Contacts of the helix formed by residues 225 - 236 (chain P) 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 LYS 225 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223P ILE 4.4 5.2 - - - +
224P PHE* 1.3 75.9 - - - +
226P PRO* 1.4 75.8 - - + +
227P GLN* 3.3 7.9 - - + +
228P GLU* 2.8 46.7 + - + +
229P ILE* 3.1 12.1 + - - +
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Residues in contact with PRO 226 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P GLN* 3.6 28.9 - - - +
62P ASP* 3.8 40.8 - - - +
207P TYR* 3.7 17.3 - - + -
224P PHE 4.4 2.0 - - - +
225P LYS* 1.4 88.6 - - + +
227P GLN* 1.3 62.7 + - - +
229P ILE* 3.3 12.0 + - + +
230P LYS* 3.1 21.7 + - - +
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Residues in contact with GLN 227 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207P TYR* 5.6 1.1 - - - -
225P LYS* 3.3 7.2 - - + +
226P PRO* 1.3 78.3 - - - +
228P GLU* 1.3 59.7 + - + +
230P LYS* 3.4 33.2 - - - +
231P ASP* 3.0 51.7 + - - +
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Residues in contact with GLU 228 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222P LYS* 2.8 31.9 + - - +
223P ILE 4.3 1.4 - - - +
224P PHE* 3.4 19.4 - - + -
225P LYS* 2.8 57.7 + - + +
227P GLN* 1.3 75.3 - - + +
229P ILE* 1.3 64.1 - - - +
231P ASP* 3.7 7.3 + - - +
232P ILE* 3.2 32.8 + - + +
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Residues in contact with ILE 229 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P GLN* 4.7 2.9 - - - +
194P LEU* 5.4 0.2 - - + -
207P TYR* 4.2 11.9 - - + +
210P LEU* 3.4 48.5 - - + +
211P GLU* 4.2 1.1 - - + -
212P PHE* 3.9 24.5 - - + +
224P PHE* 3.8 26.7 - - + +
225P LYS 3.1 15.1 + - - +
226P PRO* 3.3 11.2 + - + +
228P GLU* 1.3 74.7 - - - +
230P LYS* 1.3 67.8 + - - +
232P ILE* 3.0 8.1 + - + +
233P LEU* 3.0 39.2 + - + +
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Residues in contact with LYS 230 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207P TYR* 3.8 44.6 - - + +
226P PRO 3.1 10.7 + - - +
227P GLN* 3.4 36.6 - - - +
229P ILE* 1.3 79.8 - - - +
231P ASP* 1.3 61.9 + - - +
233P LEU* 3.2 19.1 - - + +
234P VAL* 3.5 13.8 + - + +
239P THR 5.3 0.3 - - - +
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Residues in contact with ASP 231 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227P GLN* 3.0 42.5 + - - +
228P GLU* 3.8 9.2 - - - +
230P LYS* 1.3 73.0 - - - +
232P ILE* 1.3 63.4 + - + +
233P LEU 3.0 4.3 - - - -
234P VAL* 2.9 22.9 + - - +
235P LYS* 3.2 36.9 + - - +
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Residues in contact with ILE 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P ILE* 3.8 21.1 - - + -
194P LEU* 3.6 26.5 - - + +
212P PHE* 5.2 5.6 - - + -
224P PHE* 4.3 22.7 - - + -
228P GLU* 3.2 20.7 + - + +
229P ILE* 3.0 8.9 + - + +
231P ASP* 1.3 84.7 - - + +
233P LEU* 1.3 58.2 + - + +
234P VAL 3.5 0.2 - - - -
235P LYS* 4.1 14.8 - - + +
236P THR* 3.3 26.9 + - + +
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Residues in contact with LEU 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P LEU* 3.6 30.5 - - + -
205P LEU* 3.9 24.0 - - + +
206P THR* 3.9 3.4 - - - +
207P TYR* 3.9 27.6 - - + +
210P LEU* 3.9 12.6 - - + -
229P ILE* 3.0 21.0 + - + +
230P LYS* 3.2 13.0 - - + +
231P ASP 2.9 0.4 + - - -
232P ILE* 1.3 76.9 - - + +
234P VAL* 1.3 64.4 + - - +
236P THR* 3.4 11.0 + - - -
238P ILE* 3.2 34.1 + - + +
239P THR 4.0 19.7 - - - +
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Residues in contact with VAL 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230P LYS* 3.9 13.7 - - + +
231P ASP* 2.9 9.9 + - - +
233P LEU* 1.3 74.3 - - - +
235P LYS* 1.3 83.7 + - + +
237P GLY* 2.8 16.3 + - - -
239P THR* 4.1 36.3 + - + +
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Residues in contact with LYS 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231P ASP* 3.2 43.7 + - - +
232P ILE* 4.1 17.9 - - + +
233P LEU 3.4 0.2 - - - -
234P VAL* 1.3 94.1 - - + +
236P THR* 1.3 62.2 + - + +
237P GLY* 3.3 3.8 + - - -
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Residues in contact with THR 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187P ASP 5.8 0.4 - - - +
190P ILE* 5.6 1.8 - - + -
191P GLU* 3.6 47.2 - - + +
194P LEU* 4.3 9.2 - - + +
195P LYS* 3.6 22.1 + - - -
232P ILE* 3.3 22.0 + - + +
233P LEU* 3.4 7.1 + - - -
235P LYS* 1.3 79.7 - - + +
237P GLY* 1.3 61.5 + - - +
238P ILE* 4.1 15.7 - - - +
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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