Contacts of the helix formed by residues 228 - 240 (chain D) in PDB entry 5H2U
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 HIS 228 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D LEU 3.9 0.4 + - - -
227D LEU* 1.3 77.8 - - + +
229D GLN* 1.3 64.8 + - - +
230D GLN* 3.1 45.7 + - + +
231D MET* 3.2 29.6 + - + +
232D LEU 3.0 18.7 + - - -
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Residues in contact with GLN 229 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D ARG* 2.2 41.5 + - - +
227D LEU 3.8 1.2 + - - -
228D HIS* 1.3 72.6 + - - +
230D GLN* 1.3 56.8 + - - +
232D LEU* 3.3 7.4 + - - +
233D GLN* 2.4 74.1 + - + +
255D SER* 3.4 9.5 + - - +
256D VAL* 5.1 2.2 - - - +
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Residues in contact with GLN 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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228D HIS* 3.3 23.3 + - + +
229D GLN* 1.3 78.0 - - - +
231D MET* 1.3 61.3 + - - +
233D GLN* 3.8 6.0 + - - +
234D SER* 3.4 21.3 + - - -
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Residues in contact with MET 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 LEU* 3.9 12.6 - - + -
228D HIS* 3.2 29.6 + - + +
230D GLN* 1.3 75.8 - - - +
232D LEU* 1.3 68.3 + - - +
234D SER* 3.0 17.4 + - - +
235D GLU* 2.9 56.5 + - - +
335D ARG* 2.9 34.1 - - - +
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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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223D ARG* 3.6 28.0 - - - +
226D LEU* 3.7 40.6 - - + -
227D LEU* 4.1 15.2 - - - +
228D HIS 3.0 12.4 + - - +
229D GLN* 3.4 13.7 - - - +
231D MET* 1.3 76.9 - - - +
233D GLN* 1.3 63.2 + - - +
235D GLU* 3.4 2.5 + - - +
236D ILE* 3.1 41.7 + - + +
255D SER* 4.9 3.1 - - - -
260D VAL* 4.6 8.7 - - + -
262D ILE* 5.9 0.7 - - + -
336D LEU* 3.9 29.2 - - + +
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Residues in contact with GLN 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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185D GLU* 4.1 7.1 + - - -
229D GLN* 2.4 47.5 + - + +
230D GLN* 4.0 6.7 - - - +
232D LEU* 1.3 76.2 - - - +
234D SER* 1.3 59.8 - - - +
236D ILE* 3.5 13.0 + - - +
237D GLN* 3.0 42.7 + - + +
255D SER* 2.7 31.1 + - - -
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Residues in contact with SER 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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230D GLN 3.4 11.5 + - - -
231D MET* 3.0 24.1 + - - +
233D GLN* 1.3 78.4 - - - +
235D GLU* 1.3 62.4 + - - +
237D GLN* 3.5 8.5 + - - +
238D ALA* 3.4 19.6 + - - +
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Residues in contact with GLU 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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227D LEU* 4.6 3.6 - - + -
231D MET* 2.9 43.4 + - - +
232D LEU 3.8 0.2 - - - +
234D SER* 1.3 76.2 - - - +
236D ILE* 1.3 59.1 + - - +
238D ALA* 3.3 9.9 + - - +
239D MET* 2.9 29.8 + - + +
308D TYR* 4.4 6.2 + - - +
332D GLY 5.8 0.4 - - - +
335D ARG* 2.6 42.3 + - + +
336D LEU* 3.3 25.8 - - + -
503D GOL 3.4 20.2 + - - -
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Residues in contact with ILE 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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184D CXM 4.4 0.2 - - - +
232D LEU* 3.1 40.8 + - + +
233D GLN* 3.7 12.3 - - - +
235D GLU* 1.3 76.4 - - - +
237D GLN* 1.3 70.4 - - - +
239D MET* 3.2 9.0 + - + +
240D LYS* 2.8 37.8 + - + +
250D LEU* 4.7 4.5 - - + -
253D VAL* 4.1 36.8 - - + -
255D SER* 4.1 21.8 - - - -
260D VAL* 5.9 1.8 - - + -
262D ILE* 5.5 5.2 - - + -
336D LEU* 4.5 17.0 - - + -
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Residues in contact with GLN 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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184D CXM 5.3 0.3 - - - +
233D GLN* 3.0 31.2 + - + +
234D SER* 3.8 8.3 - - - +
235D GLU 3.2 0.6 - - - -
236D ILE* 1.3 82.8 - - - +
238D ALA* 1.3 60.6 + - - +
240D LYS* 3.4 37.4 - - - +
241D LYS* 3.0 38.8 - - - +
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Residues in contact with ALA 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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234D SER 3.4 9.1 + - - +
235D GLU* 3.3 13.7 + - - +
237D GLN* 1.3 77.9 - - - +
239D MET* 1.3 62.3 + - - +
240D LYS 3.5 0.3 + - - -
241D LYS* 3.6 16.6 + - - +
242D LEU* 3.8 15.1 - - - +
308D TYR* 4.1 19.6 - - + -
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Residues in contact with MET 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 GLU* 2.9 18.7 + - + +
236D ILE* 3.5 6.3 - - - +
238D ALA* 1.3 78.7 - - - +
240D LYS* 1.3 59.4 + - - +
241D LYS 3.4 0.9 + - - -
242D LEU* 3.5 19.8 + - - +
250D LEU* 3.8 33.5 + - + +
262D ILE* 5.2 3.8 - - - -
308D TYR* 3.6 19.3 + - - +
331D PHE* 3.2 42.2 - - + +
332D GLY 3.5 24.0 - - - +
333D LEU* 3.7 7.0 - - - +
336D LEU* 3.8 28.7 - - + -
504D 1N1 5.9 1.8 - - - -
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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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184D CXM 3.4 50.6 + - - +
185D GLU 5.9 0.2 - - - +
236D ILE* 2.8 18.5 + - + +
237D GLN* 3.4 46.9 - - - +
239D MET* 1.3 75.0 - - - +
241D LYS* 1.3 67.3 + - + +
242D LEU 3.3 1.8 - - - +
243D ARG* 3.7 18.7 + - - -
250D LEU* 4.0 19.0 + - + +
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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