Contacts of the helix formed by residues 233 - 248 (chain I) in PDB entry 3KDO
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 233 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ALA 3.0 27.0 - - - +
100E ASN* 4.0 4.2 + - - -
101E LEU* 4.5 2.9 + - - +
102E PRO* 4.0 16.2 - - - +
261E TRP 4.4 6.2 - - - +
262E GLY 3.8 4.3 - - - +
265E ARG* 3.9 35.3 + - + +
266E TYR 6.2 0.4 - - - +
232I ALA* 1.3 77.7 - - - +
234I LEU* 1.3 69.4 + - - +
235I LEU 3.4 0.9 - - - +
236I GLU* 3.1 21.3 + - - +
237I MET* 2.9 19.1 + - - +
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Residues in contact with LEU 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E LEU* 3.5 23.3 - - + -
262E GLY 3.0 17.2 + - - +
263E ALA* 4.2 3.8 - - + +
266E TYR* 3.4 51.4 - - + +
233I ASP* 1.3 72.4 - - - +
235I LEU* 1.3 66.8 + - + +
237I MET* 3.0 14.4 + - + +
238I GLU* 3.0 32.3 + - + +
263I ALA* 4.5 7.9 - - + -
266I TYR* 4.0 24.9 - - + -
267I ILE* 4.2 15.5 - - + -
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Residues in contact with LEU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E TYR* 4.2 33.7 - - + -
269E ASP* 6.0 1.8 - - - +
233I ASP* 3.4 1.0 - - - +
234I LEU* 1.3 78.4 - - + +
236I GLU* 1.3 69.3 + - - +
238I GLU* 3.2 26.5 + - - +
239I GLN* 3.1 34.9 + - - +
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Residues in contact with GLU 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 4.8 3.1 - - - +
99E ALA* 5.2 6.5 - - - +
100E ASN* 6.6 0.2 - - + -
232I ALA* 3.6 17.9 - - + -
233I ASP* 3.1 30.5 + - - +
235I LEU* 1.3 79.9 - - - +
237I MET* 1.3 65.2 + - - +
239I GLN* 3.1 20.5 + - - +
240I ARG* 3.0 49.4 + - - +
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Residues in contact with MET 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E GLY* 3.9 9.6 - - - +
230I ILE* 3.2 36.8 - - + +
231I THR* 4.4 3.6 - - - -
232I ALA 3.5 27.4 - - - +
233I ASP 2.9 12.0 + - - +
234I LEU* 3.0 25.1 + - + +
236I GLU* 1.3 75.5 - - - +
238I GLU* 1.3 61.9 + - - +
240I ARG* 3.2 2.3 + - - +
241I LEU* 3.0 30.0 + - - +
254I VAL* 5.1 2.5 - - - -
259I THR* 4.3 27.8 - - + -
263I ALA* 5.3 0.9 - - + -
267I ILE* 3.9 32.5 - - + -
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Residues in contact with GLU 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I LEU* 3.0 23.9 + - + +
235I LEU* 3.2 35.2 - - - +
237I MET* 1.3 76.1 - - - +
239I GLN* 1.3 62.2 + - + +
241I LEU* 3.5 2.5 + - - +
242I GLU* 3.1 23.4 + - - +
266I TYR* 2.7 36.8 + - + -
267I ILE* 5.1 1.3 - - + +
270I LEU* 4.0 26.6 - - + +
274I TYR* 5.0 2.1 + - - -
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Residues in contact with GLN 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I LEU* 3.1 21.8 + - - +
236I GLU* 3.1 24.9 + - - +
238I GLU* 1.3 77.5 - - + +
240I ARG* 1.3 62.8 + - + +
242I GLU* 3.6 10.9 + - - +
243I VAL* 3.1 32.6 + - + +
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Residues in contact with ARG 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 2.5 43.6 + - - -
195I THR* 4.2 4.2 - - - +
196I SER* 3.4 23.1 + - - +
202I PHE* 3.5 40.0 - - + +
203I GLU* 6.3 0.9 - - + -
229I ASN 4.9 1.2 + - - -
230I ILE* 3.9 24.9 + - + +
231I THR 3.9 7.1 + - - -
232I ALA* 3.8 19.5 - - - +
236I GLU* 3.0 33.0 + - - +
237I MET 3.2 3.1 + - - +
239I GLN* 1.3 79.6 - - + +
241I LEU* 1.3 65.1 + - - +
243I VAL* 3.5 4.6 + - + -
244I LEU* 3.2 28.3 + - - +
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Residues in contact with LEU 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230I ILE* 3.7 20.9 - - + -
237I MET 3.0 19.9 + - - +
238I GLU 3.8 3.8 - - - +
240I ARG* 1.3 76.1 - - - +
242I GLU* 1.3 65.3 + - - +
244I LEU* 3.1 7.3 + - + +
245I ALA* 3.0 22.5 + - - +
252I ALA* 3.5 32.1 - - + -
254I VAL* 6.0 0.2 - - + -
267I ILE* 4.2 19.7 - - + +
270I LEU* 3.6 34.1 - - + -
271I ALA* 4.2 9.9 - - + +
274I TYR* 3.9 13.9 - - + -
276I LEU* 3.9 15.1 - - + +
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Residues in contact with GLU 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I GLU 3.1 15.1 + - - +
239I GLN* 3.6 9.7 - - - +
241I LEU* 1.3 79.3 - - - +
243I VAL* 1.3 60.4 + - + +
245I ALA* 3.3 2.5 + - - +
246I ASP* 2.8 53.6 + - - +
274I TYR* 3.9 26.7 + - + +
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Residues in contact with VAL 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202I PHE* 4.2 9.9 - - + -
203I GLU* 3.9 36.6 - - + +
206I ALA* 3.9 26.7 - - + -
239I GLN* 3.1 24.1 + - + +
240I ARG* 3.6 10.3 - - + +
241I LEU 3.3 0.2 - - - -
242I GLU* 1.3 77.9 - - + +
244I LEU* 1.3 63.4 + - - +
246I ASP* 3.4 7.1 + - - +
247I LEU* 3.1 30.2 + - + +
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Residues in contact with LEU 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202I PHE* 3.7 8.7 - - + -
206I ALA* 4.6 1.8 - - + -
226I TRP* 3.6 17.7 - - + -
228I ALA* 3.6 15.0 - - + -
230I ILE* 4.1 9.4 - - + -
240I ARG 3.2 14.8 - - - +
241I LEU* 3.1 8.3 + - - +
243I VAL* 1.3 75.3 - - - +
245I ALA* 1.3 64.7 + - - +
247I LEU 3.3 1.7 + - - -
248I GLY 3.2 3.6 + - - -
249I LEU* 3.0 57.3 + - + +
251I HIS 3.3 22.2 - - - +
252I ALA* 3.9 19.3 - - + -
276I LEU* 4.1 15.3 - - + -
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Residues in contact with ALA 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241I LEU 3.0 8.2 + - - +
242I GLU 3.6 7.0 - - - +
244I LEU* 1.3 74.5 - - - +
246I ASP* 1.3 67.0 + - - +
248I GLY* 3.0 15.6 + - - -
249I LEU 5.2 0.7 - - - -
274I TYR* 3.5 48.5 - - + +
276I LEU* 4.5 7.7 - - - +
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Residues in contact with ASP 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242I GLU* 2.8 43.1 + - - +
243I VAL* 3.7 7.4 - - - +
245I ALA* 1.3 79.0 - - - +
247I LEU* 1.3 63.0 + - + +
248I GLY 3.4 0.5 + - - -
274I TYR* 6.0 0.5 - - - -
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Residues in contact with LEU 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206I ALA* 3.5 45.8 - - + +
207I GLU* 3.6 20.0 - - + +
210I ALA* 4.3 23.1 - - + +
243I VAL* 3.1 24.7 + - + +
244I LEU 3.9 3.6 - - - +
245I ALA 3.2 0.2 - - - -
246I ASP* 1.3 79.2 - - + +
248I GLY* 1.3 62.0 + - - +
249I LEU* 3.3 10.9 + - + +
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Residues in contact with GLY 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245I ALA 3.0 15.4 + - - -
246I ASP 3.2 1.4 + - - -
247I LEU* 1.3 79.1 - - - +
249I LEU* 1.3 66.9 + - - +
250I LYS* 4.2 9.0 - - - +
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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