Contacts of the helix formed by residues 231 - 245 (chain D) in PDB entry 4KEU
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 PRO 231 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D ASP* 3.4 22.9 - - + +
230D LEU* 1.4 102.2 - - + +
232D VAL* 1.3 64.3 + - - +
233D ASP* 3.2 19.1 - - - +
234D LYS* 3.3 17.5 + - + +
235D ARG* 3.1 19.1 + - - +
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Residues in contact with VAL 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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224D TYR* 4.3 8.5 - - + -
225D GLY* 3.9 23.8 - - - +
227D ASP* 3.1 16.6 + - - +
231D PRO* 1.3 72.4 - - - +
233D ASP* 1.3 57.3 + - - +
235D ARG* 3.3 10.1 + - - +
236D ASN* 2.8 37.5 + - - +
277D ARG* 3.5 29.5 - - - +
282D LEU* 3.9 10.1 - - + -
286D ASP* 3.2 33.7 - - + +
287D THR* 5.0 0.2 - - - +
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Residues in contact with ASP 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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231D PRO* 3.2 21.4 - - - +
232D VAL* 1.3 76.4 - - - +
234D LYS* 1.4 66.6 + - - +
236D ASN* 3.5 10.7 + - - +
237D GLU* 3.0 27.3 + - - +
277D ARG* 5.2 1.2 - - - +
290D PHE* 5.6 0.7 - - - -
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Residues in contact with LYS 234 (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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204D ASP* 3.8 24.1 - - + +
230D LEU* 3.9 31.2 - - + -
231D PRO* 3.3 18.6 + - + +
233D ASP* 1.4 84.8 + - - +
235D ARG* 1.3 57.7 + - - +
237D GLU* 3.4 16.6 + - - +
238D THR* 2.8 38.1 + - - -
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Residues in contact with ARG 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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201D GLY* 3.1 40.0 + - - +
202D ASP* 2.8 21.2 + - - -
221D LEU 5.1 1.4 - - - -
222D ASP 4.8 0.6 - - - +
223D ARG* 3.2 43.8 + - - +
224D TYR* 3.4 39.6 - - + +
225D GLY 4.7 1.5 - - - +
226D LEU 3.5 15.2 + - - -
229D PHE* 3.6 8.9 - - - +
230D LEU* 2.9 28.4 + - + +
231D PRO 3.1 14.6 + - - +
232D VAL* 3.4 10.5 - - - +
234D LYS* 1.3 76.1 - - - +
236D ASN* 1.3 57.4 + - - +
238D THR* 3.1 6.7 + - - -
239D THR* 2.8 32.3 + - - +
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Residues in contact with ASN 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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224D TYR* 3.0 29.3 + - - -
232D VAL* 2.8 25.4 + - - +
233D ASP* 3.7 9.0 - - - +
235D ARG* 1.3 74.7 - - - +
237D GLU* 1.3 58.1 + - - +
239D THR* 3.3 2.3 + - - -
240D LEU* 2.8 32.2 + - - +
286D ASP* 3.0 26.3 + - - -
287D THR* 3.4 13.1 + - - +
290D PHE* 3.4 41.6 - - + +
291D LEU* 4.7 0.4 - - - +
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Residues in contact with GLU 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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204D ASP* 6.4 1.8 - - - -
233D ASP 3.0 17.2 + - - +
234D LYS* 3.6 20.1 - - - +
235D ARG 3.2 0.2 - - - -
236D ASN* 1.3 76.3 - - - +
238D THR* 1.3 60.1 + - - +
240D LEU* 3.8 6.4 - - - +
241D ARG* 3.0 29.9 + - + +
290D PHE* 4.5 6.0 - - + -
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Residues in contact with THR 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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201D GLY* 6.0 1.6 - - - -
203D THR 4.1 8.5 + - - +
204D ASP* 3.7 26.1 + - - +
206D ILE* 3.9 20.9 - - + -
209D ILE* 4.1 19.7 - - + -
221D LEU* 5.4 4.5 - - + -
230D LEU* 4.8 0.9 - - - +
234D LYS 2.8 21.7 + - - -
235D ARG* 3.4 7.5 - - - -
237D GLU* 1.3 77.4 - - - +
239D THR* 1.3 59.6 + - - +
241D ARG* 3.3 7.0 + - - +
242D LEU* 2.9 32.5 + - + +
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Residues in contact with THR 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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221D LEU* 3.5 31.3 - - + +
224D TYR* 2.6 29.3 + - - +
235D ARG 2.8 9.1 + - - -
236D ASN* 3.6 3.6 - - - -
238D THR* 1.3 73.0 - - - +
240D LEU* 1.3 65.6 - - - +
242D LEU* 3.2 3.8 + - - +
243D ILE* 2.9 46.1 + - + +
251D ILE* 4.7 2.7 - - + -
253D ILE* 4.0 20.4 - - + -
291D LEU* 4.4 10.1 - - + -
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Residues in contact with LEU 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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236D ASN 2.8 20.0 + - - +
237D GLU* 3.8 5.6 - - - +
239D THR* 1.3 73.3 - - - +
241D ARG* 1.3 58.2 + - - +
243D ILE* 3.3 11.1 + - + +
244D LYS* 2.9 65.1 + - + +
290D PHE* 4.1 18.6 - - + -
291D LEU* 4.1 21.0 - - + +
294D ASN* 3.9 35.9 - - + +
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Residues in contact with ARG 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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206D ILE* 4.4 32.5 - - + +
210D LYS* 5.1 2.8 - - - +
237D GLU* 3.0 20.6 + - + +
238D THR* 3.5 7.2 - - - +
240D LEU* 1.3 78.2 - - - +
242D LEU* 1.3 57.2 + - - +
244D LYS* 3.2 10.5 + - - +
245D ASP* 3.0 52.4 + - - +
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Residues in contact with LEU 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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206D ILE* 2.8 40.2 - - + -
209D ILE* 4.0 23.8 - - + -
210D LYS* 3.8 23.1 - - + -
219D ILE* 4.1 7.6 - - + -
221D LEU* 3.9 25.6 - - + -
238D THR* 2.9 20.5 + - + +
239D THR 3.6 5.8 - - - +
241D ARG* 1.3 76.0 - - - +
243D ILE* 1.3 64.0 + - - +
245D ASP* 3.2 9.1 + - - -
246D GLY 3.2 0.3 + - - -
247D TYR* 3.0 36.1 + - + +
251D ILE* 3.7 11.2 - - + -
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Residues in contact with ILE 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 THR* 2.9 35.8 + - + +
240D LEU* 3.5 9.0 - - + +
242D LEU* 1.3 75.8 - - - +
244D LYS* 1.3 60.9 + - + +
246D GLY* 3.0 19.8 + - - -
247D TYR 4.1 1.3 + - - +
248D SER* 3.5 26.4 + - - +
251D ILE* 3.8 15.5 - - + -
253D ILE* 5.9 0.9 - - + -
291D LEU* 4.0 26.0 - - + -
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Residues in contact with LYS 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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240D LEU* 2.9 54.0 + - + +
241D ARG* 3.2 10.1 + - - +
243D ILE* 1.3 79.0 - - + +
245D ASP* 1.3 64.2 + - - +
246D GLY 3.2 1.2 + - - -
294D ASN* 4.3 12.1 + - - +
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Residues in contact with ASP 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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210D LYS* 2.6 28.7 + - - +
241D ARG* 3.0 40.9 + - - +
242D LEU 3.7 4.9 - - - +
243D ILE 3.1 0.2 - - - -
244D LYS* 1.3 81.9 - - - +
246D GLY* 1.3 60.5 + - - +
247D TYR* 3.6 24.6 - - + -
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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