALA* 3.0 29.8 + - - +
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Residues in contact with GLU 227 (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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225D ASP* 3.4 15.3 - - - +
226D ASN* 1.3 83.9 + - - +
228D LYS* 1.3 62.1 + - - +
230D ALA* 3.5 7.5 - - - +
231D GLU* 3.2 36.3 + - - +
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Residues in contact with LYS 228 (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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190D GLU* 5.0 4.7 + - - -
224D TYR* 4.0 46.5 + - + -
225D ASP* 3.2 21.3 + - - +
227D GLU* 1.3 77.5 - - - +
229D THR* 1.3 64.2 + - - +
231D GLU* 3.6 9.7 + - + +
232D LEU* 3.3 33.4 + - + +
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Residues in contact with THR 229 (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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194D LEU* 4.4 18.4 - - + -
208D ASP 5.6 0.2 - - - +
209D GLU* 4.5 11.0 - - - -
210D ALA* 4.7 11.8 + - + +
211D GLN* 5.4 0.5 - - - -
212D LEU* 4.4 19.4 + - + +
224D TYR* 3.8 18.4 + - - +
225D ASP 3.3 11.9 + - - -
226D ASN* 4.0 8.8 + - - -
227D GLU 3.4 0.2 - - - -
228D LYS* 1.3 74.6 - - - +
230D ALA* 1.3 67.9 + - - +
232D LEU* 2.9 10.1 + - + +
233D ILE* 2.9 37.7 + - + +
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Residues in contact with ALA 230 (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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209D GLU* 4.0 29.0 - - - +
226D ASN 3.0 17.7 + - - +
227D GLU* 3.5 9.6 - - - +
229D THR* 1.3 74.6 - - - +
231D GLU* 1.3 58.7 + - + +
233D ILE* 2.9 23.2 + - - +
235D LYS* 3.0 15.6 + - - +
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Residues in contact with GLU 231 (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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227D GLU* 3.2 25.3 + - - +
228D LYS* 4.0 8.6 - - + +
229D THR 3.3 0.4 - - - -
230D ALA* 1.3 78.2 - - + +
232D LEU* 1.3 60.8 + - - +
235D LYS* 4.1 15.1 - - + +
236D GLU* 3.5 22.5 + - - +
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Residues in contact with LEU 232 (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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187D LYS* 4.3 18.4 - - - +
190D GLU* 3.6 22.7 - - + +
191D LEU* 3.9 18.8 - - + +
194D LEU* 4.3 13.0 - - + +
212D LEU* 4.2 13.2 - - + -
224D TYR* 4.1 31.2 - - + -
228D LYS* 3.3 25.1 - - + +
229D THR* 2.9 9.9 + - - +
231D GLU* 1.3 78.2 - - - +
233D ILE* 1.3 61.2 + - - +
235D LYS 3.5 0.2 - - - -
236D GLU* 3.6 13.1 + - - +
237D LEU* 3.2 24.4 + - - +
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Residues in contact with ILE 233 (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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194D LEU* 4.4 9.9 - - + -
198D LYS* 5.8 4.5 - - - +
207D LEU* 3.9 31.4 - - + +
208D ASP* 3.6 11.4 - - - +
209D GLU* 3.5 35.4 - - - +
210D ALA* 6.3 0.7 - - + -
229D THR* 2.9 30.2 + - + +
230D ALA* 3.5 8.5 - - - +
232D LEU* 1.3 75.1 - - - +
235D LYS* 1.3 60.5 + - - +
237D LEU* 2.9 29.3 + - + +
238D LYS* 2.9 18.1 + - + +
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Residues in contact with LYS 235 (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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230D ALA 3.0 15.8 + - - +
231D GLU* 4.1 14.1 - - + +
233D ILE* 1.3 78.7 - - - +
236D GLU* 1.3 61.1 + - - +
238D LYS* 3.3 21.4 + - + +
239D GLU* 3.4 30.5 + - - +
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Residues in contact with GLU 236 (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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187D LYS* 3.5 26.3 + - - +
191D LEU* 4.2 24.0 - - - +
231D GLU 3.5 17.1 + - - +
232D LEU* 3.6 13.0 + - - +
233D ILE 3.2 1.0 - - - -
235D LYS* 1.3 80.3 - - - +
237D LEU* 1.3 55.8 + - - +
239D GLU* 3.7 13.2 + - + +
240D LYS* 3.3 40.1 + - + +
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Residues in contact with LEU 237 (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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191D LEU* 4.3 36.6 - - + +
194D LEU* 4.6 10.1 - - + -
195D LYS* 4.5 19.5 - - + +
198D LYS* 4.0 19.7 - - + -
207D LEU* 6.1 1.6 - - + -
232D LEU 3.2 12.7 + - - +
233D ILE* 2.9 15.3 + - + +
236D GLU* 1.3 75.5 - - - +
238D LYS* 1.3 67.8 + - - +
239D GLU 3.2 0.4 - - - -
240D LYS* 4.4 8.3 - - + +
241D GLU* 3.1 58.4 + - + +
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Residues in contact with LYS 238 (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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198D LYS* 5.6 10.8 - - - +
206D LYS* 3.6 27.1 - - - +
233D ILE* 2.9 16.0 + - + +
235D LYS* 3.3 15.0 - - - +
237D LEU* 1.3 81.4 - - - +
239D GLU* 1.3 64.3 + - + +
241D GLU* 4.0 5.1 - - - +
242D ALA* 3.4 22.1 + - + +
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Residues in contact with GLU 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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235D LYS* 3.4 41.1 + - - +
236D GLU* 3.7 14.4 + - + +
237D LEU 3.2 0.4 - - - -
238D LYS* 1.3 79.1 - - + +
240D LYS* 1.3 65.1 + - + +
241D GLU 3.6 0.2 + - - -
242D ALA* 3.6 19.7 + - - +
243D ALA* 4.7 1.9 - - - +
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Residues in contact with LYS 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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188D GLU* 6.4 0.4 - - - +
191D LEU* 4.5 19.2 - - + +
236D GLU* 3.3 35.8 + - + +
237D LEU* 3.4 12.0 + - + +
239D GLU* 1.3 75.0 - - + +
241D GLU* 1.3 65.8 + - - +
243D ALA* 3.3 21.4 - - - +
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Residues in contact with GLU 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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195D LYS* 4.7 23.8 - - + +
198D LYS* 3.7 18.9 - - - +
237D LEU* 3.1 48.9 + - + +
238D LYS* 4.0 4.8 - - - +
240D LYS* 1.3 75.6 - - - +
242D ALA* 1.3 58.1 + - - +
243D ALA 2.8 7.6 + - - -
244D GLU 3.9 13.0 + - - -
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Residues in contact with ALA 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* 3.4 15.1 + - + +
239D GLU* 3.6 13.0 + - - +
240D LYS 3.3 0.4 - - - -
241D GLU* 1.3 74.7 - - - +
243D ALA* 1.3 56.8 + - - +
244D GLU 5.7 0.2 - - - -
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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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239D GLU 4.7 2.0 - - - +
240D LYS* 3.3 18.4 - - - +
241D GLU 2.8 8.9 + - - -
242D ALA* 1.3 76.0 - - - +
244D GLU* 1.3 71.9 + - + +
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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