Contacts of the helix formed by residues 232 - 238 (chain D) in PDB entry 1EJI
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 ILE 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D ASN* 6.3 0.9 - - - +
211D TYR* 4.0 20.2 - - + +
229D MSE 3.7 19.5 - - + -
230D ALA 3.2 0.4 - - - -
231D HIS* 1.3 86.0 - - + +
233D SER* 1.3 65.8 + - - +
234D GLY 3.1 2.9 - - - -
235D LEU* 3.8 24.0 - - + -
236D VAL* 2.9 43.9 + - + +
241D VAL* 4.6 8.3 - - + -
242D PRO 4.9 4.3 - - - +
244D PRO* 5.1 1.3 - - + -
258D THR* 3.5 2.2 - - - -
356D ASN* 4.8 10.8 - - + +
357D HIS* 4.3 8.1 - - + -
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Residues in contact with SER 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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104D TYR* 2.9 30.9 + - - -
229D MSE 2.8 17.9 + - - -
230D ALA 3.3 10.4 + - - -
232D ILE* 1.3 77.4 - - - +
234D GLY* 1.3 62.0 + - - +
236D VAL 3.5 0.2 + - - -
237D ALA* 3.0 19.6 + - - +
253D THR* 3.3 24.9 - - - -
254D THR 3.8 3.6 + - - -
256D HIS 4.0 1.4 + - - -
258D THR* 3.3 3.3 + - - -
259D LEU* 3.4 24.4 + - - +
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Residues in contact with GLY 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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233D SER* 1.3 76.7 + - - +
235D LEU* 1.3 64.4 + - - -
236D VAL 3.1 1.6 - - - -
237D ALA* 3.2 2.1 + - - +
238D ALA* 2.9 26.5 + - - +
258D THR* 2.8 33.5 + - - -
259D LEU* 3.9 12.3 - - - -
324D PHE* 3.9 3.5 - - - -
328D GLN* 3.8 8.2 - - - +
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Residues in contact with LEU 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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232D ILE* 3.3 19.2 + - + +
234D GLY* 1.3 75.5 - - - +
236D VAL* 1.3 61.5 + - - +
238D ALA 3.5 0.3 + - - -
239D GLY 3.2 2.9 + - - -
240D VAL* 3.1 41.2 + - + +
241D VAL* 3.6 21.3 + - + -
258D THR* 4.4 8.1 - - + -
328D GLN* 2.9 49.1 - - + +
331D VAL* 4.6 8.7 - - + -
332D LEU* 4.4 4.9 - - + -
356D ASN* 3.9 18.8 - - + -
357D HIS* 3.8 28.7 - - + +
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Residues in contact with VAL 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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104D TYR* 4.0 18.5 - - + -
229D MSE 4.4 5.8 - - - -
232D ILE* 2.9 52.3 + - + +
233D SER 3.7 3.8 - - - +
235D LEU* 1.3 73.4 - - - +
237D ALA* 1.3 67.3 + - - +
238D ALA 3.1 1.3 - - - -
239D GLY* 2.9 14.0 + - - -
241D VAL* 3.6 17.2 - - + +
242D PRO 4.2 1.6 - - - +
243D SER* 3.8 33.7 - - - +
244D PRO* 4.0 13.7 - - + -
245D PHE* 4.8 0.2 - - + -
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Residues in contact with ALA 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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103D ALA* 3.7 22.7 - - + +
104D TYR* 3.7 25.1 - - + +
105D HIS* 5.3 6.9 + - - -
233D SER 3.0 18.6 + - - +
234D GLY* 3.8 6.5 - - - +
236D VAL* 1.3 77.1 - - - +
238D ALA* 1.3 60.7 + - - +
239D GLY* 3.3 1.0 + - - -
259D LEU* 4.7 5.4 - - + -
319D ALA* 4.7 13.0 - - + +
324D PHE* 4.6 9.0 - - + -
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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 GLY 2.9 16.2 + - - +
235D LEU 3.8 2.2 - - - +
237D ALA* 1.3 78.0 - - - +
239D GLY* 1.3 56.5 + - - +
240D VAL* 3.3 7.5 + - + +
319D ALA 5.1 1.1 - - - -
324D PHE* 4.2 12.3 - - + -
325D LYS* 3.0 45.5 + - - +
328D GLN* 3.6 30.1 - - + -
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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